Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies

BACKGROUND

Clinical, molecular, and genetic epidemiology studies displayed remarkable differences between ever- and never-smoking lung cancer.

METHODS

We conducted a stratified multi-population (European, East Asian, and African descent) association study on 44,823 ever-smokers and 20,074 never-smokers to identify novel variants that were missed in the non-stratified analysis. Functional analysis including expression quantitative trait loci (eQTL) colocalization and DNA damage assays, and annotation studies were conducted to evaluate the functional roles of the variants. We further evaluated the impact of smoking quantity on lung cancer risk for the variants associated with ever-smoking lung cancer.

RESULTS

Five novel independent loci, GABRA4, intergenic region 12q24.33, LRRC4C, LINC01088, and LCNL1 were identified with the association at two or three populations (P < 5 × 10-8). Further functional analysis provided multiple lines of evidence suggesting the variants affect lung cancer risk through excessive DNA damage (GABRA4) or cis-regulation of gene expression (LCNL1). The risk of variants from 12 independent regions, including the well-known CHRNA5, associated with ever-smoking lung cancer was evaluated for never-smokers, light-smokers (packyear ≤ 20), and moderate-to-heavy-smokers (packyear > 20). Different risk patterns were observed for the variants among the different groups by smoking behavior.

CONCLUSIONS

We identified novel variants associated with lung cancer in only ever- or never-smoking groups that were missed by prior main-effect association studies.

IMPACT

Our study highlights the genetic heterogeneity between ever- and never-smoking lung cancer and provides etiologic insights into the complicated genetic architecture of this deadly cancer.

Life, the genome and everything

In this issue of the Journal of Bacteriology, N. J. Bonde, E. A. Wood, K. S. Myers, M. Place, J. L. Keck, and M. M. Cox (J Bacteriol 205:e00184-23, 2023, https//doi.org/10.1128/jb.00184-23) used an unbiased transposon-sequencing (Tn-seq) screen to identify proteins required for life when cells lose the RecG branched-DNA helicase (synthetic lethality). The proteins' identities indicate pathways that prevent endogenous DNA damage, pathways that prevent its homology-directed repair (HDR) "strand-exchange" intermediates between sister chromosomes, and pathways that resolve those intermediates. All avoid intermediate pile-up, which blocks chromosome segregation, causing "death-by-recombination." DNA damage is managed to regulate crucial but potentially lethal HDR.

Drugging evolution of antibiotic resistance at a regulatory network hub

Evolution of antibiotic resistance is a world health crisis, fueled by new mutations. Drugs to slow mutagenesis could, as cotherapies, prolong the shelf-life of antibiotics, yet evolution-slowing drugs and drug targets have been underexplored and ineffective. Here, we used a network-based strategy to identify drugs that block hubs of fluoroquinolone antibiotic-induced mutagenesis. We identify a U.S. Food and Drug Administration- and European Medicines Agency-approved drug, dequalinium chloride (DEQ), that inhibits activation of the Escherichia coli general stress response, which promotes ciprofloxacin-induced (stress-induced) mutagenic DNA break repair. We uncover the step in the pathway inhibited: activation of the upstream "stringent" starvation stress response, and find that DEQ slows evolution without favoring proliferation of DEQ-resistant mutants. Furthermore, we demonstrate stress-induced mutagenesis during mouse infections and its inhibition by DEQ. Our work provides a proof-of-concept strategy for drugs to slow evolution in bacteria and generally.

Rapid profiling of DNA replication dynamics using mass spectrometry-based analysis of nascent DNA

The primary method for probing DNA replication dynamics is DNA fiber analysis, which utilizes thymidine analog incorporation into nascent DNA, followed by immunofluorescent microscopy of DNA fibers. Besides being time-consuming and prone to experimenter bias, it is not suitable for studying DNA replication dynamics in mitochondria or bacteria, nor is it adaptable for higher-throughput analysis. Here, we present mass spectrometry-based analysis of nascent DNA (MS-BAND) as a rapid, unbiased, quantitative alternative to DNA fiber analysis. In this method, incorporation of thymidine analogs is quantified from DNA using triple quadrupole tandem mass spectrometry. MS-BAND accurately detects DNA replication alterations in both the nucleus and mitochondria of human cells, as well as bacteria. The high-throughput capability of MS-BAND captured replication alterations in an E. coli DNA damage-inducing gene library. Therefore, MS-BAND may serve as an alternative to the DNA fiber technique, with potential for high-throughput analysis of replication dynamics in diverse model systems.

ppGpp and RNA-polymerase backtracking guide antibiotic-induced mutable gambler cells

Antibiotic resistance is a global health threat and often results from new mutations. Antibiotics can induce mutations via mechanisms activated by stress responses, which both reveal environmental cues of mutagenesis and are weak links in mutagenesis networks. Network inhibition could slow the evolution of resistance during antibiotic therapies. Despite its pivotal importance, few identities and fewer functions of stress responses in mutagenesis are clear. Here, we identify the Escherichia coli stringent starvation response in fluoroquinolone-antibiotic ciprofloxacin-induced mutagenesis. Binding of response-activator ppGpp to RNA polymerase (RNAP) at two sites leads to an antibiotic-induced mutable gambler-cell subpopulation. Each activates a stress response required for mutagenic DNA-break repair: surprisingly, ppGpp-site-1-RNAP triggers the DNA-damage response, and ppGpp-site-2-RNAP induces σ^S-response activity. We propose that RNAP regulates DNA-damage processing in transcribed regions. The data demonstrate a critical node in ciprofloxacin-induced mutagenesis, imply RNAP-regulation of DNA-break repair, and identify promising targets for resistance-resisting drugs.

Interdependent progression of bidirectional sister replisomes in E. coli

Bidirectional DNA replication complexes initiated from the same origin remain colocalized in a factory configuration for part or all their lifetimes. However, there is little evidence that sister replisomes are functionally interdependent, and the consequence of factory replication is unknown. Here, we investigated the functional relationship between sister replisomes in Escherichia coli, which naturally exhibits both factory and solitary configurations in the same replication cycle. Using an inducible transcription factor roadblocking system, we found that blocking one replisome caused a significant decrease in overall progression and velocity of the sister replisome. Remarkably, progression was impaired only if the block occurred while sister replisomes were still in a factory configuration - blocking one fork had no significant effect on the other replisome when sister replisomes were physically separate. Disruption of factory replication also led to increased fork stalling and requirement of fork restart mechanisms. These results suggest that physical association between sister replisomes is important for establishing an efficient and uninterrupted replication program. We discuss the implications of our findings on mechanisms of replication factory structure and function, and cellular strategies of replicating problematic DNA such as highly transcribed segments.

Looking on the horizon; potential and unique approaches to developing radiation countermeasures for deep space travel

Future lunar missions and beyond will require new and innovative approaches to radiation countermeasures. The Translational Research Institute for Space Health (TRISH) is focused on identifying and supporting unique approaches to reduce risks to human health and performance on future missions beyond low Earth orbit. This paper will describe three funded and complementary avenues for reducing the risk to humans from radiation exposure experienced in deep space. The first focus is on identifying new therapeutic targets to reduce the damaging effects of radiation by focusing on high throughput genetic screens in accessible, sometimes called lower, organism models. The second focus is to design innovative approaches for countermeasure development with special attention to nucleotide-based methodologies that may constitute a more agile way to design therapeutics. The final focus is to develop new and innovative ways to test radiation countermeasures in a human model system. While animal studies continue to be beneficial in the study of space radiation, they can have imperfect translation to humans. The use of three-dimensional (3D) complex in vitro models is a promising approach to aid the development of new countermeasures and personalized assessments of radiation risks. These three distinct and unique approaches complement traditional space radiation efforts and should provide future space explorers with more options to safeguard their short and long-term health.

Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer

To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung fibroblasts indicated that a subset of these genes, including the pleiotropic gene IRF4, potentially exert effects by promoting endogenous DNA damage.

Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli

Since antibiotic development lags, we search for potential drug targets through directed evolution experiments. A challenge is that many resistance genes hide in a noisy mutational background as mutator clones emerge in the adaptive population. Here, to overcome this noise, we quantify the impact of mutations through evolutionary action (EA). After sequencing ciprofloxacin or colistin resistance strains grown under different mutational regimes, we find that an elevated sum of the evolutionary action of mutations in a gene identifies known resistance drivers. This EA integration approach also suggests new antibiotic resistance genes which are then shown to provide a fitness advantage in competition experiments. Moreover, EA integration analysis of clinical and environmental isolates of antibiotic resistant of E. coli identifies gene drivers of resistance where a standard approach fails. Together these results inform the genetic basis of de novo colistin resistance and support the robust discovery of phenotype-driving genes via the evolutionary action of genetic perturbations in fitness landscapes.

Genomic mapping of DNA-repair reaction intermediates in living cells with engineered DNA structure-trap proteins

Diverse DNA structures occur as reaction intermediates in various DNA-damage and -repair mechanisms, most of which results from replication stress. We harness the power of proteins evolutionarily optimized to bind and "trap" specific DNA reaction-intermediate structures, to quantify the structures, and discern the mechanisms of their occurrence in cells. The engineered proteins also allow genomic mapping of sites at which specific DNA structures occur preferentially, using a structure-trapping protein and ChIP-seq- or Cut-and-Tag-like methods. Genome-wide identification of sites with recurrent DNA-damage intermediates has illuminated mechanisms implicated in genome instability, replication stress, and chromosome fragility. Here, we describe X-seq, for identifying sites of recurrent four-way DNA junctions or Holliday-junctions (HJs). X-seq uses an engineered, catalysis-defective mutant of Escherichia coli RuvC HJ-specific endonuclease, RuvCDefGFP. X-seq signal indicates sites of recombinational DNA repair or replication-fork stalling and reversal. We also describe methods for genomic mapping of 3'-single-stranded DNA ends with SsEND-seq, in E. coli. Both methods allow genomic profiling of DNA-damage and -repair intermediates, which can precede genome instability, and are expected to have many additional applications including in other cells and organisms.

Biology before the SOS Response-DNA Damage Mechanisms at Chromosome Fragile Sites

The Escherichia coli SOS response to DNA damage, discovered and conceptualized by Evelyn Witkin and Miroslav Radman, is the prototypic DNA-damage stress response that upregulates proteins of DNA protection and repair, a radical idea when formulated in the late 1960s and early 1970s. SOS-like responses are now described across the tree of life, and similar mechanisms of DNA-damage tolerance and repair underlie the genome instability that drives human cancer and aging. The DNA damage that precedes damage responses constitutes upstream threats to genome integrity and arises mostly from endogenous biology. Radman's vision and work on SOS, mismatch repair, and their regulation of genome and species evolution, were extrapolated directly from bacteria to humans, at a conceptual level, by Radman, then many others. We follow his lead in exploring bacterial molecular genomic mechanisms to illuminate universal biology, including in human disease, and focus here on some events upstream of SOS: the origins of DNA damage, specifically at chromosome fragile sites, and the engineered proteins that allow us to identify mechanisms. Two fragility mechanisms dominate: one at replication barriers and another associated with the decatenation of sister chromosomes following replication. DNA structures in E. coli, additionally, suggest new interpretations of pathways in cancer evolution, and that Holliday junctions may be universal molecular markers of chromosome fragility.

Two mechanisms of chromosome fragility at replication-termination sites in bacteria

Chromosomal fragile sites are implicated in promoting genome instability, which drives cancers and neurological diseases. Yet, the causes and mechanisms of chromosome fragility remain speculative. Here, we identify three spontaneous fragile sites in the Escherichia coli genome and define their DNA damage and repair intermediates at high resolution. We find that all three sites, all in the region of replication termination, display recurrent four-way DNA or Holliday junctions (HJs) and recurrent DNA breaks. Homology-directed double-strand break repair generates the recurrent HJs at all of these sites; however, distinct mechanisms of DNA breakage are implicated: replication fork collapse at natural replication barriers and, unexpectedly, frequent shearing of unsegregated sister chromosomes at cell division. We propose that mechanisms such as both of these may occur ubiquitously, including in humans, and may constitute some of the earliest events that underlie somatic cell mosaicism, cancers, and other diseases of genome instability.

Rare deleterious germline variants and risk of lung cancer

Recent studies suggest that rare variants exhibit stronger effect sizes and might play a crucial role in the etiology of lung cancers (LC). Whole exome plus targeted sequencing of germline DNA was performed on 1045 LC cases and 885 controls in the discovery set. To unveil the inherited causal variants, we focused on rare and predicted deleterious variants and small indels enriched in cases or controls. Promising candidates were further validated in a series of 26,803 LCs and 555,107 controls. During discovery, we identified 25 rare deleterious variants associated with LC susceptibility, including 13 reported in ClinVar. Of the five validated candidates, we discovered two pathogenic variants in known LC susceptibility loci, ATM p.V2716A (Odds Ratio [OR] 19.55, 95%CI 5.04-75.6) and MPZL2 p.I24M frameshift deletion (OR 3.88, 95%CI 1.71-8.8); and three in novel LC susceptibility genes, POMC c.*28delT at 3' UTR (OR 4.33, 95%CI 2.03-9.24), STAU2 p.N364M frameshift deletion (OR 4.48, 95%CI 1.73-11.55), and MLNR p.Q334V frameshift deletion (OR 2.69, 95%CI 1.33-5.43). The potential cancer-promoting role of selected candidate genes and variants was further supported by endogenous DNA damage assays. Our analyses led to the identification of new rare deleterious variants with LC susceptibility. However, in-depth mechanistic studies are still needed to evaluate the pathogenic effects of these specific alleles.

Transcriptome-wide association study reveals candidate causal genes for lung cancer

We have recently completed the largest GWAS on lung cancer including 29,266 cases and 56,450 controls of European descent. The goal of our study has been to integrate the complete GWAS results with a large-scale expression quantitative trait loci (eQTL) mapping study in human lung tissues (n = 1,038) to identify candidate causal genes for lung cancer. We performed transcriptome-wide association study (TWAS) for lung cancer overall, by histology (adenocarcinoma, squamous cell carcinoma and small cell lung cancer) and smoking subgroups (never- and ever-smokers). We performed replication analysis using lung data from the Genotype-Tissue Expression (GTEx) project. DNA damage assays were performed in human lung fibroblasts for selected TWAS genes. As expected, the main TWAS signal for all histological subtypes and ever-smokers was on chromosome 15q25. The gene most strongly associated with lung cancer at this locus using the TWAS approach was IREB2 (pTWAS = 1.09E-99), where lower predicted expression increased lung cancer risk. A new lung adenocarcinoma susceptibility locus was revealed on 9p13.3 and associated with higher predicted expression of AQP3 (pTWAS = 3.72E-6). Among the 45 previously described lung cancer GWAS loci, we mapped candidate target gene for 17 of them. The association AQP3-adenocarcinoma on 9p13.3 was replicated using GTEx (pTWAS = 6.55E-5). Consistent with the effect of risk alleles on gene expression levels, IREB2 knockdown and AQP3 overproduction promote endogenous DNA damage. These findings indicate genes whose expression in lung tissue directly influences lung cancer risk.

Gamblers: An Antibiotic-Induced Evolvable Cell Subpopulation Differentiated by Reactive-Oxygen-Induced General Stress Response

Antibiotics can induce mutations that cause antibiotic resistance. Yet, despite their importance, mechanisms of antibiotic-promoted mutagenesis remain elusive. We report that the fluoroquinolone antibiotic ciprofloxacin (cipro) induces mutations by triggering transient differentiation of a mutant-generating cell subpopulation, using reactive oxygen species (ROS). Cipro-induced DNA breaks activate the Escherichia coli SOS DNA-damage response and error-prone DNA polymerases in all cells. However, mutagenesis is limited to a cell subpopulation in which electron transfer together with SOS induce ROS, which activate the sigma-S (σS) general-stress response, which allows mutagenic DNA-break repair. When sorted, this small σS-response-"on" subpopulation produces most antibiotic cross-resistant mutants. A U.S. Food and Drug Administration (FDA)-approved drug prevents σS induction, specifically inhibiting antibiotic-promoted mutagenesis. Further, SOS-inhibited cell division, which causes multi-chromosome cells, promotes mutagenesis. The data support a model in which within-cell chromosome cooperation together with development of a "gambler" cell subpopulation promote resistance evolution without risking most cells.

Tools To Live By: Bacterial DNA Structures Illuminate Cancer

Holliday junctions (HJs) are DNA intermediates in homology-directed DNA repair and replication stalling, but until recently were undetectable in living cells. We review how an engineered protein that traps and labels HJs in Escherichia coli illuminates the biology of DNA and cancer. HJ chromatin immunoprecipitation with deep sequencing (ChIP-seq) analysis showed the directionality of double-strand break (DSB) repair in the E. coli genome. Quantification of HJs as fluorescent foci in live cells revealed that the commonest spontaneous problem repaired via HJs is replication-dependent single-stranded DNA gaps, not DSBs. Focus quantification also indicates that RecQ DNA helicase plays dual roles in promoting repair HJs and preventing replication-stall HJs in an E. coli model of RAD51-overexpressing (most) cancers. Moreover, cancer transcriptomes imply that most cancers suffer frequent fork stalls that are reduced by the HJ removers EME1 and GEN1, as well as by the human RecQ orthologs BLM and RECQL4-surprising potential procancer roles for these known cancer-preventing proteins.

What is mutation? A chapter in the series: How microbes "jeopardize" the modern synthesis

Mutations drive evolution and were assumed to occur by chance: constantly, gradually, roughly uniformly in genomes, and without regard to environmental inputs, but this view is being revised by discoveries of molecular mechanisms of mutation in bacteria, now translated across the tree of life. These mechanisms reveal a picture of highly regulated mutagenesis, up-regulated temporally by stress responses and activated when cells/organisms are maladapted to their environments-when stressed-potentially accelerating adaptation. Mutation is also nonrandom in genomic space, with multiple simultaneous mutations falling in local clusters, which may allow concerted evolution-the multiple changes needed to adapt protein functions and protein machines encoded by linked genes. Molecular mechanisms of stress-inducible mutation change ideas about evolution and suggest different ways to model and address cancer development, infectious disease, and evolution generally.

Abstract GS6-05: The impact of breast cancer surgery on quality of life: Long term results from E5103

Background: Breast cancer (BC) treatment, including surgery, can impact not only short-term health outcomes but may also affect longer term health-related and psychosocial quality of life (QOL). We sought to describe the impact of BC surgery on QOL among breast cancer survivors followed in a large randomized trial.

Methods: The ECOG-ACRIN protocol E5103 was a phase III trial that randomized BC patients (pts) who had undergone definitive BC surgery to receive adjuvant doxorubicin, cyclophosphamide, and paclitaxel with either bevacizumab (bev) or placebo. Telephone based surveys were administered to all pts enrolled between 01/Jan/10 and 08/Jun/10 as part of a Decision-Making/QOL component until 18 mos post enrollment. Functional/psychosocial QOL domains were assessed by the EQ-5D-3L and the FACT B+G. Fisher's exact test compared categorical and Wilcoxon rank sum test compared continuous variables between subgroups. Multivariable regression was used to evaluate factors in addition to primary surgery at enrollment (age, race, ER/PgR status, tumor size, nodal status) associated with overall FACT score at 18 mos.

Results: Patient reported outcomes at 18 mos were available from 89.6% (465/519) pts. At enrollment, 57% (266/465) had a mastectomy; 43% (199/465) breast conserving surgery (BCS). Median age at enrollment was 52 (range: 25-76) years. There were no differences in QOL between bev vs placebo treatment arms (EQ-5D-3L Index Score p=0.65; FACT B+G Score p=0.23) at 18 mos so groups were combined. Using EQ-5D-3L, over half of the pts (58%) reported at least some pain/discomfort; 38% symptoms of anxiety/depression. A higher proportion of mastectomy pts reported problems with usual activities compared to BCS pts (Table). Compared to BCS pts, mastectomy pts had lower average EQ5D-3L scores 0.80 vs. 0.84, p=0.04 and FACT B+G scores 109 vs. 114, p=0.01, indicating worse QOL. In univariate analyses, non-white race (p=0.03), ER/PgR+ status (p=0.04) and mastectomy as primary surgery (p=0.01) were significantly associated with worse QOL (lower FACT B+G scores). In multivariable analyses, non-white race (p=0.02) and ER/PgR+ status (p=0.05) remained associated with worse QOL; mastectomy was borderline significant (p=0.06).

Conclusions: Among women participating in a contemporary adjuvant BC chemotherapy trial, a substantial proportion of survivors experience symptoms that may be amenable to intervention, including referral to physical rehabilitation, especially among pts undergoing more extensive surgery. Attention to psychosocial health is also essential both during and after completion of active treatment to optimize QOL outcomes.

 N(%) reporting problems*  5 DimensionsBCSMastectomyOverallp**Mobility44(23)59(23)103(23)1.00Self-care11(6)23(9)34(7)0.21Usual activities49(25)90(34)139(30)0.04Pain/discomfort104(53)161(61)265(58)0.08Anxiety/depression70(36)105(40)175(38)0.44*3L: 3 possible answers: 1) no problems 2) some/moderate problems 3) problems; responses then collapsed into no problems vs. any problems' (=some/moderate problems and problems). ** Fisher's exact test p-value.

Citation Format: Rosenberg SM, O'Neill A, Sepucha K, Miller KD, Dang CT, Northfelt DW, Sledge GW, Schneider BP, Partridge AH. The impact of breast cancer surgery on quality of life: Long term results from E5103 [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 GS6-05.

Abstract P6-22-03: Tumor phenotype and concordance in synchronous bilateral breast cancer in young women

Background: Synchronous bilateral breast cancer is rare, with reported incidence from 0.3-12%; the incidence and pattern of bilateral breast cancer among younger women is unknown. Here we report the incidence and phenotypes of bilateral breast cancer in women ≤40 years of age enrolled in the Young Women's Study (YWS) cohort.

Methods: The YWS is a multi-center, prospective cohort study that enrolled women with newly diagnosed breast cancer at age ≤40 years from 2006-2016. Those with synchronous bilateral breast cancer (in-situ and/or invasive) formed our study cohort. Disease characteristics and treatment were obtained by medical record review. Central pathology review was performed to capture histologic features and categorize the tumor phenotype as either luminal A (hormone receptor (HR)+, HER2-, grade 1 or 2), luminal B (HR+, HER2+, or HER2- and grade 3), HER2-type (HR-, HER2+), or triple negative (TNC; HR/HER2-). Tumor phenotypes of bilateral breast cancers were compared and evaluated for concordance.

Results: Among 1302 patients enrolled in the YWS, 20 (1.5%) patients presented with bilateral disease, with median age of diagnosis of 38 years (range 18-40). The majority of patients (13 (65%)) presented with unilateral symptoms and contralateral disease was identified on subsequent imaging. 12 (60%) reported a positive family history of breast cancer and 17 (85%) underwent genetic testing; resulting in the identification of 6 mutation carriers (2 BRCA1, 3 BRCA2, 1 TP53). The majority of patients (15 (75%)) underwent bilateral mastectomy, 1 underwent unilateral mastectomy with contralateral lumpectomy, and 4 underwent bilateral lumpectomy. On pathology, 2 patients had bilateral in-situ disease, 5 had unilateral invasive and contralateral in-situ disease, and 13 had bilateral invasive disease. Of those with bilateral invasive disease, all had concordant tumor histology (92% ductal, 8% ductal and lobular), 10 (77%) patients had bilateral luminal tumors and when fully characterized 6 were of the same luminal type. Only one patient had bilateral basal-like breast cancer.

Patient ID ERPRHer2 amplifiedGradePhenotype1Left++-2Luminal A Right++-3Luminal B3Left++-3Luminal B Right++-3Luminal B6Left++-3Luminal B Right++-3Luminal B9Left++-2Luminal A Right++-2Luminal A10Left+++3Luminal B Right++-2Luminal A12Left+--3Luminal B Right+--2Luminal A13Left---NABasal-like Right++-NALuminal A or B14Left+++2Luminal B Right++-3Luminal B15Left++-3Luminal B Right+++3Luminal B16Left+++3Luminal B Right--+NAHEr2-type17Left---3Basal-like Right---3Basal-like19Left++-2Luminal A Right++-3Luminal B20Left++-1Luminal A Right++-2Luminal A

Conclusions: Among a large cohort of young women, only 20 (1.5%) had bilateral disease, and the majority of the invasive tumors were of the luminal phenotype, yet frequently differed by grade or HER2 status; supporting the need for thorough pathologic evaluation of bilateral disease to determine risk and tailor treatment. Overall the low incidence of bilateral disease and preponderance of the luminal phenotype in this population is reassuring.

Citation Format: Pak LM, Rosenberg SM, Ruddy KJ, Tamimi RM, Peppercorn J, Schapira L, Borges VF, Come SE, Warner E, Snow C, Collins L, King TA, Partridge AH. Tumor phenotype and concordance in synchronous bilateral breast cancer in young women [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 P6-22-03.

Abstract P2-14-03: Longitudinal changes in psychosocial health in young women following breast cancer surgery: Results from a multi-center cohort study

Background: Young women with breast cancer (BC) are increasingly choosing contralateral prophylactic mastectomy (CPM), yet little is known about the impact of surgical choices on quality of life (QOL) and psychological health. Using a large, prospective cohort of young women with BC, we sought to evaluate psychosocial outcomes following surgery.

Methods: Among participants of the Young Women's BC Study, a multi-center cohort of women dx'd with BC at age ≤40, we identified women with Stage 0-3 unilateral BC who had surgery and completed surveys that included measures of QOL (CARES) and psychological health (HADS). Linear mixed-effects models were fit to assess changes from 1 to 3 years (yrs) post-dx in anxiety, depression, psychosocial, body image, and sexual scores. Adjusted (stage, hormone receptor status, chemotherapy, age) means were estimated and differences compared (Bonferroni adjusted p-values) between CPM vs breast conserving surgery (BCS) and unilateral mastectomy (UM) at 1, 2, and 3 yrs.

Results: Of 863 women, 30% had BCS, 24% UM, 46% CPM. Median age at dx was 37 (range: 22-40). Of women who had UM/CPM, 84% had reconstruction. Among women who had CPM, mean body image (p=.02), psychosocial (p&lt;.0001), sexual (p&lt;.0001), and depression p=.0007) scores decreased, indicating improvement, from yr 1 to 2 but remained stable from yr 2 to 3 (Table). Anxiety decreased from yr 1 to 2 for women who had BCS (p=.0007) and M (p=.03), and from yr 2 to 3 for women who had CPM (p=.003). Body image scores did not change significantly between any time points among women who had M or BCS. Overall change trajectories for sexual (p=.03) and anxiety scores (p=.008) differed by surgery. Compared to BCS and UM, psychosocial scores were higher in women who had CPM at 1 yr (p&lt;.05) and remained higher compared to BCS at 2 yrs (p=.04). Anxiety was higher among women who had CPM vs UM at 1 and 2 yrs (p&lt;.01), vs BCS at 2 yrs (p=.004). Depression was higher among women who had CPM vs UM in yr 1 (p=.05). By yr 3, there were no significant differences in anxiety, depression, and overall psychosocial scores between groups. Compared to BCS, women who had CPM had higher sexual and body image scores (p&lt;.01), indicating worse QOL, at all timepoints. Compared to UM, women who had CPM had higher sexual scores at 1 and 3 yrs (p&lt;.05) and body image scores at 3 yrs (p=.02).

Conclusions: While psychosocial health improves over time, differences by surgery persist, with women who have CPM experiencing more sexual and body image issues compared to women who undergo BCS or M in the years following surgery. Given that surgical choices may be affected by distress experienced before or at dx, ensuring young women receive adequate support when making surgical decisions as well as after surgery is warranted.

Mean CARES and HADS scores  Year 123Psychosocial*CPM.89.78.76 UM.75.69.66 BCS.72.65.66     Sexual*CPM1.641.371.40 UM1.411.291.08 BCS1.181.071.04     Body image*CPM1.331.221.30 UM1.161.131.04 BCS.64.57.56     Anxiety**CPM7.657.406.79 UM6.505.916.39 BCS7.036.226.50     Depression**CPM3.723.213.25 UM3.022.802.70 BCS3.332.823.13**CARES range: 0-4;higher scores=worse QOL **HADS range 0-21;higher scores=more anxiety/depression

Citation Format: Rosenberg SM, Hu J, Dominici LS, Poorvu PD, Ruddy KJ, Tamimi RM, Schapira L, Come S, Peppercorn JM, Borges VF, Partridge AH. Longitudinal changes in psychosocial health in young women following breast cancer surgery: Results from a multi-center cohort study [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 P2-14-03.

Abstract GS6-06: Local therapy and quality of life outcomes in young women with breast cancer

Background: Increasing rates of mastectomy, primarily bilateral mastectomy (BMx), have been most dramatic in young women with breast cancer (BC). Impact on long-term quality of life (QOL) is largely unknown.

Methods: Between 10/2016-11/2017, we administered the BREAST-Q, a validated patient-reported outcomes measure, to women dx with BC at age ≤40 in a large prospective cohort study. Demographic and treatment information was obtained by surveys and chart review. Mean BREAST-Q scores for each domain (breast satisfaction, physical, psychosocial, and sexual) were compared by surgery types; higher BREAST-Q scores (range: 0-100) indicate better QOL. Linear regression was used to identify predictors of BREAST-Q domain scores.

Results: 581 women with stage 0-3 BC completed the BREAST-Q a median of 5.8 years from dx. Median age at dx was 37 (range: 26-40) years; 86% had stage 0, 1 or 2 disease; 28% had breast-conserving surgery (BCS); 72% had mastectomy (Mx), among whom 72% underwent BMx and 89% had reconstruction. Mean BREAST-Q scores (unadjusted) for breast satisfaction, psychosocial, and sexual well-being were lower for patients having unilateral mastectomy (UMx) or BMx compared to BCS; physical function was similar among groups. In multivariate analysis, lower BREAST-Q psychosocial scores were associated with radiation and Mx (UMx or BMx). Lower sexual well-being scores were also associated with Mx. Lower satisfaction with breast scores following radiation were of a clinically significant magnitude (β -8.1 95% CI -11.9- -4.3, p-value 0.03). Lower scores for physical well-being were seen for patients reporting lymphedema and higher for those who had undergone surgery more than 5 years prior. Lower scores across all 4 domains were associated with reported financial distress.

BREAST-Q domain mean scores (SD) BMxUMxBCSp-valueBreast satisfaction60.3 (18.9)59.5 (21.3)65.9 (20.7)0.008Physical well-being78.6 (14.9)79.7 (15.1)78.9 (15.5)0.8Psychosocial well-being68.1 (20.8)70.5 (21.2)76.1 (20.5)&lt;0.001Sexual well-being48.6 (21.3)53.2 (21.7)57.5 (18.7)&lt;0.001SD Standard deviation

Conclusion: Local therapy in young breast cancer survivors may have a persistent impact on their breast satisfaction, psychosocial, and sexual outcomes, with particular effects from UMx or BMx. Socio-economic stressors also appear to play a role. When counseling young women about their surgical decisions, knowledge of potential long-term QOL impact is of critical importance.

Citation Format: Dominici LS, Hu J, King TA, Ruddy KJ, Tamimi RM, Peppercorn J, Schapira L, Borges VF, Come SE, Warner E, Partridge AH, Rosenberg SM. Local therapy and quality of life outcomes in young women with 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 GS6-06.

Abstract P2-08-07: Prognostic impact of the 21-gene recurrence score assay among young women with node-negative and node-positive ER+/HER2- breast cancer

Background: The 21-gene Recurrence Score (RS) assay is prognostic among women with early-stage estrogen receptor (ER) positive and human epidermal growth factor receptor 2 (HER2) negative breast cancer (BC) and is used to select patients for chemotherapy (CT). Young women (age &lt;40) have represented a minority in studies evaluating gene expression assays, including TAILORx, and additional data in young women are needed.

Methods: In the Young Women's Breast Cancer Study, a prospective cohort study of women diagnosed with BC at age &lt;40 enrolling between 2006-2016 (N=1302), we identified those with stage I-III ER+/HER2- BC. Disease and treatment information were obtained through serial surveys and medical record review. The RS was performed on banked specimens for those not tested clinically. Distant recurrence free interval (DRFI), defined as distant recurrence or BC specific death, by risk group was assessed using Cox regression and Kaplan-Meier survival estimates. Outcomes by receipt of CT were explored in the RS 11-25 group, and due to small number of events, reported descriptively.

Results: Among eligible women (N=577), 189 (33%) had undergone RS testing and 320 (56%) had banked specimens sufficient for testing. Median follow-up was 6 years. Median age at diagnosis was 37, most had N0 BC (300/509, 59%), and the majority had RS 11-25 (306/509, 60%). RS result was significantly associated with DRFI in N0 BC, with hazard ratio (HR) (95% CI) of 0.29 (0.07,1.30) and 0.21 (0.09,0.50) for RS&lt;11 and RS 11-25, respectively, relative to RS&gt;26 (and trended towards significance in N1 BC). Results were similar using conventional RS groups. Among women with N0 BC and RS 11-25, 44% received CT, with two events in the 86 receiving CT (2.3%) and 6 events in the 109 without CT (5.5%); 5/8 (63%) occurred in those with RS 20-25.

Table 1 N0N1Total Cohort N%N%N% 3005916332509100Median Age37.137.537.2Tumor Stage      T120869694229358T28227784817635T3103159357T4001151Grade      I4716855711II16555794926652III8829754618536Not assessed  1 1 PR status by IHC      Negative (&lt;1%)2071710398Positive (&gt;=1%)280931469047092Chemotherapy      No1414712715430Yes159531519335570Ovarian Suppression      No263881499145289Yes37121495711TAILORx RS Groups      RS &lt;1133111495411RS 11-2519565885430660RS &gt;=267224613714929Conventional RS Groups      RS &lt;1812742543319939RS 18-3012542694221142RS &gt;=31481640259919

Table 2 6-year freedom from distant recurrence or breast cancer deathDRFI HR (95% CI) N0N1N0N1TAILORx RS Groups    RS &lt;1194.4%92.3%0.29 (0.07,1.30)0.21 (0.03,1.61)RS 11-2596.9%85.2%0.21 (0.09, 0.50)0.55 (0.27,1.12)RS &gt;=2685.1%71.3%RefRefConventional RS Groups    RS &lt;1897.5%85.9%0.19 (0.06,0.59)0.31 (0.13,0.74)RS 18-3093.1%87.3%0.39 (0.16,1.00)0.32 (0.14,0.73)RS &gt;=3186.4%62.8%RefRef

Conclusions: The RS is prognostic among young women with node-negative and node-positive BC, and is a valuable tool for risk stratification. Disease outcomes among young women with N0 disease and RS 11-25, a minority of whom received CT, are very good. Evaluation of the effect of ovarian suppression/CT-induced amenorrhea by RS/treatment strata is ongoing.

Citation Format: Poorvu PD, Gelber SI, Rosenberg SM, Ruddy KJ, Tamimi RM, Collins LC, Peppercorn J, Schapira L, Borges VF, Come SE, Warner E, Jakubowski DM, Russell C, Winer EP, Partridge AH. Prognostic impact of the 21-gene recurrence score assay among young women with node-negative and node-positive ER+/HER2- 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 P2-08-07.

Abstract P1-12-05: A qualitative exploration of self-developed and peer-recommended techniques used by women with breast cancer to improve sexual functioning during and after treatment

Background: Coping with sexual dysfunction during and after breast cancer treatment is a persistent challenge for many women, even if clinicians offer standard sexual rehabilitative therapies (e.g. lubricants, counseling). This study sought to explore how women with breast cancer supplement clinician recommendations with self-developed and peer-recommended techniques for improving sexual function, what those techniques are, and how well they work.

Methods: We conducted a cross-sectional, online survey of 501 adult women with stage I-IV breast cancer who were members of the Breastcancer.org community. Open-ended survey items asked women to describe any techniques used to improve sexual function during and after breast cancer treatment beyond those recommended by clinicians. Closed-ended items asked women to assess the source and perceived efficacy of their techniques. We used qualitative content analysis to extract themes that described women's techniques and calculated frequencies in StataMP 15 to quantify sources and efficacy levels.

Results: Participants were, on average, age 53 (range 30-79) and 10 years from diagnosis. Most were partnered (90%), heterosexual (96%), with stage I/II disease (73%). 174/501 (35%) women reported using a sexual self-management technique they developed themselves or that was recommended by someone other than a clinician. Emergent themes in techniques included: 1) pain reduction: trial-and-error to find an effective lubricant or moisturizer (e.g. coconut oil), changing sex positions, choosing oral sex over intercourse 2) intimacy enhancement: open partner communication, planning sex 3) arousal enhancement: masturbation, erotica, vibrator use 4) emotional coping: adopting an attitude of persistence vs. acceptance of loss of sex life, encouraging partners to use sexual surrogates. 77 women developed the technique themselves, 54 with partners, 37 heard about it from survivors, 36 read about it online. 45% of women rated their techniques as moderately or more effective when used in addition to or instead of standard therapies offered by clinicians.

Conclusion: In a survey of an Internet-based community of women treated for breast cancer, women reported a variety of successful techniques for increasing intimacy and arousal, reducing vaginal pain, and coping emotionally with changes in sexual life after breast cancer. More women reported developing these techniques on their own or with partners vs. learning them from others. Given that standard therapies are often insufficient to manage sexual dysfunction during and after breast cancer treatment, clinicians should address sexual function during follow-up care and encourage women's safe experimentation with techniques for improving sexual function. Clinicians can refer patients to platforms like Breastcancer.org for peer-to-peer support and information exchange. Existing self-developed and peer-recommended techniques should be evaluated for safety, quality, and generalizability. Future research can then assess the effectiveness of particularly novel techniques as a complement to standard, clinician-developed therapies for the broader population of women with breast cancer experiencing sexual dysfunction.

Citation Format: von Hippel CD, Rosenberg SM, Jenkins MB, Weiss MC, Partridge AH. A qualitative exploration of self-developed and peer-recommended techniques used by women with breast cancer to improve sexual functioning during and after treatment [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 P1-12-05.

Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage

DNA damage provokes mutations and cancer and results from external carcinogens or endogenous cellular processes. However, the intrinsic instigators of endogenous DNA damage are poorly understood. Here, we identify proteins that promote endogenous DNA damage when overproduced: the DNA "damage-up" proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six function clusters, demonstrating DDP mechanisms in three: reactive oxygen increase by transmembrane transporters, chromosome loss by replisome binding, and replication stalling by transcription factors. Their 284 human homologs are over-represented among known cancer drivers, and their RNAs in tumors predict heavy mutagenesis and a poor prognosis. Half of the tested human homologs promote DNA damage and mutation when overproduced in human cells, with DNA damage-elevating mechanisms like those in E. coli. Our work identifies networks of DDPs that provoke endogenous DNA damage and may reveal DNA damage-associated functions of many human known and newly implicated cancer-promoting proteins.

Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways

Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.

Fluorescent fusions of the N protein of phage Mu label DNA damage in living cells

The N protein of phage Mu was indicated from studies in Escherichia coli to hold linear Mu chromosomes in a circular conformation by non-covalent association, and thus suggested potentially to bind DNA double-stranded ends. Because of its role in association with linear Mu DNA, we tested whether fluorescent-protein fusions to N might provide a useful tool for labeling DNA damage including double-strand break (DSB) ends in single cells. We compared N-GFP with a biochemically well documented DSB-end binding protein, the Gam protein of phage Mu, also fused to GFP. We find that N-GFP produced in live E. coli forms foci in response to DNA damage induced by radiomimetic drug phleomycin, indicating that it labels damaged DNA. N-GFP also labels specific DSBs created enzymatically by I-SceI double-strand endonuclease, and by X-rays, with the numbers of foci corresponding with the numbers of DSBs generated, indicating DSB labeling. However, whereas N-GFP forms about half as many foci as GamGFP with phleomycin, its labeling of I-SceI- and X-ray-induced DSBs is far less efficient than that of GamGFP. The data imply that N-GFP binds and labels DNA damage including DSBs, but may additionally label phleomycin-induced non-DSB damage, with which DSB-specific GamGFP does not interact. The data indicate that N-GFP labels DNA damage, and may be useful for general, not DSB-specific, DNA-damage detection.

Abstract P4-15-11: “Is it cancer or not?” A qualitative exploration of patient perspectives surrounding the diagnosis and treatment of DCIS

Background: Approximately 53,000 women in the US undergo treatment for ductal carcinoma in situ (DCIS) each year, of whom only 20-30% may benefit. To better understand both the clinical and psychosocial impact of a DCIS diagnosis and different management approaches, we sought to engage women with DCIS regarding their experience surrounding diagnosis (dx) and treatment.

Methods: In July 2014, we administered a web-based survey through an email listserv to the Susan Love Army of Women that resulted in over 2000 respondents self-identified as patients with DCIS. The survey included open-ended questions designed to assess patients' perspectives on their experiences with the dx and treatment of their DCIS. Responses were coded using an inductive coding schema; common themes were identified and summarized. Women who reported an invasive cancer, a second primary or recurrent tumor, or other benign breast lesions (in absence of DCIS) were excluded from analysis.

Results: Among 1,857 women included in the analytic sample, the average age at dx was 60 years; 18% women were ≤2 years from their dx; most women (93%) identified as white. Four primary themes were identified: 1) uncertainty about DCIS dx; 2) uncertainty surrounding treatment; 3) concern about side effects from treatment; and 4) concern about recurrence and invasive breast cancer. Uncertainty about treatment often manifested as women questioning whether they were over-treated for their DCIS, “over-reacting by having surgery,” or wondering if “watchful waiting might be better.” In addition to recalling bothersome side effects and sequelae from both their local and systemic (hormonal) therapy, women also expressed doubt about their treatment choices, specifically, that they were not necessarily “doing enough” with many women citing recurrence, the “cancer spreading”, or becoming invasive, as primary concerns. Uncertainty about whether DCIS was cancer or not, was noted by many women, with one calling it a “grey zone” and others articulating that DCIS is “having a dx that's not really cancer… yet you might still lose your breast,” and experiencing “confusion about my status as a cancer patient - as in I wasn't sure if I even was a cancer patient. I had no idea where I fit in…”

Conclusion: A DCIS dx can be confusing and distressing, with women making treatment decisions based on a limited understanding of the disease, its risks, and pros and cons of treatment options. There is a need to develop additional strategies to improve the management of this disease and other screen-detected conditions, through better understanding of the disease and its outcomes, coupled with improved methods to communicate this information to those affected. Our study highlights the potential value of collecting patient reported outcomes (PROs) to inform clinical research and care. Ongoing clinical trials like the COMET, LORIS, and LORD studies, which incorporate robust PROs, should provide additional evidence for patients, health care providers and other stakeholders regarding the medical and psychosocial benefits and harms of different DCIS management options.

Citation Format: Rosenberg SM, Gierisch JM, Lowenstein C, Frank ES, Collyer D, Partridge AH, Hwang ES. “Is it cancer or not?” A qualitative exploration of patient perspectives surrounding the diagnosis and treatment of DCIS [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 P4-15-11.

Abstract P3-12-06: Fertility concerns and their impact on hormonal therapy decisions in young breast cancer survivors

Background: Fertility is a critical issue for young breast cancer (BC) survivors and can be diminished by adjuvant chemotherapy or by age-related decline in ovarian reserve over time. Little is known about how fertility concerns affect decision-making and persistence with endocrine therapy (ET) given the standard 5-10 year duration of therapy during which pregnancy is contraindicated.

Methods: As part of a multi-center, prospective cohort study enrolling women with newly diagnosed (dx) BC at age ≤40 years between 2006-2016, we identified participants with HR+, Stage I-III BC, without documented recurrence and with at least 3 years of follow-up. Participants completed serial surveys that include questions about socio-demographics, fertility issues and outcomes, treatment, and decision-making. ET use and pregnancy outcomes were evaluated up to 5 years post-dx (mean follow-up: 4.4 years). We used t-tests and chi-square tests to evaluate differences between women who indicated at least once in the first 2 years following diagnosis that fertility concerns affected their ET decisions and those who did not, and multi-variable logistic regression to identify factors independently associated (p≤0.05) with indicating ET decisions were affected by fertility concerns.

Results: Among 479 women included in this analysis, 33% (156/479) indicated that fertility concerns affected their decision regarding hormonal therapy – by choosing to defer treatment, stop early, or indicating that they may stop early or interrupt at a future time. Among these women, 44% (67/156) did not initiate or stopped ET (at least temporarily) vs. 21% (68/323) among women who did not indicate that fertility concerns affected their decision (p&lt;0.0001). Among the 67 women with fertility concerns who did not initiate/discontinued ET, 29 (43%) subsequently reported a pregnancy within 5 years of dx. Women who were younger at dx, not partnered, nulliparous, and those who had a pre-treatment discussion about fertility with a provider were more likely to indicate that fertility concerns affected their ET decision (Table). In multi-variable analyses, only no or low parity remained significant: no children at diagnosis vs. ≥2 OR 9.86, 95% CI: 5.19-18.75, 1 child at diagnosis vs. ≥2: OR 6.28, 95% CI: 3.18-12.39.

Conclusion: Concern about fertility is a contributor to ET decisions among a significant number of young women with HR+ BC. Ongoing research, including the POSITIVE trial (NCT 02308085), an international study that is exploring the safety and feasibility of interrupting ET for pregnancy after HR+ BC, will provide much needed evidence that will help inform and guide both patients and providers as they make fertility and treatment decisions.

Table Fertility concerns affected decisionFertility concerns did not affect decisionpAge at dx - mean (SD)34.0 (3.8)36.3 (3.8)&lt;0.0001Stage  0.17172 (46)128 (40) 269 (44)146 (45) 315 (10)49 (15) Chemo  0.41Yes112 (73)247 (77) No41 (27)75 (23) Radiation  0.96Yes98 (64)205 (64) No56 (36)116 (36) Partnered  &lt;0.0001Yes106 (69)272 (84) No48 (31)50 (16) Children pre-diagnosis  &lt;0.0001094 (64)73 (23) 131 (21)43 (14) &gt; 2 children22 (15)197 (63) Pre-treatment fertility discussion  0.0003Yes127 (88)225 (73) No17 (12)84 (27) 

Citation Format: Poorvu PD, Ruddy KJ, Gelber SI, Tamimi RM, Peppercorn J, Schapira L, Borges VF, Come SE, Partridge AH, Rosenberg SM. Fertility concerns and their impact on hormonal therapy decisions in young breast cancer survivors [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 P3-12-06.

Abstract P6-12-08: Fertility interest, management and outcomes in young BRCA+ breast cancer survivors

Background: Young women with BRCA mutations may face fertility issues given the standard recommendation for risk-reducing oophorectomy after childbearing has been completed or before age 40. Potential transmission of the affected gene to future progeny may also be a concern. Little is known regarding the perspectives, management, and outcomes of young breast cancer survivors with BRCA mutations, who also face risks of recurrent disease and treatment effects on fertility.

Methods: As part of a multi-center, prospective cohort study of newly diagnosed breast cancer (BC) at age ≤40 years enrolling between 2006-2016, we identified women with stage I-III BC who had self-reported results of genetic testing. Participants are surveyed at baseline then annually regarding their breast cancer treatment, genetic testing, fertility interest, pregnancy attempts, and pregnancies. Chi-square tests were used to compare proportions of carriers vs non-carriers who were interested in future biologic children, took steps to preserve fertility, underwent bilateral oophorectomy, attempted pregnancy, and became pregnant in the 5 years following diagnosis.

Results: Carriers (n=104) and non-carriers (n=662) were similar in age and stage, but greater proportions of carriers had ER negative disease and received chemotherapy (Table 1). The proportion of carriers and non-carriers interested in future biologic children was similar prior to diagnosis (51% vs 38%; p=0.18), 1 year following diagnosis (30% vs 27%; p=0.44), and 5 years following diagnosis (14% vs 15%; p=0.26). Similar proportions of carriers (12%) and non-carriers (14%) took steps to prevent infertility prior to treatment. Greater proportions of carriers indicated that concern about having a child at higher risk of breast cancer affected their interest in future biologic children (15% vs 4%, p=0.02) and underwent bilateral oophorectomy (61% vs 9%, p&lt;0.0001), but there was no difference in rates of pregnancy attempts (15% vs 11%, p=0.62), or pregnancies (12% vs 8%, p=0.36) in the five years following diagnosis.

Conclusion: Young breast cancer survivors with known BRCA mutations have similar interest in future fertility and both attempt and become pregnant at similar rates to non-carriers in the five years following diagnosis. Impact of specific BRCA mutation (1 or 2), ER status of tumor, and timing of pregnancy attempts will be explored in future analyses.

Table 1: BRCA mutation carriers, n (%)Non-carriers, n (%)X2 p-valueAge  0.47&lt;3018 (17)86 (13) 31-3529 (28)201 (30) 36-4057 (55)375 (57) Stage  0.73I40 (39)260 (39) II46 (44)307 (46) III18 (17)95 (14) Partnered  0.44Yes77 (74)509 (77) No27 (26)148 (22) Missing0 (0)5 (1) Children pre-diagnosis  0.33Yes62 (60)427 (64) No42 (40)235 (36) Phenotype  &lt;0.0001ER and/or PR+48 (46)490 (74) ER and PR-56 (54)171 (26) Missing0 (0)1 (0) Adjuvant hormones  &lt;0.0001Yes44 (42)488 (74) No60 (58)174 (26) Chemotherapy  0.003Yes96 (92)529 (80) No8 (8)132 (2) Missing0 (0)1 (0) 

Citation Format: Poorvu PD, Gelber SI, Ruddy KJ, Seiger K, Tamimi RM, Peppercorn J, Schapira L, Borges VF, Come SE, Partridge AH, Rosenberg SM. Fertility interest, management and outcomes in young BRCA+ breast cancer survivors [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 P6-12-08.

Persistent damaged bases in DNA allow mutagenic break repair in Escherichia coli

Bacteria, yeast and human cancer cells possess mechanisms of mutagenesis upregulated by stress responses. Stress-inducible mutagenesis potentially accelerates adaptation, and may provide important models for mutagenesis that drives cancers, host pathogen interactions, antibiotic resistance and possibly much of evolution generally. In Escherichia coli repair of double-strand breaks (DSBs) becomes mutagenic, using low-fidelity DNA polymerases under the control of the SOS DNA-damage response and RpoS general stress response, which upregulate and allow the action of error-prone DNA polymerases IV (DinB), II and V to make mutations during repair. Pol IV is implied to compete with and replace high-fidelity DNA polymerases at the DSB-repair replisome, causing mutagenesis. We report that up-regulated Pol IV is not sufficient for mutagenic break repair (MBR); damaged bases in the DNA are also required, and that in starvation-stressed cells, these are caused by reactive-oxygen species (ROS). First, MBR is reduced by either ROS-scavenging agents or constitutive activation of oxidative-damage responses, both of which reduce cellular ROS levels. The ROS promote MBR other than by causing DSBs, saturating mismatch repair, oxidizing proteins, or inducing the SOS response or the general stress response. We find that ROS drive MBR through oxidized guanines (8-oxo-dG) in DNA, in that overproduction of a glycosylase that removes 8-oxo-dG from DNA prevents MBR. Further, other damaged DNA bases can substitute for 8-oxo-dG because ROS-scavenged cells resume MBR if either DNA pyrimidine dimers or alkylated bases are induced. We hypothesize that damaged bases in DNA pause the replisome and allow the critical switch from high fidelity to error-prone DNA polymerases in the DSB-repair replisome, thus allowing MBR. The data imply that in addition to the indirect stress-response controlled switch to MBR, a direct cis-acting switch to MBR occurs independently of DNA breakage, caused by ROS oxidation of DNA potentially regulated by ROS regulators.

Driving cancer evolution

Tumor-growth-factor-beta signaling helps cancer cells to evolve and become resistant to drugs by down-regulating accurate DNA repair.

Stress-Induced Mutagenesis: Implications in Cancer and Drug Resistance

Genomic instability underlies many cancers and generates genetic variation that drives cancer initiation, progression, and therapy resistance. In contrast with classical assumptions that mutations occur purely stochastically at constant, gradual rates, microbes, plants, flies, and human cancer cells possess mechanisms of mutagenesis that are upregulated by stress responses. These generate transient, genetic-diversity bursts that can propel evolution, specifically when cells are poorly adapted to their environments-that is, when stressed. We review molecular mechanisms of stress-response-dependent (stress-induced) mutagenesis that occur from bacteria to cancer, and are activated by starvation, drugs, hypoxia, and other stressors. We discuss mutagenic DNA break repair in Escherichia coli as a model for mechanisms in cancers. The temporal regulation of mutagenesis by stress responses and spatial restriction in genomes are common themes across the tree of life. Both can accelerate evolution, including the evolution of cancers. We discuss possible anti-evolvability drugs, aimed at targeting mutagenesis and other variation generators, that could be used to delay the evolution of cancer progression and therapy resistance.

Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase

DNA repair by homologous recombination (HR) underpins cell survival and fuels genome instability, cancer, and evolution. However, the main kinds and sources of DNA damage repaired by HR in somatic cells and the roles of important HR proteins remain elusive. We present engineered proteins that trap, map, and quantify Holliday junctions (HJs), a central DNA intermediate in HR, based on catalytically deficient mutant RuvC protein of Escherichia coli. We use RuvCDefGFP (RDG) to map genomic footprints of HR at defined DNA breaks in E. coli and demonstrate genome-scale directionality of double-strand break (DSB) repair along the chromosome. Unexpectedly, most spontaneous HR-HJ foci are instigated, not by DSBs, but rather by single-stranded DNA damage generated by replication. We show that RecQ, the E. coli ortholog of five human cancer proteins, nonredundantly promotes HR-HJ formation in single cells and, in a novel junction-guardian role, also prevents apparent non-HR-HJs promoted by RecA overproduction. We propose that one or more human RecQ orthologs may act similarly in human cancers overexpressing the RecA ortholog RAD51 and find that cancer genome expression data implicate the orthologs BLM and RECQL4 in conjunction with EME1 and GEN1 as probable HJ reducers in such cancers. Our results support RecA-overproducing E. coli as a model of the many human tumors with up-regulated RAD51 and provide the first glimpses of important, previously elusive reaction intermediates in DNA replication and repair in single living cells.

Abstract P4-10-04: Employment trends in young women following a breast cancer diagnosis

Background: Workplace concerns are particularly salient for young women with breast cancer (BC), and a cancer diagnosis (dx) and treatment may affect their careers. We sought to evaluate the perceived impact of dx on employment, describe job changes, and identify factors associated with transition out of the workforce after dx of BC at a young age.

Methods: As part of an ongoing, multi-center cohort of young women diagnosed with BC at age ≤ 40, we surveyed women with early-stage BC about their pre- and post-dx employment status. Additional items assessed socio-demographic and treatment information; tumor characteristics were ascertained via pathology and medical record review. We used logistic regression to identify predictors of transitioning from pre-dx employment to unemployment at 1 year after dx. Among women employed 1 year after dx, we evaluated job satisfaction, perceived impact of dx on job performance, accommodations made by employers, and perceived likelihood of employment in the future.

Results: 76% of women (555/730) were employed both before dx and at 1 year; 13% were not employed at either time point; 7% were employed pre-dx but unemployed at 1 year; 4% were not employed prior to dx but reported employment at 1 year. Among women employed 1 year after dx, 74% (427/581) were somewhat or completely satisfied with their job. Only 6% said cancer or treatment limited their ability to perform their job quite a bit or very much; 38% said their ability was affected a little bit. Most (63%) said their employers had made accommodations for them, and almost all women (93%) said it was very likely they would be working in 1 year. In multivariable analyses (Table 1), women with stage 3 disease (vs. stage 1), were more likely to transition out of the workforce following dx, while women with a college or graduate degree (vs. no college degree) were less likely to transition out.

Conclusion: Most young women with early stage BC remain employed and report a willingness by their employer to make accommodations following a breast cancer dx. While few women reported that their dx or treatment limited their job performance, the finding that women with more advanced disease were more likely to transition out of the workforce suggests an impact of dx/treatment burden on employment. Women without a college degree were also at risk for unemployment post-dx, suggesting that job type, socioeconomic status, and environment affect employment outcomes. Attention to these subgroups of women is warranted to ensure that they are sufficiently supported given the potential adverse psychosocial and financial impacts of unemployment on patients, families, communities, and society.

Table 1. Multivariable analysis of factors associated with transition out of workforce 1year post-dx (N=634) OR (95% CI)Stage (ref=1) 04.52 (0.60-33.85)21.11 (0.48-2.58)34.05 (1.53-10.72)*White non-Hispanic (ref=non-WNH)1.47 (0.56-3.81)College graduate (ref=no college degree)0.44 (0.22-0.90)*Married/Living as married (ref=unmarried)0.95 (0.43-2.08)Parous (ref=nulliparous)1.75 (0.83-3.69)Age at diagnosis (years)0.98 (0.90-1.06)Mastectomy (ref=lumpectomy)1.74 (0.75-4.05)Endocrine therapy (ref=none)0.75 (0.41-1.39)Chemotherapy (ref=none)5.20 (0.93-29.22)Radiation (ref=none)1.38 (0.64-2.96)*p&lt;0.05

Citation Format: Partridge AH, Rosenberg SM, Rajagopal PS, Ruddy KJ, Tamimi RM, Schapira L, Come S, Borges V, Gelber S. Employment trends in young women following a breast cancer diagnosis. [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 P4-10-04.

Abstract P1-10-18: Contraception use in young women with breast cancer

Background: Young women with breast cancer need highly effective contraception given the potential implications of unplanned pregnancy for optimal treatment, and the teratogenic risks. We sought to determine the contraceptive methods used by young women after diagnosis (dx) of breast cancer and factors associated with use of less effective methods or no contraceptive method, which confers a 6-90% annual risk of pregnancy in sexually active women in contrast to highly effective methods (risk &lt;1%).

Methods: As part of a randomized trial conducted in 54 sites to test an education and support intervention for young women with breast cancer and their oncologists, we surveyed women about their pre-dx, current, and planned contraceptive use, and about communication with their providers regarding contraception. Women enrolled within 3 months of dx; contraception items were included on 3- and 12-month post-enrollment surveys. Intrauterine device (IUD) use, tubal sterilization, hysterectomy or bilateral salpingo-oophorectomy (hyst/BSO) after dx, or male partner vasectomy were classified as highly effective methods; all other methods and non-use were categorized as less effective. We excluded women not at risk of pregnancy: hyst/BSO prior to dx, or no indication for contraception. We used logistic regression to explore factors associated with use of less effective methods.

Results: Of 424 women who completed the 3-month post-enrollment survey, median age at dx was 39 (range 22-45). 312 women at risk of pregnancy were included in this analysis, including 291 reporting sexual activity with a male partner within the last 6 months, and 21 reporting no recent sexual activity but reporting use of birth control. 123 women (39%) used highly effective contraceptive methods prior to dx; after dx, 161 (52%) reported current use of or a plan to use a highly effective method. 19 women (6%) reported use of a hormonal birth control method since dx; 7 (2%) reported withdrawal as their only contraceptive method; 25 (8%) reported no contraception. 30% of women did not recall a discussion of avoiding pregnancy or need for contraception during treatment with their providers. In multivariable analyses (N=310), desire for additional biologic children (OR 7.54, 95% CI 3.88-14.66) and provider discussion of contraception and pregnancy (OR 2.13 95% CI 1.20-3.78) were associated with use of less effective contraception. Age, race/ethnicity, disease stage, and partner status were not significantly associated with use of less effective methods.

Conclusion: About half of women who are at risk of pregnancy reported use or planned use of less effective contraceptive methods or no method of contraception following dx of breast cancer. Women with breast cancer and their providers may benefit from targeted education on contraceptive options and method effectiveness.

Citation Format: Rosenberg SM, Dutton CR, Ligibel J, Barry W, Ruddy KJ, Sprunck-Harrild K, Emmons KM, Partridge AH. Contraception use in young women with breast cancer. [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 P1-10-18.

The DNA polymerase III holoenzyme contains γ and is not a trimeric polymerase

There is widespread agreement that the clamp loader of the Escherichia coli replicase has the composition DnaX₃δδ’χψ. Two DnaX proteins exist in E. coli, full length τ and a truncated γ that is created by ribosomal frameshifting. τ binds DNA polymerase III tightly; γ does not. There is a controversy as to whether or not DNA polymerase III holoenzyme (Pol III HE) contains γ. A three-τ form of Pol III HE would contain three Pol IIIs. Proponents of the three-τ hypothesis have claimed that γ found in Pol III HE might be a proteolysis product of τ. To resolve this controversy, we constructed a strain that expressed only τ from a mutated chromosomal dnaX. γ containing a C-terminal biotinylation tag (γ-C_tag) was provided in trans at physiological levels from a plasmid. A 2000-fold purification of Pol III* (all Pol III HE subunits except β) from this strain contained one molecule of γ-C_tag per Pol III* assembly, indicating that the dominant form of Pol III* in cells is Pol III₂τ₂ γδδ’χψ. Revealing a role for γ in cells, mutants that express only τ display sensitivity to ultraviolet light and reduction in DNA Pol IV-dependent mutagenesis associated with double-strand-break repair, and impaired maintenance of an F’ episome.

Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in Starving Escherichia coli

The mutagenicity of DNA double-strand break repair in Escherichia coli is controlled by DNA-damage (SOS) and general (RpoS) stress responses, which let error-prone DNA polymerases participate, potentially accelerating evolution during stress. Either base substitutions and indels or genome rearrangements result. Here we discovered that most small basic proteins that compact the genome, nucleoid-associated proteins (NAPs), promote or inhibit mutagenic break repair (MBR) via different routes. Of 15 NAPs, H-NS, Fis, CspE, and CbpA were required for MBR; Dps inhibited MBR; StpA and Hha did neither; and five others were characterized previously. Three essential genes were not tested. Using multiple tests, we found the following: First, Dps, which reduces reactive oxygen species (ROS), inhibited MBR, implicating ROS in MBR. Second, CbpA promoted F' plasmid maintenance, allowing MBR to be measured in an F'-based assay. Third, Fis was required for activation of the SOS DNA-damage response and could be substituted in MBR by SOS-induced levels of DinB error-prone DNA polymerase. Thus, Fis promoted MBR by allowing SOS activation. Fourth, H-NS represses ROS detoxifier sodB and was substituted in MBR by deletion of sodB, which was not otherwise mutagenic. We conclude that normal ROS levels promote MBR and that H-NS promotes MBR by maintaining ROS. CspE positively regulates RpoS, which is required for MBR. Four of five previously characterized NAPs promoted stress responses that enhance MBR. Hence, most NAPs affect MBR, the majority via regulatory functions. The data show that a total of six NAPs promote MBR by regulating stress responses, indicating the importance of nucleoid structure and function to the regulation of MBR and of coupling mutagenesis to stress, creating genetic diversity responsively.

An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli

With the wide availability of whole-genome sequencing (WGS), genetic mapping has become the rate-limiting step, inhibiting unbiased forward genetics in even the most tractable model organisms. We introduce a rapid deconvolution resource and method for untagged causative mutations after mutagenesis, screens, and WGS in Escherichia coli. We created Deconvoluter—ordered libraries with selectable insertions every 50 kb in the E. coli genome. The Deconvoluter method uses these for replacement of untagged mutations in the genome using a phage-P1-based gene-replacement strategy. We validate the Deconvoluter resource by deconvolution of 17 of 17 phenotype-altering mutations from a screen of N-ethyl-N-nitrosourea-induced mutants. The Deconvoluter resource permits rapid unbiased screens and gene/function identification and will enable exploration of functions of essential genes and undiscovered genes/sites/alleles not represented in existing deletion collections. This resource for unbiased forward-genetic screens with mapping-by-sequencing (‘forward genomics’) demonstrates a strategy that could similarly enable rapid screens in many other microbes.

Atypical Role for PhoU in Mutagenic Break Repair under Stress in Escherichia coli

Mechanisms of mutagenesis activated by stress responses drive pathogen/host adaptation, antibiotic and anti-fungal-drug resistance, and perhaps much of evolution generally. In Escherichia coli, repair of double-strand breaks (DSBs) by homologous recombination is high fidelity in unstressed cells, but switches to a mutagenic mode using error-prone DNA polymerases when the both the SOS and general (σS) stress responses are activated. Additionally, the σE response promotes spontaneous DNA breakage that leads to mutagenic break repair (MBR). We identified the regulatory protein PhoU in a genetic screen for functions required for MBR. PhoU negatively regulates the phosphate-transport and utilization (Pho) regulon when phosphate is in excess, including the PstB and PstC subunits of the phosphate-specific ABC transporter PstSCAB. Here, we characterize the PhoU mutation-promoting role. First, some mutations that affect phosphate transport and Pho transcriptional regulation decrease mutagenesis. Second, the mutagenesis and regulon-expression phenotypes do not correspond, revealing an apparent new function(s) for PhoU. Third, the PhoU mutagenic role is not via activation of the σS, SOS or σE responses, because mutations (or DSBs) that restore mutagenesis to cells defective in these stress responses do not restore mutagenesis to phoU cells. Fourth, the mutagenesis defect in phoU-mutant cells is partially restored by deletion of arcA, a gene normally repressed by PhoU, implying that a gene(s) repressed by ArcA promotes mutagenic break repair. The data show a new role for PhoU in regulation, and a new regulatory branch of the stress-response signaling web that activates mutagenic break repair in E. coli.

Medicine. Combating evolution to fight disease

Molecular mechanisms that generate biological diversity are rewriting ideas about how evolution proceeds, with implications for treating disease.

Abstract P2-18-02: Factors associated with contralateral prophylactic mastectomy in young women with breast cancer

Background: While younger age at diagnosis has consistently been identified as a predictor of contralateral prophylactic mastectomy (CPM), little is known about how clinical, decisional, and psychosocial factors are related to the decision to undergo CPM in young women with breast cancer.

Methods: As part of an ongoing, multi-center cohort study of young women diagnosed with breast cancer at age 40 or younger, we identified 428 women with unilateral Stage I-III disease. Participants were asked to complete surveys by mail that included questions about decision-making and treatments. Tumor characteristics were ascertained via medical record review. Multinomial logistic regression was used to identify predictors of: 1) CPM vs. unilateral mastectomy (UM); 2) CPM vs. breast conserving surgery (BCS). Independent variables with a p-value ≤ 0.15 in bi-variate analyses were included in the final multivariable model.

Results: 41% of women had CPM, 29% had UM and 31% had BCS. Median age at diagnosis was 37 (range: 17-40). Most women had stage I or II disease (87%), and estrogen receptor (ER) positive tumors (69%); approximately 14% were carriers of a BRCA 1 or 2 mutation. In the multivariable analysis (Table 1), having a cancer-predisposing mutation, having at least one child, anxiety as measured by the Hospital Anxiety and Depression Scale (HADS), and patient-driven decision making were all associated with a greater likelihood of undergoing CPM, while women who reported their physician made the final decision about surgery were less likely to undergo CPM, compared to both UM and BCS. Additional factors significantly associated with undergoing CPM vs. BCS included nodal involvement, Her2 positivity, and lower BMI. Race/ethnicity, marital status, tumor size, tumor grade, depression (as measured by the HADS), fear of recurrence, and having a first-degree relative with breast or ovarian cancer were not associated with undergoing CPM.

Conclusion: Many young women with early stage breast cancer are choosing to undergo CPM. Our findings point to the need for improved communication with patients regarding surgical choices as well as better management of anxiety surrounding diagnosis. Interventions aimed at enhancing risk communication and encouraging shared patient-physician decision-making might be beneficial in this setting.

Table 1. Factors associated with: 1) CPM vs. UM; 2) CPM vs. BCS CPM vs. UMCPM vs. BCS OR (95% CI)OR (95% CI)Age at diagnosis0.92 (0.86-1.00)0.97 (0.90-1.04)Mutation positive3.83 (1.60-9.15)14.51 (5.02-41.92)Any nodal involvement0.79 (0.45-1.38)1.93 (1.05-3.55)Her2 positivity0.71 (0.40-1.26)2.24 (1.18-4.25)Having ≥ 1 child2.08 (1.04-4.14)3.25 (1.63-6.48)BMI0.98 (0.92-1.03)0.92 (0.87-0.97)Anxiety1.93 (1.05-3.56)2.31 (1.22-4.35)Decisional involvement (ref = shared)  Mainly patient's decision3.47 (1.99-6.06)3.71 (2.09-6.58)Mainly doctor's decision0.14 (0.03-0.63)0.16 (0.03-0.77)

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-18-02.

Engineered proteins detect spontaneous DNA breakage in human and bacterial cells

Spontaneous DNA breaks instigate genomic changes that fuel cancer and evolution, yet direct quantification of double-strand breaks (DSBs) has been limited. Predominant sources of spontaneous DSBs remain elusive. We report synthetic technology for quantifying DSBs using fluorescent-protein fusions of double-strand DNA end-binding protein, Gam of bacteriophage Mu. In Escherichia coli GamGFP forms foci at chromosomal DSBs and pinpoints their subgenomic locations. Spontaneous DSBs occur mostly one per cell, and correspond with generations, supporting replicative models for spontaneous breakage, and providing the first true breakage rates. In mammalian cells GamGFP-labels laser-induced DSBs antagonized by end-binding protein Ku; co-localizes incompletely with DSB marker 53BP1 suggesting superior DSB-specificity; blocks resection; and demonstrates DNA breakage via APOBEC3A cytosine deaminase. We demonstrate directly that some spontaneous DSBs occur outside of S phase. The data illuminate spontaneous DNA breakage in E. coli and human cells and illustrate the versatility of fluorescent-Gam for interrogation of DSBs in living cells. DOI:http://dx.doi.org/10.7554/eLife.01222.001.

Thymineless death is inhibited by CsrA in Escherichia coli lacking the SOS response

Thymineless death (TLD) is the rapid loss of colony-forming ability in bacterial, yeast and human cells starved for thymine, and is the mechanism of action of common chemotherapeutic drugs. In Escherichia coli, significant loss of viability during TLD requires the SOS replication-stress/DNA-damage response, specifically its role in inducing the inhibitor of cell division, SulA. An independent RecQ- and RecJ-dependent TLD pathway accounts for a similarly large additional component of TLD, and a third SOS- and RecQ/J-independent TLD pathway has also been observed. Although two groups have implicated the SOS-response in TLD, an SOS-deficient mutant strain from an earlier study was found to be sensitive to thymine deprivation. We performed whole-genome resequencing on that SOS-deficient strain and find that, compared with the SOS-proficient control strain, it contains five mutations in addition to the SOS-blocking lexA(Ind(-)) mutation. One of the additional mutations, csrA, confers TLD sensitivity specifically in SOS-defective strains. We find that CsrA, a carbon storage regulator, reduces TLD in SOS- or SulA-defective cells, and that the increased TLD that occurs in csrA(-) SOS-defective cells is dependent on RecQ. We consider a hypothesis in which the modulation of nucleotide pools by CsrA might inhibit TLD specifically in SOS-deficient (SulA-deficient) cells.

R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli

Double-stranded DNA ends, often from replication, drive genomic instability, yet their origin in non-replicating cells is unknown. Here we show that transcriptional RNA/DNA hybrids (R-loops) generate DNA ends that underlie stress-induced mutation and amplification. Depleting RNA/DNA hybrids with overproduced RNase HI reduces both genomic changes, indicating RNA/DNA hybrids as intermediates in both. An Mfd requirement and inhibition by translation implicate transcriptional R-loops. R-loops promote instability by generating DNA ends, shown by their dispensability when ends are provided by I-SceI endonuclease. Both R-loops and single-stranded endonuclease TraI are required for end formation, visualized as foci of a fluorescent end-binding protein. The data suggest that R-loops prime replication forks that collapse at single-stranded nicks, producing ends that instigate genomic instability. The results illuminate how DNA ends form in non-replicating cells, identify R-loops as the earliest known mutation/amplification intermediate, and suggest that genomic instability during stress could be targeted to transcribed regions, accelerating adaptation.

Identity and function of a large gene network underlying mutagenic repair of DNA breaks

Mechanisms of DNA repair and mutagenesis are defined on the basis of relatively few proteins acting on DNA, yet the identities and functions of all proteins required are unknown. Here, we identify the network that underlies mutagenic repair of DNA breaks in stressed Escherichia coli and define functions for much of it. Using a comprehensive screen, we identified a network of ≥93 genes that function in mutation. Most operate upstream of activation of three required stress responses (RpoS, RpoE, and SOS, key network hubs), apparently sensing stress. The results reveal how a network integrates mutagenic repair into the biology of the cell, show specific pathways of environmental sensing, demonstrate the centrality of stress responses, and imply that these responses are attractive as potential drug targets for blocking the evolution of pathogens.

Gross chromosomal rearrangement mediated by DNA replication in stressed cells: evidence from Escherichia coli

Gross chromosomal rearrangements (GCRs), or changes in chromosome structure, play central roles in evolution and are central to cancer formation and progression. GCRs underlie copy number variation (CNV), and therefore genomic disorders that stem from CNV. We study amplification in Escherichia coli as a model system to understand mechanisms and circumstances of GCR formation. Here, we summarize observations that led us to postulate that GCR occurs by a replicative mechanism as part of activated stress responses. We report that we do not find RecA to be downregulated by stress on a population basis and that constitutive expression of RecA does not inhibit amplification, as would be expected if downregulation of RecA made cells permissive for nonhomologous recombination. Strains deleted for the genes for three proteins that inhibit RecA activity, psiB, dinI, and recX, all show unaltered amplification, suggesting that if they do downregulate RecA indirectly, this activity does not promote amplification.

Two mechanisms produce mutation hotspots at DNA breaks in Escherichia coli

Mutation hotspots and showers occur across phylogeny and profoundly influence genome evolution, yet the mechanisms that produce hotspots remain obscure. We report that DNA double-strand breaks (DSBs) provoke mutation hotspots via stress-induced mutation in Escherichia coli. With tet reporters placed 2 kb to 2 Mb (half the genome) away from an I-SceI site, RpoS/DinB-dependent mutations occur maximally within the first 2 kb and decrease logarithmically to ∼60 kb. A weak mutation tail extends to 1 Mb. Hotspotting occurs independently of I-site/tet-reporter-pair position in the genome, upstream and downstream in the replication path. RecD, which allows RecBCD DSB-exonuclease activity, is required for strong local but not long-distance hotspotting, indicating that double-strand resection and gap-filling synthesis underlie local hotspotting, and newly illuminating DSB resection in vivo. Hotspotting near DSBs opens the possibility that specific genomic regions could be targeted for mutagenesis, and could also promote concerted evolution (coincident mutations) within genes/gene clusters, an important issue in the evolution of protein functions.