Reversion Of Mutation Research Articles

A nuanced role of the small loop of hepatitis B virus small envelope protein in virion morphogenesis and secretion

BackgroundThe virion secretion mechanism of human hepatitis B virus (HBV) remains to be investigated. In our current study, we characterized a reverse transcriptase mutant, which changed from the YMDD motif to YMHA. We noted that this mutant YMHA secreted no virions in the medium. Because of the overlapping open reading frame (ORF) between the polymerase and the envelope genes, the lack of virion secretion is likely due to corresponding concurrent mutations in a small loop of the envelope protein (HBsAg, HBV surface antigen). In literature, small loop mutations are thought to affect virion secretion of hepatitis delta virus (HDV), but not HBV.MethodsHere, we revisited the relationship between the small loop and virion secretion by site-directed mutagenesis and native agarose gel electrophoresis.ResultsA proline substitution at residue 196 or 198 in the small loop blocked both HBV genome-containing and genome-free virion secretion, but not the secretion of 22-nm HBsAg subviral particles. Surprisingly, a leucine substitution at residue 196 enhanced genome-containing virion secretion. It is also intriguing that a proline-197, sandwiched by residue 196 and 198, exhibited no apparent defect in secreted virions, with or without containing an HBV genome. By complementation assay, we demonstrated that the wild type small envelope protein alone is sufficient to rescue the virion secretion defect of a small loop mutant M198P.ConclusionsThe effect of the small loop mutation of HBV small envelope protein on virion secretion is position-dependent. It warrants further investigation how the small loop of HBsAg plays a subtle role in HBV morphogenesis and secretion of virions with or without containing an HBV genome.

Abstract P068: Different treatment schemes cause distinct PARP inhibitor resistance mechanisms in BRCA2-mutant ovarian cancer cells

Abstract Poly (ADP-ribose) polymerase inhibitors (PARPis) represent a major advance in ovarian cancer management, now as treatment for recurrent ovarian cancer and as a maintenance therapy following platinum-based chemotherapy in the upfront and platinum-sensitive recurrent settings. Yet, a growing number of patients progress through PARPis, creating a need for further understanding on resistance mechanisms. We hypothesized that different treatment dosing/timing schemes would cause distinct mechanisms of acquired resistance to PARPis. To test this hypothesis, we exposed BRCA2-mutant PEO1 ovarian cancer cells to 0.5 μM olaparib, doubling its concentration up to 40 μM over 3–4 months (PEO1/OlaJR). The second PARPi-resistant PEO1 cell line (PEO1/OlaR) was developed using a relatively low initial dose of 5 nM olaparib, and gradually increasing its concentration up to 20 μM over 6 months. To confirm PARPi resistance, cell proliferation and viability were measured by MTT and colony formation assay, respectively. Both cell lines were resistant to two different PARPis beyond clinically achievable concentrations (olaparib IC50 141.7–372.8 μM and rucaparib IC50 37.1–51.2 μM) and demonstrated restored homologous recombination (HR) repair as evidenced by increased HR-reporter activity (1.32 to 1.45-fold compared to PEO1, p < 0.05) and RAD51 foci formation (5.2 to 6.1-fold compared to PEO1, p < 0.001). For PEO1/OlaJR, distinct resistance mechanisms to PARPi were noted: 1) promoting drug efflux confirmed by increased MDR efflux activity (1.92-fold compared to PEO1, p < 0.001) and increased protein levels of an ABCB1 transporter (7.2-fold compared to PEO1); and 2) enhancing HR repair restoration, likely via reduced REV7 protein expression (0.43-fold compared to PEO1). On the other hand, PEO1/OlaR exhibited a mesenchymal cell phenotype with greater invasion ability as measured by transwell invasion assay (2.25-fold compared to PEO1, p < 0.001) and restored HR repair with upregulation of TRIP13 protein (1.85-fold compared to PEO1). PEO1/OlaR also showed increased cell survival, possibly via activation of PI3K/AKT signaling, as evidenced by increased p-AKT (2.12-fold compared to PEO1). No loss of 53BP1 was observed in either PEO1/OlaJR or PEO1/OlaR based on whole exome sequencing and immunoblotting of 53BP1. BRCA2 reversion mutation status is currently under investigation. Altogether, our findings suggest that mechanisms of resistance to PARPis arise differently based on the duration and concentrations of drug treatment, highlighting the importance of appreciating interplay between specific treatment schemes and the downstream consequences. Thus, developing tailored therapeutic strategies should consider various mechanisms of PARPi resistance. Citation Format: Tzu-Ting Huang, Jayakumar R. Nair, Nitasha Gupta, Tomomi M. Yamamoto, Benjamin G. Bitler, Jung-Min Lee. Different treatment schemes cause distinct PARP inhibitor resistance mechanisms in BRCA2-mutant ovarian cancer cells [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P068.

Identification of Complement-Related Missense Variants in Pediatric Patients with Acute and Post COVID-19 Syndromes

Background: Complement dysregulation has been documented in the molecular pathophysiology of COVID-19 and recently implicated in the relevant pediatric patient inflammatory responses.Aims: Based on our previous data in adults, we hypothesized that signatures of complement genetic variants would also be detectable in pediatric patients exhibiting COVID-19 signs and symptoms.Methods: We prospectively studied consecutive pediatric patients from our COVID-19 Units (November 2020-March 2021). COVID-19 was confirmed by reverse-transcriptase polymerase chain reaction (RT-PCR). Patient data were recorded by treating physicians that followed patients up to discharge. DNA was obtained from peripheral blood samples. Probes were designed using the Design studio (Illumina). Amplicons cover exons of complement-associated genes (C3, C5, CFB, CFD, CFH, CFHR1, CFI, CD46, CD55, MBL2, MASP1, MASP2, COLEC11, FCN1, FCN3 as well as ADAMTS13 and ΤHBD) spanning 15 bases into introns. We used 10ng of initial DNA material. Libraries were quantified using Qubit and sequenced on a MiniSeq System in a 2x150 bp run. Analysis was performed using the TruSeq Amplicon application (BaseSpace). Alignment was based on the banded Smith-Waterman algorithm in the targeted regions (specified in a manifest file). We performed variant calling with the Illumina-developed Somatic Variant Caller in germline mode and variant allele frequency higher than 20%. Both Ensembl and Refseq were used for annotation of the output files. A preliminary analysis (A) for the identification of variants of clinical significance was based on annotated ClinVar data, while a further and more selective analysis (B) was performed to identify missense complement coding variants that may biochemically contribute to the deregulation of innate responses during infection. This analysis was mainly based on the dbSNP and UniProt databases and available literature.Results: We studied 80 children and adolescents, 8 of whom developed inflammatory syndromes (MIS-C group). Among them, 41 were hospitalized and eventually all survived. 1.In our preliminary analysis, patients exhibited heterogeneous variant profiles including pathogenic, benign, likely benign, and variants of unknown significance (median number of variants: 97, range: 61-103). We found a variant of ADAMTS13 (rs2301612, missense) in 39 patients. We also detected two missense risk factor variants, previously detected in complement-related diseases: rs2230199 in C3 (33 patients); and rs800292 in CFH (36 patients). Among them, 40 patients had a combination of these characterized variants. This combination was significantly associated with the presence of dyspnea (p=0.031) and cough (p=0.042). Furthermore, 27 patients had a pathogenic variant in MBL2 (rs1800450), and 7 a pathogenic deletion in FCN3 that have been previously associated with inflammatory syndromes.2.The results of our further analysis are summarized in Figure. We identified common variants, some well represented by relatively high frequencies (>70%) (rs11098044 in CFI, rs1061170 in CFH and rs12711521 in MASP2) and others less abundant, but varying considerably between the hospitalized group, the non-admitted group and the MIS-C individuals (rs2230199 in C3, rs1065489 in CFH, rs12614 and rs641153 in CFB, rs1800450 in MBL2, rs2273346 and rs72550870 in MASP2, rs72549154 in MASP3 and rs7567833 in COLEC11, all highlighted in Figure in red).). Structurally, the majority of these common variants of interest encode charge reversal mutations. These may influence protein-protein interactions in complex formations that are important for complement activation and/or regulation.Conclusion: In pediatric COVID-19 we have detected a novel set of complement missense coding variants some of which have been implicated earlier in inflammatory syndromes and endothelial stress responses. Certain combinations of mutations of alternative and/or lectin pathway components may increase the threshold dynamics of complement consumption and therefore alter COVID-19 phenotypes. [Display omitted] DisclosuresGavriilaki: Alexion, Omeros, Sanofi Corporation: Consultancy; Gilead Corporation: Honoraria; Pfizer Corporation: Research Funding. Anagnostopoulos: Abbvie: Other: clinical trials; Sanofi: Other: clinical trials ; Ocopeptides: Other: clinical trials ; GSK: Other: clinical trials; Incyte: Other: clinical trials ; Takeda: Other: clinical trials ; Amgen: Other: clinical trials ; Janssen: Other: clinical trials; novartis: Other: clinical trials; Celgene: Other: clinical trials; Roche: Other: clinical trials; Astellas: Other: clinical trials .

Six decades of infectious bursal disease in poultry: The journey so far and challenges ahead


 
 
 Despite six decades of concerted efforts, Infectious bursal disease (IBD) still remains a major threat to the poultry industry worldwide. Most importantly, the emergence of variant and very virulent strains of infectious bursal disease virus (IBDV) has dramatically changed the epidemiology of the disease, thus resulting in the renewed efforts in the search for effective control measures. Currently, live attenuated, inactivated, and immune-complex vaccines are among the immune-therapeutic approaches employed for the control of IBD in the field alongside adequate biosecurity, albeit with various degrees of success and limitations. Progress in genetic engineering has allowed the generation of reverse genetic IBDV mutants, recombinant live viral vectors expressing the IBDV VP2 immunodominant protein, intra-serotypic recombinant IBDV viral-like particle co-expressing the outer capsid protein structures derived from 2 or more serotype 1 strains or the incorporation of either VP2 or VP2-4-3 polyprotein sequences alongside molecular adjuvants that can be used as IBD vaccine candidates to elicit an immune response. However, despite these advances, outbreaks are still reported even in flocks that have up to date vaccination records and somewhat excellent management practices. This paper reviews aspect of genetic characteristics of IBDV and reflects on the progress and future challenges in providing effective IBD vaccine to achieve effective control of both classical and very-virulent IBDV serotypes that constitute a major devastation to poultry production and health.
 
 

The Clinical Challenges, Trials, and Errors of Combatting Poly(ADP-Ribose) Polymerase Inhibitors Resistance.

The use of poly(ADP-ribose) polymerase inhibitor (PARPi) exploits synthetic lethality in solid tumors with homologous recombination repair (HRR) defects. Significant clinical benefit has been established in breast and ovarian cancers harboring BRCA1/2 mutations, as well as tumors harboring characteristics of "BRCAness." However, the durability of treatment responses is limited, and emerging data have demonstrated the clinical challenge of PARPi resistance. With the expanding use of PARPi, the significance of PARP therapy in patients pretreated with PARPi remains in need of significant further investigation. Molecular mechanisms contributing to this phenomenon include restoration of HRR function, replication fork stabilization, BRCA1/2 reversion mutations, and epigenetic changes. Current studies are evaluating the utility of combination therapies of PARPi with cell cycle checkpoint inhibitors, antiangiogenic agents, phosphatidylinositol 3-kinase/AKT pathway inhibitors, MEK inhibitors, and epigenetic modifiers to overcome this resistance. In this review, we address the mechanisms of PARPi resistance supported by preclinical models, examine current clinical trials applying combination therapy to overcome PARPi resistance, and discuss future directions to enhance the clinical efficacy of PARPi.

A Non-Rogue Mutant Line Induced by ENU Mutagenesis in Paramutated Rogue Peas (Pisum sativum L.) Is Still Sensitive to the Rogue Paramutation.

The spontaneously emerging rogue phenotype in peas (Pisum sativum L.), characterized by narrow and pointed leaf stipula and leaflets, was the first identified case of the epigenetic phenomenon paramutation. The crosses of homozygous or heterozygous (e.g., F1) rogue plants with non-rogue (wild type) plants, produce exclusively rogue plants in the first and all subsequent generations. The fact that the wild phenotype disappears forever, is in clear contradiction with the Mendelian rules of inheritance, a situation that impedes the positional cloning of genes involved in this epigenetic phenomenon. One way of overcoming this obstacle is the identification of plant genotypes harboring naturally occurring or artificially induced neutral alleles, non-sensitive to paramutation. So far, such alleles have never been described for the pea rogue paramutation. Here, we report the induction via 1-ethyl-1-nitrosourea (ENU) mutagenesis of a non-rogue revertant mutant in the rogue cv. Progreta, and the completely unusual fixation of the induced non-rogue phenotype through several generations. The reversion of the methylation status of two previously identified differentially methylated genomic sequences in the induced non-rogue mutant, confirms that the rogue paramutation is accompanied by alterations in DNA methylation. Nevertheless, unexpectedly, the induced non-rogue mutant showed to be still sensitive to paramutation.

Suppression of telomere capping defects of Saccharomyces cerevisiae yku70 and yku80 mutants by telomerase.

The Ku complex performs multiple functions inside eukaryotic cells, including protection of chromosomal DNA ends from degradation and fusion events, recruitment of telomerase, and repair of double-strand breaks (DSBs). Inactivation of Ku complex genes YKU70 or YKU80 in cells of the yeast Saccharomyces cerevisiae gives rise to mutants that exhibit shortened telomeres and temperature-sensitive growth. In this study, we have investigated the mechanism by which overexpression of telomerase suppresses the temperature sensitivity of yku mutants. Viability of yku cells was restored by overexpression of the Est2 reverse transcriptase and TLC1 RNA template subunits of telomerase, but not the Est1 or Est3 proteins. Overexpression of other telomerase- and telomere-associated proteins (Cdc13, Stn1, Ten1, Rif1, Rif2, Sir3, and Sir4) did not suppress the growth defects of yku70 cells. Mechanistic features of suppression were assessed using several TLC1 RNA deletion derivatives and Est2 enzyme mutants. Supraphysiological levels of three catalytically inactive reverse transcriptase mutants (Est2-D530A, Est2-D670A, and Est2-D671A) suppressed the loss of viability as efficiently as the wild-type Est2 protein, without inducing cell senescence. Roles of proteins regulating telomere length were also determined. The results support a model in which chromosomes in yku mutants are stabilized via a replication-independent mechanism involving structural reinforcement of protective telomere cap structures.

MuWU: Mutant-seq library analysis and annotation.

MotivationInsertional mutagenesis allows for the creation of loss-of-function mutations on a genome-wide scale. In theory, every gene can be ‘knocked out’ via the insertion of an additional DNA sequence. Resources of sequence-indexed mutants of plant and animal model organisms are instrumental for functional genomics studies. Such repositories significantly speed up the acquisition of interesting genotypes and allow for the validation of hypotheses regarding phenotypic consequences in reverse genetics. To create such resources, comprehensive sequencing of flanking sequence tags using protocols such as Mutant-seq requires various downstream computational tasks, and these need to be performed in an efficient and reproducible manner.ResultsHere, we present MuWU, an automated Mutant-seq workflow utility initially created for the identification of Mutator insertion sites of the BonnMu resource, representing a reverse genetics mutant collection for functional genetics in maize (Zea mays). MuWU functions as a fast, one-stop downstream processing pipeline of Mutant-seq reads. It takes care of all complex bioinformatic tasks, such as identifying tagged genes and differentiating between germinal and somatic mutations/insertions. Furthermore, MuWU automatically assigns insertions to the corresponding mutated seed stocks. We discuss the implementation and how parameters can easily be adapted to use MuWU for other species/transposable elements.Availability and implementationMuWU is a Snakemake-based workflow and freely available at https://github.com/tgstoecker/MuWU.Supplementary information Supplementary data are available at Bioinformatics online.

Somatic reversion impacts myelodysplastic syndromes and acute myeloid leukemia evolution in the short telomere disorders

BACKGROUNDGermline mutations in telomerase and other telomere maintenance genes manifest in the premature aging short telomere syndromes. Myelodysplastic syndromes and acute myeloid leukemia (MDS/AML) account for 75% of associated malignancies, but how these cancers overcome the inherited telomere defect is unknown.METHODSWe used ultra-deep targeted sequencing to detect somatic reversion mutations in 17 candidate telomere lengthening genes among controls and patients with short telomere syndromes with and without MDS/AML, and we tested the functional significance of these mutations.RESULTSWhile no controls carried somatic mutations in telomere maintenance genes, 29% (16 of 56) of adults with germline telomere maintenance defects carried at least 1 (P < 0.001), and 13% (7 of 56) had 2 or more. In addition to TERT promoter mutations, which were present in 19%, another 13% of patients carried a mutation in POT1 or TERF2IP. POT1 mutations impaired telomere binding in vitro and some mutations were identical to ones seen in familial melanoma associated with longer telomere length. Exclusively in patients with germline defects in telomerase RNA (TR), we identified somatic mutations in nuclear RNA exosome genes RBM7, SKIV2L2, and DIS3, where loss-of-function upregulates mature TR levels. Somatic reversion events in 6 telomere-related genes were more prevalent in patients who were MDS/AML-free (P = 0.02, RR 4.4, 95% CI 1.2-16.7), and no patient with MDS/AML had more than 1 reversion mutation.CONCLUSIONOur data indicate that diverse adaptive somatic mutations arise in the short telomere syndromes. Their presence may alleviate the telomere crisis that promotes transformation to MDS/AML.FUNDINGThis work was supported by the NIH, the Commonwealth Foundation, the S&R Foundation Kuno Award, the Williams Foundation, the Vera and Joseph Dresner Foundation, the MacMillan Pathway to Independence Award, the American Society of Hematology Scholar Award, the Johns Hopkins Research Program for Medical Students, and the Turock Scholars Fund.

Revertant mutation V48G alters conformational dynamics of highly drug resistant HIV protease PRS17

Drug resistance is a serious problem for controlling the HIV/AIDS pandemic. Current antiviral drugs show several orders of magnitude worse inhibition of highly resistant clinical variant PRS17 of HIV-1 protease compared with wild-type protease. We have analyzed the effects of a common resistance mutation G48V in the flexible flaps of the protease by assessing the revertant PRS17V48G for changes in enzyme kinetics, inhibition, structure, and dynamics. Both PRS17 and the revertant showed about 10-fold poorer catalytic efficiency than wild-type enzyme (0.55 and 0.39 μM−1min−1 compared to 6.3 μM−1min−1). Clinical inhibitors, amprenavir and darunavir, showed 2-fold and 8-fold better inhibition, respectively, of the revertant than of PRS17, although the inhibition constants for PRS17V48G were still 25 to 1,200-fold worse than for wild-type protease. Crystal structures of inhibitor-free revertant and amprenavir complexes with revertant and PRS17 were solved at 1.3–1.5 Å resolution. The amprenavir complexes of PRS17V48G and PRS17 showed no significant differences in the interactions with inhibitor, although changes were observed in the conformation of Phe53 and the interactions of the flaps. The inhibitor-free structure of the revertant showed flaps in an open conformation, however, the flap tips do not have the unusual curled conformation seen in inhibitor-free PRS17. Molecular dynamics simulations were run for 1 μs on the two inhibitor-free mutants and wild-type protease. PRS17 exhibited higher conformational fluctuations than the revertant, while the wild-type protease adopted the closed conformation and showed the least variation. The second half of the simulations captured the transition of the flaps of PRS17 from a closed to a semi-open state, whereas the flaps of PRS17V48G tucked into the active site and the wild-type protease retained the closed conformation. These results suggest that mutation G48V contributes to drug resistance by altering the conformational dynamics of the flaps.

Analyses of DNA repair protein expression in BRCA1 mutant patient-derived xenografts

<h3>Objectives:</h3> To evaluate the potential of DNA damage response protein expression and foci formation to serve as biomarkers of resistance to platinum chemotherpay or Poly-(ADP)-Ribose Polymerase Inhibitors (PARPi) using immunohistochemistry (IHC). <h3>Methods:</h3> A collection of four patient-derived xenografts (PDX) mouse models with <i>BRCA1</i> mutations in exon 11, a <i>BRCA1</i> exon 13 mutant, and a <i>BRCA1</i> wild-type tumor were analyzed. <i>BRCA1</i> exon 11 mutants included: PDX196, mutation: c1961delA; PDX124, mutation: c196delA; PDX017, mutation: c1105_1106insTC; PDX056, mutation: c895_896delGT; <i>BRCA1</i> WT control: PDX036 and <i>BRCA1</i> exon 13 mutant: PDX1126, mutation: c4327C>T. Mice harboring PDX tumors were subjected to vehicle, PARPi (rucaparib), or platinum (cisplatin) treatment. Passaging and re-treatment of tumors was performed until minimal therapy response. Formalin-fixed paraffin embedded tumor samples was prepared for IHC analyses. IHC protocols were optimized to evaluate expression and foci formation for the following proteins: phosphorylated-RPA32, Rad51, phosphorylated-53BP1, 53BP1, <i>BRCA1,</i> Ki67. <h3>Results:</h3> <i>BRCA1</i> foci formation was observed by IHC in PARPi and cisplatin resistant tumors. Reversion mutations were not detected and <i>BRCA1</i> protein expression was due to increased levels of <i>BRCA1</i>-D11q. Increased RPA32 and RAD51 foci were also observed in several therapy resistant PDX models, which indicate active HR repair. Interestingly, acquired resistance to cisplatin and PARPi was associated with a reduction in 53BP1 and phosphorylated-53BP1. Finally, PARPi and cisplatin resistant tumors exhibited similar levels of <i>BRCA1</i> and RAD51 foci. <h3>Conclusions:</h3> <i>BRCA1</i>-D11q protein expression correlates with platinum and PARPi response in several <i>BRCA1</i> exon 11 mutant PDX models. We predict that increased <i>BRCA1</i>-D11q in combination with decreased 53BP1 expression drives RPA and RAD51 foci, resulting in active homologous recombination and therapy resistance. Our results suggest that IHC can be utilized for detection of DNA damage repair protein expression as well as foci formation, and could lead to the development of biomarkers that are predictive of therapy response.

1Rucaparib versus chemotherapy in patients with advanced, relapsed ovarian cancer and a deleterious BRCA mutation: efficacy and safety from ARIEL4, a randomized phase III study

Objectives: Prospective studies comparing poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitors with standard-of-care (SOC) chemotherapy (CT) in patients (pts) with relapsed ovarian cancer (OC) are currently limited. ARIEL4 (NCT02855944) is a phase III, randomized, open-label, international, multicenter study of the efficacy and safety of rucaparib vs SOC CT as treatment for PARP-inhibitor naïve pts with relapsed high-grade epithelial ovarian, fallopian tube or primary peritoneal cancer, who had a deleterious BRCA1/2 (BRCA) mutation and had received ≥2 prior CT regimens. Methods: Pts were randomized 2:1 to oral rucaparib 600 mg twice daily or SOC CT and stratified based on progression-free interval (≥1 to <6 months = platinum resistant; ≥6 to <12 months = partially platinum sensitive; ≥12 months = fully platinum sensitive). Pts in the CT arm with platinum-resistant or partially platinum-sensitive disease received weekly paclitaxel 60-80 mg/m2; pts with fully platinum-sensitive disease received investigator's choice of platinum-based CT (single-agent carboplatin or cisplatin, or platinum doublet [carboplatin + paclitaxel, carboplatin + gemcitabine, or cisplatin + gemcitabine]). Pre-study-treatment plasma samples were assessed for BRCA reversion mutations. The primary endpoint was investigator-assessed progression-free survival (PFS). Secondary endpoints included objective response rate (ORR) per RECIST and safety. Each efficacy endpoint was first evaluated in the efficacy population (randomized pts with deleterious BRCA mutations excluding those with BRCA reversion mutations), stepping down to the intent-to-treat (ITT) population (all randomized pts). Results: Conclusions: Patients with BRCA-mutated advanced, relapsed OC who received rucaparib had a significant improvement in PFS vs SOC CT. No new safety signals were identified. This is the first prospective report from a randomized trial demonstrating that the presence of a BRCA reversion mutation predicts for primary resistance to rucaparib. Prospective studies comparing poly(adenosine diphosphate-ribose) polymerase (PARP) inhibitors with standard-of-care (SOC) chemotherapy (CT) in patients (pts) with relapsed ovarian cancer (OC) are currently limited. ARIEL4 (NCT02855944) is a phase III, randomized, open-label, international, multicenter study of the efficacy and safety of rucaparib vs SOC CT as treatment for PARP-inhibitor naïve pts with relapsed high-grade epithelial ovarian, fallopian tube or primary peritoneal cancer, who had a deleterious BRCA1/2 (BRCA) mutation and had received ≥2 prior CT regimens. Pts were randomized 2:1 to oral rucaparib 600 mg twice daily or SOC CT and stratified based on progression-free interval (≥1 to <6 months = platinum resistant; ≥6 to <12 months = partially platinum sensitive; ≥12 months = fully platinum sensitive). Pts in the CT arm with platinum-resistant or partially platinum-sensitive disease received weekly paclitaxel 60-80 mg/m2; pts with fully platinum-sensitive disease received investigator's choice of platinum-based CT (single-agent carboplatin or cisplatin, or platinum doublet [carboplatin + paclitaxel, carboplatin + gemcitabine, or cisplatin + gemcitabine]). Pre-study-treatment plasma samples were assessed for BRCA reversion mutations. The primary endpoint was investigator-assessed progression-free survival (PFS). Secondary endpoints included objective response rate (ORR) per RECIST and safety. Each efficacy endpoint was first evaluated in the efficacy population (randomized pts with deleterious BRCA mutations excluding those with BRCA reversion mutations), stepping down to the intent-to-treat (ITT) population (all randomized pts). Patients with BRCA-mutated advanced, relapsed OC who received rucaparib had a significant improvement in PFS vs SOC CT. No new safety signals were identified. This is the first prospective report from a randomized trial demonstrating that the presence of a BRCA reversion mutation predicts for primary resistance to rucaparib.

Safety Evaluation of Bifidobacterium lactis BL-99 and Lacticaseibacillus paracasei K56 and ET-22 in vitro and in vivo.

Probiotics have been reported to play a major role in maintaining the balance of microbiota in host. Consumption of food with probiotics has increased with consumer concerns regarding healthy diets and wellness. Correspondingly, safety evaluation of probiotics for human consumption has become increasingly important in food industry. Herein, we aimed to test the safety of Bifidobacterium lactis BL-99 and Lacticaseibacillus paracasei K56 and ET-22 strains in vitro and in vivo. In results, these strains were found to be negative for mucin degradation and platelet aggregation test. Additionally, the three strains were susceptible to eight antibiotics. In accordance with bacterial reversion mutation (Ames) assay, the tested strains had no genetic mutagenicity. Finally, it was confirmed that there were no dose-dependent mortality and toxicity throughout multidose oral toxicity tests in rats. Our findings demonstrated that B. lactis BL-99 and L. paracasei K56 and ET-22 can achieve the generally recognized as safe (GRAS) status as probiotics in the future.

Usefulness of Cell-Free Human Telomerase Reverse Transcriptase Mutant DNA Quantification in Blood for Predicting Hepatocellular Carcinoma Treatment Efficacy.

Although the usefulness of liquid biopsy as a biomarker in the treatment of hepatocellular carcinoma (HCC) has been suggested, its usefulness in transcatheter arterial chemoembolization (TACE) or tyrosine kinase inhibitor (TKI) therapies has not been reported in detail. In this study, we investigated the clinical value of a cell‐free (cf)DNA quantification system targeting the human telomerase reverse transcriptase (hTERT) promoter mutation in advanced HCC treatment. Plasma from 67 patients with advanced HCC, treated with TACE and TKI, was used for extraction of cfDNA. We defined cfDNA with the hTERT promoter C228T mutation as circulating mutant DNA (mutant DNA) and without the mutation as circulating wild‐type DNA (wild‐type DNA). We analyzed the changes in mutant and wild‐type DNA levels during HCC treatment and examined the relationship between changes in the cfDNA level and the clinical course. Mutant DNA was detected in 73.1% (49/67) of the patients during HCC treatment. In univariate analysis, factors associated with detection of mutant DNA before treatment were the intrahepatic maximum tumor diameter (P = 0.015) and protein induced by vitamin K absence (PIVKAII) (P = 0.006). The degree of mutant DNA change after TACE was significantly correlated with tumor volume (P < 0.001), reflecting the treated tumor volume. Responders with peak cfDNA levels within 1 week of TKI initiation had significantly better progression‐free survival than nonresponders (P = 0.004). Conclusion: Changes in blood hTERT promoter mutant DNA levels during TACE or TKI treatment indirectly reflect the amount of HCCs and are useful for predicting long‐term treatment responses.

Abstract 25: Reversion patterns in homologous recombination repair genes in metastatic cancer patients profiled by cell-free DNA

Abstract Background: Inactivating mutations in homologous recombination repair (HRR) genes are associated with a response to PARP inhibitors and platinum-based therapies. However, secondary reversion mutations in HRR genes remain a major mechanism of resistance. We sought to characterize the prevalence and spectrum of these reversions in advanced cancer patients in BRCA1/2 and other HRR genes, such as ATM and CDK12. Methods: We analyzed cfDNA from &amp;gt;75,000 late-stage cancer patients previously tested as part of routine clinical care using Guardant360®, a 73- to 74-gene panel. This assay detects single-nucleotide variants (SNVs), indels, fusions, and copy-number alterations in cfDNA with a reportable range of ≥0.04%, 0.02%, 0.04%, and ≥2.12 copies, respectively. Secondary reversion mutations were identified by re-analysis using a bespoke HRR deficiency (HRD) Module, which annotates SNV/indels and calls multi-exon deletions and copy-number loss with a 95% limit of detection of ≥ 0.1% and 10 to 25% tumor fraction, respectively. Results: Among &amp;gt;20,000 breast, ovarian, prostate and pancreatic cancer patients, deleterious germline or somatic mutations were detected in BRCA1 (2.7%), BRCA2 (4.8%), ATM (2.9%) and CDK12 (1.7%). The majority of reversions occurred in BRCA1/2-mut (8.7%), compared to 0.07% of CDK12-mut and none in ATM. Reversions showed selective gene and allele representation. In breast cancer, reversions in BRCA2-mut patients were twice as frequent as those in BRCA1-mut (12.9% vs 5.5%, p-value=0.0046), while the near opposite was true for ovarian (7.6% vs 12.8%, p-value=0.73). In pancreatic cancer (&amp;gt;7,500 patients), reversions presented exclusively in BRCA2-mut (8.4%, n=131 vs 0 in BRCA1-mut, n=63). CDK12 reversions were relatively rare: 1 detected in &amp;gt;5,000 prostate cancer patients. Across all genes, the majority of reversions were small indels while 18% of reversions removed the exon entirely. Pathogenic hotspots BRCA2 codons A938 and S1982 - accounted for ≥10% of reversions and were more likely to revert compared to other deleterious sites (p-value&amp;lt;1.0×10-6). Overall, 16.0% of BRCA1/2 mutant breast, ovarian, pancreatic, prostate patients reverted, consistent with previous reports (Lin et al. 2018). Conclusions: cfDNA has been previously shown to detect BRCA1/2 germline, somatic and polyclonal reversion mutations acquired over PARP and platinum-based therapy. We demonstrate that the Guardant HRD Module can robustly identify these reversions in the cfDNA of metastatic patients. We emphasize that reversions were frequent among BRCA1/2-mut breast, ovarian, prostate and pancreatic cancers, with preferential enrichment based on gene and tumor type. Understanding resistance patterns may aid in the treatment selection for progressing patients. Further work is needed to define these ideal treatment options. Citation Format: Yu Fu, Jennifer Yen, Alexander Aartyomenko, Sante Gnerre, Caroline Weiport, Elena Helman, Arielle Yablonovitch, Stephen Pettitt, Christopher Llord, Andrew Tutt, Rebecca Nagy, Justin Odegaard, Darya Chudova, AmirAli Talasaz. Reversion patterns in homologous recombination repair genes in metastatic cancer patients profiled by cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 25.

Relevance of Platinum-free Interval and BRCA Reversion Mutations for Veliparib Monotherapy after Progression on Carboplatin/Paclitaxel for gBRCA Advanced Breast Cancer (BROCADE3 Crossover).

Safety, efficacy, and exploratory biomarker analyses were evaluated in patients with advanced HER2-negative germline breast cancer susceptibility gene (gBRCA)-associated breast cancer enrolled in the BROCADE3 trial who received crossover veliparib monotherapy after disease progression on placebo plus carboplatin/paclitaxel. Eligible patients (N = 513) were randomized 2:1 to veliparib plus carboplatin/paclitaxel or placebo plus carboplatin/paclitaxel; patients had variable platinum-free intervals (PFI) at progression. In the placebo arm, patients were eligible to receive crossover veliparib monotherapy (300-400 mg twice daily continuous). Antitumor activity and adverse events were assessed during crossover veliparib treatment. BRCA reversion mutations at crossover were analyzed retrospectively using next-generation sequencing on plasma circulating tumor DNA (ctDNA). Seventy-five patients in the placebo plus carboplatin/paclitaxel arm received ≥1 dose of crossover veliparib postprogression (mean treatment duration: 154 days). Eight of 50 (16%) patients with measurable disease had a RECIST v1.1 response. Activity was greater in patients with PFI ≥180 days compared with <180 days [responses in 23.1% (3/13) vs. 13.5% (5/37) of patients]. BRCA reversion mutations that restored protein function were detected in ctDNA from 4 of 28 patients tested, and the mean duration of crossover veliparib monotherapy was <1 month in these 4 patients versus 7.49 months in patients lacking reversion mutations. The most frequent adverse events were nausea (61%), vomiting (29%), and fatigue (24%). Crossover veliparib monotherapy demonstrated limited antitumor activity in patients who experienced disease progression on placebo plus carboplatin/paclitaxel. PFI appeared to affect veliparib activity. BRCA reversion mutations may promote cross-resistance and limit veliparib activity following progression on platinum.

Comprehensive analysis of somatic reversion mutations in homologous recombination repair genes in a large cohort of Chinese pan-cancer patients.

e15093 Background: Mutations leading to homologous recombination deficiency increases the sensitivity towards platinum-based chemotherapy, as well as the PARP inhibitor. The acquired resistance caused by reversion mutations diminishes the prolonged benefit from the treatment. Herein, we aimed to investigate the prevalence and characteristics of reversion mutations in Chinese population. Methods: The next-generation sequencing data from 23,712 pan-cancer patients (including over 17 cancer types) were retrospectively analyzed for pathogenic/likely pathogenic (P/LP) germline mutations in homologous recombination repair (HRR) genes and possible somatic reversion mutations emerged later. Somatic mutations predicted to restore the open reading frame were identified and further classified into definitive or putative reversion mutations depending on whether the somatic mutation could be confirmed to occur on the same allele as the germline mutation by sequencing reads. Results: From the 23,712 patients, 685 (2.9%) were identified with P/LP germline HRR gene mutations, among which we identified 11 cases with 21 definitive and 4 putative somatic reversion mutations upon treatment, including 8 cases of breast cancer, 3 cases of ovarian cancer, 1 case of pancreatic cancers, and another case of lung cancer. The reversion mutations occurred in 3 genes: BRCA1 (7 cases), BRCA2 (5 cases) and PALB2 (1 case), but not in any other HRR genes in our cohort. Therefore, the incidence of reversion mutations in HRR genes was 1.6% (11/685), with the highest incidence observed in BRCA1 (5.26%) followed by BRCA2 (2.7%) and PALB2 (1.96%). Interestingly, multiple somatic reversion mutations could be observed in 3 patients, indicating heterogeneity in the resistance mechanisms. Among 6 patients with detailed treatment history available, 5 of them had reversion mutations detected after systemic platinum-based chemotherapy and/or PARP inhibitor treatment. The other patient of metastatic breast cancer had 6 prior lines of treatment including 2 cycles of thoracic perfusion of endostatin and lobaplatin before BRCA2 reversion mutation was detected. This patient subsequently received olaparib monotherapy with a progression free survival of only 2 months. Conclusions: This retrospective study demonstrated that the reversion mutations were observed in three HRR-associated genes ( BRCA1, BRCA2 and PALB2) with four cancer types (breast cancer, ovarian cancer, lung cancer and pancreatic cancer) from this Chinese patient cohort. The reversion mutations frequently occurred after resistance to platinum-based chemotherapy and/or PARP inhibitor, and may predict poor outcome from ensuing PARP inhibition therapy. Therefore, monitoring HRR mutation status along the course of the disease could be beneficial especially to informing resistance mechanism and guiding subsequent therapies.

BRCA reversion mutations in a pan-cancer cohort to reveal BRCA-dependence in select noncanonical BRCA-mutant histologies.

3012 Background: Loss of BRCA1/2 function leads to homologous recombination deficiency (HRD) and can enhance platinum and PARP inhibitor sensitivity in breast, pancreas, prostate, and ovarian cancers. In BRCA-associated cancers, resistance can result from the development of BRCA1/2 reversion mutations, which restore BRCA1/2 function. By contrast, a BRCA mutation may be an incidental finding in other tumor histologies. Methods: To determine the distribution of reversion mutations in a pan-cancer cohort, the MSK-IMPACT clinical sequencing cohort was mined to identify patients who had both a germline BRCA1/2 mutation and a frameshift somatic reversion mutation that restored BRCA1/2 function. Whole exome resequencing was used to detect HRD signatures. Chart review enabled collection of data on treatment history in patients consented to germline testing. Results: Of the 33,277 patients with matched tumor and normal sequencing profiled in this study, 861 patients were found to have germline pathogenic BRCA1/2 alterations, including 347 (40%) in BRCA1 and 514 (60%) in BRCA2. Somatic BRCA1/2 driver alterations were also found in tumor tissue from an additional 447 patients, with 156 (35%) having BRCA1 mutations, and the remainder having alterations in BRCA2 (65%) . Among the 1,308 germline or somatic BRCA1/2 mutant tumors, we identified reversion mutations in 12 patients, all of whom were germline carriers of BRCA1/2, comprising 3 BRCA1 and 9 BRCA2 tumors. 7 patients consented to germline testing enabling review of clinical characteristics and treatment history, 5 of whom received PARP inhibitor or platinum-therapy prior to reversion detection. Ten of 12 tumors with reversion mutations were in canonical BRCA-associated cancers. Interestingly, reversion mutations were also found in patients with lung adenocarcinoma (n=1) and gastroesophageal junction adenocarcinoma (n=1). In both these non-canonical histologies, the reversion was detected following progression on platinum-based therapy. Whole exome resequencing of the lung tumor revealed the classic somatic molecular phenotypes of HRD that are characteristic of BRCA-dependent tumors, including in terms of large-scale transitions, HRD-loss of heterozygosity, signature 3, and the number of telomeric allelic imbalance score. Conclusions: Matched tumor and normal sequencing from a large cohort of patients with diverse cancer histologies reveals that reversion mutations are found across BRCA-associated cancer types. In rare cases, reversion mutations in BRCA1/2 following platinum-based therapy may be indicative of prior BRCA-dependence in select non-canonical tumor histologies.

Subgroup analysis of rucaparib versus chemotherapy as treatment for BRCA-mutated, advanced, relapsed ovarian carcinoma: Effect of platinum sensitivity in the randomized, phase 3 study ARIEL4.

5517 Background: In ARIEL4 (NCT02855944), rucaparib significantly improved the primary endpoint of progression-free survival (PFS) vs chemotherapy (CT) in patients with advanced, relapsed ovarian carcinoma (OC) harboring a deleterious BRCA1/2 (BRCA) mutation (median PFS 7.4 [95% CI 7.3–9.1] vs 5.7 [5.5–7.3] months; hazard ratio (HR) 0.64 [95% CI 0.49–0.84]; P=0.001). This prespecified exploratory analysis investigated the effect of platinum sensitivity on the efficacy of rucaparib vs CT in ARIEL4. Methods: Patients were randomized 2:1 to oral rucaparib 600 mg twice daily or CT and stratified based on progression-free interval (≥1 to &lt;6 months = platinum resistant; ≥6 to &lt;12 months = partially platinum sensitive; ≥12 months = fully platinum sensitive). In the CT group, patients with platinum-resistant or partially platinum-sensitive disease received weekly paclitaxel 60–80 mg/m2; patients with fully platinum-sensitive disease received investigator’s choice of platinum-based CT (single-agent carboplatin or cisplatin, or platinum doublet). Patients could crossover from CT to rucaparib following radiologic disease progression. Efficacy endpoints were explored in patients with a confirmed BRCA mutation (patients with a reversion mutation were excluded), based on the randomization strata of platinum sensitivity. Results: The visit cutoff date was September 30, 2020. PFS and objective response rates (ORR) per RECIST v1.1 for rucaparib vs CT across subgroups are presented in the Table. The most common treatment-emergent adverse events in the rucaparib group were anemia/decreased hemoglobin (platinum-resistant patients: rucaparib 47% vs CT 40%; partially platinum-sensitive patients: 63% vs 27%; fully platinum-sensitive patients: 58% vs 20%) and nausea (52% vs 21%; 51% vs 23%; 60% vs 68%). In the intent-to-treat population, 74/116 (64%) patients in the CT group crossed over to receive rucaparib: 39/59 (66%) with platinum-resistant, 25/31 (81%) with partially platinum-sensitive, and 10/26 (38%) with fully platinum-sensitive disease. Conclusions: Results from this exploratory subgroup analysis suggest that rucaparib is a reasonable treatment option for heavily pretreated patients across all platinum sensitivity subgroups. Safety was consistent with prior rucaparib studies. Clinical trial information: NCT02855944. [Table: see text]

Phase II multicenter study of talazoparib for somatic BRCA1/2 mutant metastatic breast cancer.

TPS1110 Background: PARP inhibitors are approved for the treatment of HER2 negative metastatic breast cancer (MBC) with germline BRCA1/2 mutations, based on phase III studies demonstrating an improvement in progression-free survival (PFS) compared to chemotherapy in this population and better patient reported outcomes (Robson, NEJM, 2017; Litton, NEJM, 2018). However, germline BRCA1/2 mutations account for only 5-10% of breast cancer, limiting the current clinical applicability of PARP inhibitors. Somatic BRCA1/2 mutations are detectable in circulating cell-free DNA (cfDNA) in ̃13.5% of patients with MBC; in pre-clinical models, pathogenic somatic BRCA1/2 mutations have been shown to respond to PARP inhibition (Vidula, CCR, 2020). The purpose of this study is to evaluate the efficacy of talazoparib, a PARP inhibitor, in patients with MBC who have somatic BRCA1/2 mutations detectable in cfDNA, in the absence of a germline BRCA1/2 mutation, which we hypothesize will be effective in this setting. This study may help expand the population of patients with MBC who benefit from PARP inhibitors. Methods: This is an investigator initiated multicenter, single arm, phase II clinical trial studying the efficacy of talazoparib in 30 patients with MBC who have pathogenic somatic BRCA1/2 mutations detected in cfDNA. Patients with MBC who are found to have pathogenic somatic BRCA1/2 mutations detected in cfDNA in the absence of a germline BRCA1/2 mutation are eligible. Patients may have triple negative (with ≥ 1 prior chemotherapy), or hormone receptor positive/HER2 negative breast cancer (with ≥ 1 prior hormone therapy). Patients may have received any number of prior lines of chemotherapy, including a prior platinum (in the absence of progression). They must have adequate organ function and ECOG performance status ≤2, and should not have previously received a PARP inhibitor. Patients are treated with talazoparib 1 mg daily until disease progression or intolerability, with serial imaging using CT chest/abdomen/pelvis and bone scan performed at baseline and every 12 weeks, and cfDNA collection every 4 weeks. Primary endpoint is PFS by RECIST 1.1. Patients are being enrolled in a two-stage design with 80% power to demonstrate that the treatment is associated with “success” (PFS &gt; 12 weeks) in ≥53% patients (4% alpha). Secondary endpoints include objective response rate and safety (NCI CTCAE v 5.0). Exploratory analyses include studying serial changes in cfDNA BRCA1/2 mutant allelic frequency and comparing pre-and post-treatment cfDNA for the emergence of BRCA1/2 reversion and resistance mutations. This study is activated and open at Massachusetts General Hospital, where 2 patients are completing screening. It is also opening soon at 6 other academic centers (NCT03990896). Grant support includes a Pfizer ASPIRE award and 2020 Conquer Cancer Foundation of ASCO – Breast Cancer Research Foundation – Career Development Award. Clinical trial information: NCT03990896 .