bims-ovdlit Biomed News
on Ovarian cancer: early diagnosis, liquid biopsy and therapy
Issue of 2022–10–30
eight papers selected by
Lara Paracchini, Humanitas Research
  1. The application of circulating tumor cell and cell-free DNA liquid biopsies in ovarian cancer.
  2. Clinical and molecular characteristics of ARIEL3 patients who derived exceptional benefit from rucaparib maintenance treatment for high-grade ovarian carcinoma.
  3. Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer.
  4. PAX8 as a Potential Target for Ovarian Cancer: What We Know so Far.
  5. Rules for the conduct of clinical trials need revision, but "good clinical practice" requires much more.
  6. scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells.
  7. Spatially resolved epigenomic profiling of single cells in complex tissues.
  8. Single-cell genomic variation induced by mutational processes in cancer.
  1. Mol Cell Probes. 2022 Oct 22. pii: S0890-8508(22)00082-2. [Epub ahead of print] 101871
    The application of circulating tumor cell and cell-free DNA liquid biopsies in ovarian cancer.
    Abigél Balla, Jong Bhak, Orsolya Biró.
      Ovarian cancer is the deadliest gynecological cancer. 70% of the cases are diagnosed at late stages with already developed metastases due to the absence of easily noticeable symptoms. Early-stage ovarian cancer has a good prognosis with a 5-year survival rate reaching 95%, hence the identification of effective biomarkers for early diagnosis is important. Advances in liquid biopsy-based methods can have a significant impact not just on the development of an efficient screening strategy, but also in clinical decision-making with additional molecular profiling and genetic alterations linked to therapy resistance. Despite the well-known advantages of liquid biopsy, there are still challenges that need to be addressed before its routine use in clinical practice. Various liquid biopsy-based biomarkers have been investigated in ovarian cancer; however, in this review, we are concentrating on the current use of cell-free DNA (cfDNA) and circulating tumor cells (CTCs) in disease management, focusing on their emerging importance in clinical practice. We also discuss the technical aspects of these workflows. The analysis of cfDNA is often chosen for the detection of mutations, copy number aberrations, and DNA methylation changes, whereas CTC analysis provides a unique opportunity to study whole cells, thus allowing DNA, RNA, and protein-based molecular profiling as well as in vivo studies. Combined solutions which merge the strengths of cfDNA and CTC approaches should be developed to maximize the potential of liquid biopsy technology.
    Keywords:  Circulating cell-free DNA (cfDNA); Circulating tumor cell (CTC); Liquid biopsy; Ovarian cancer
    DOI:  https://doi.org/10.1016/j.mcp.2022.101871
  2. Gynecol Oncol. 2022 Oct 20. pii: S0090-8258(22)00575-3. [Epub ahead of print]
    Clinical and molecular characteristics of ARIEL3 patients who derived exceptional benefit from rucaparib maintenance treatment for high-grade ovarian carcinoma.
    David M O'Malley, Amit M Oza, Domenica Lorusso, Carol Aghajanian, Ana Oaknin, Andrew Dean, Nicoletta Colombo, Johanne I Weberpals, Andrew R Clamp, Giovanni Scambia, Alexandra Leary, Robert W Holloway, Margarita Amenedo Gancedo, Peter C Fong, Jeffrey C Goh, Elizabeth M Swisher, Lara Maloney, Sandra Goble, Kevin K Lin, Tanya Kwan, Jonathan A Ledermann, Robert L Coleman.
       OBJECTIVE: ARIEL3 (NCT01968213) is a placebo-controlled randomized trial of the poly(ADP-ribose) polymerase inhibitor rucaparib as maintenance treatment in patients with recurrent high-grade ovarian carcinoma who responded to their latest line of platinum therapy. Rucaparib improved progression-free survival across all predefined subgroups. Here, we present an exploratory analysis of clinical and molecular characteristics associated with exceptional benefit from rucaparib.
    METHODS: Patients were randomized 2:1 to receive rucaparib 600 mg twice daily or placebo. Molecular features (genomic alterations, BRCA1 promoter methylation) and baseline clinical characteristics were evaluated for association with exceptional benefit (progression-free survival ≥2 years) versus progression on first scan (short-term subgroup) and other efficacy outcomes.
    RESULTS: Rucaparib treatment was significantly associated with exceptional benefit compared with placebo: 79/375 (21.1%) vs 4/189 (2.1%), respectively (p < 0.0001). Exceptional benefit was more frequent among patients with favorable baseline clinical characteristics and with carcinomas harboring molecular evidence of homologous recombination deficiency (HRD). A comparison between patients who derived exceptional benefit from rucaparib and those in the short-term subgroup revealed both clinical markers (no measurable disease at baseline, complete response to latest platinum, longer penultimate platinum-free interval) and molecular markers (BRCA1, BRCA2, RAD51C, and RAD51D alterations and genome-wide loss of heterozygosity) significantly associated with exceptional benefit.
    CONCLUSIONS: Exceptional benefit in ARIEL3 was more common in, but not exclusive to, patients with favorable clinical characteristics or molecular features associated with HRD. Our results suggest that rucaparib can deliver exceptional benefit to a diverse set of patients with recurrent high-grade ovarian carcinoma.
    Keywords:  Genomics; Ovarian carcinoma; Rucaparib; Safety
    DOI:  https://doi.org/10.1016/j.ygyno.2022.08.021
  3. Nat Commun. 2022 Oct 26. 13(1): 6360
    Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer.
    Filipe Correia Martins, Dominique-Laurent Couturier, Ines de Santiago, Carolin Margarethe Sauer, Maria Vias, Mihaela Angelova, Deborah Sanders, Anna Piskorz, James Hall, Karen Hosking, Anumithra Amirthanayagam, Sabina Cosulich, Larissa Carnevalli, Barry Davies, Thomas B K Watkins, Ionut G Funingana, Helen Bolton, Krishnayan Haldar, John Latimer, Peter Baldwin, Robin Crawford, Matthew Eldridge, Bristi Basu, Mercedes Jimenez-Linan, Andrew W Mcpherson, Nicholas McGranahan, Kevin Litchfield, Sohrab P Shah, Iain McNeish, Carlos Caldas, Gerard Evan, Charles Swanton, James D Brenton.
      Chromosomal instability is a major challenge to patient stratification and targeted drug development for high-grade serous ovarian carcinoma (HGSOC). Here we show that somatic copy number alterations (SCNAs) in frequently amplified HGSOC cancer genes significantly correlate with gene expression and methylation status. We identify five prevalent clonal driver SCNAs (chromosomal amplifications encompassing MYC, PIK3CA, CCNE1, KRAS and TERT) from multi-regional HGSOC data and reason that their strong selection should prioritise them as key biomarkers for targeted therapies. We use primary HGSOC spheroid models to test interactions between in vitro targeted therapy and SCNAs. MYC chromosomal copy number is associated with in-vitro and clinical response to paclitaxel and in-vitro response to mTORC1/2 inhibition. Activation of the mTOR survival pathway in the context of MYC-amplified HGSOC is statistically associated with increased prevalence of SCNAs in genes from the PI3K pathway. Co-occurrence of amplifications in MYC and genes from the PI3K pathway is independently observed in squamous lung cancer and triple negative breast cancer. In this work, we show that identifying co-occurrence of clonal driver SCNA genes could be used to tailor therapeutics for precision medicine.
    DOI:  https://doi.org/10.1038/s41467-022-33870-0
  4. Onco Targets Ther. 2022 ;15 1273-1280
    PAX8 as a Potential Target for Ovarian Cancer: What We Know so Far.
    Tina Di Palma, Mariastella Zannini.
      The Fallopian tube epithelium harbors the origin cells for the majority of high-grade serous ovarian carcinomas (HGSCs), the most lethal form of gynecologic malignancies. PAX8 belongs to the paired-box gene family of transcription factors and it is a marker of the FTE secretory cell lineage. Its role has been investigated in migration, invasion, proliferation, cell survival, stem cell maintenance, angiogenesis and tumor growth. In this review, we focus on the pro-tumorigenic role of PAX8 in ovarian cancer; in this context, PAX8 possibly continues to exert its transcriptional activity on its physiological targets but may also function on newly available targets after the tumorigenic hits. Acquiring new insights into the different PAX8 mechanism(s) of action in the tumor microenvironment could uncover new viable therapeutic targets and thus improve the current treatment regimen.
    Keywords:  Fallopian tube; PAX8; STICs; ovarian cancer; transcription factor
    DOI:  https://doi.org/10.2147/OTT.S361511
  5. Ann Oncol. 2022 Oct 20. pii: S0923-7534(22)04194-1. [Epub ahead of print]
    Rules for the conduct of clinical trials need revision, but "good clinical practice" requires much more.
    A Salawu, I F Tannock.
      
    DOI:  https://doi.org/10.1016/j.annonc.2022.10.005
  6. Genome Biol. 2022 Oct 28. 23(1): 229
    scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells.
    Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten, Renée Beekman.
      Single-cell DNA methylation profiling currently suffers from excessive noise and/or limited cellular throughput. We developed scTAM-seq, a targeted bisulfite-free method for profiling up to 650 CpGs in up to 10,000 cells per experiment, with a dropout rate as low as 7%. We demonstrate that scTAM-seq can resolve DNA methylation dynamics across B-cell differentiation in blood and bone marrow, identifying intermediate differentiation states that were previously masked. scTAM-seq additionally queries surface-protein expression, thus enabling integration of single-cell DNA methylation information with cell atlas data. In summary, scTAM-seq is a high-throughput, high-confidence method for analyzing DNA methylation at single-CpG resolution across thousands of single cells.
    Keywords:  DNA methylation; Epigenetics; Hematopoiesis; Multi-omic analysis; Single-cell profiling
    DOI:  https://doi.org/10.1186/s13059-022-02796-7
  7. Cell. 2022 Oct 14. pii: S0092-8674(22)01254-5. [Epub ahead of print]
    Spatially resolved epigenomic profiling of single cells in complex tissues.
    Tian Lu, Cheen Euong Ang, Xiaowei Zhuang.
      The recent development of spatial omics methods has enabled single-cell profiling of the transcriptome and 3D genome organization with high spatial resolution. Expanding the repertoire of spatial omics tools, a spatially resolved single-cell epigenomics method will accelerate understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved epigenomic profiling of single cells using in situ tagmentation and transcription followed by multiplexed imaging. We demonstrated the ability to profile histone modifications marking active promoters, putative enhancers, and silent promoters in individual cells, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results suggested putative promoter-enhancer pairs and enhancer hubs regulating developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.
    Keywords:  MERFISH; brain; development; enhancer; enhancer hub; enhancer-promoter interaction; epigenomic MERFISH; promoter; single-cell epigenomics; spatial epigenomic
    DOI:  https://doi.org/10.1016/j.cell.2022.09.035
  8. Nature. 2022 Oct 26.
    Single-cell genomic variation induced by mutational processes in cancer.
    IMAXT Consortium
      How cell-to-cell copy number alterations that underpin genomic instability1 in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer2, remains understudied. Here, by applying scaled single-cell whole-genome sequencing3 to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient mammary epithelial cells (13,818 genomes), and to primary triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSC) cells (22,057 genomes), we identify three distinct 'foreground' mutational patterns that are defined by cell-to-cell structural variation. Cell- and clone-specific high-level amplifications, parallel haplotype-specific copy number alterations and copy number segment length variation (serrate structural variations) had measurable phenotypic and evolutionary consequences. In TNBC and HGSC, clone-specific high-level amplifications in known oncogenes were highly prevalent in tumours bearing fold-back inversions, relative to tumours with homologous recombination deficiency, and were associated with increased clone-to-clone phenotypic variation. Parallel haplotype-specific alterations were also commonly observed, leading to phylogenetic evolutionary diversity and clone-specific mono-allelic expression. Serrate variants were increased in tumours with fold-back inversions and were highly correlated with increased genomic diversity of cellular populations. Together, our findings show that cell-to-cell structural variation contributes to the origins of phenotypic and evolutionary diversity in TNBC and HGSC, and provide insight into the genomic and mutational states of individual cancer cells.
    DOI:  https://doi.org/10.1038/s41586-022-05249-0
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