bims-ovdlit Biomed News
on Ovarian cancer: early diagnosis, liquid biopsy and therapy
Issue of 2022–06–26
seven papers selected by
Lara Paracchini, Humanitas Research
  1. Integrating chromatin accessibility states in the design of targeted sequencing panels for liquid biopsy.
  2. Current and Emerging Methods for Ovarian Cancer Screening and Diagnostics: A Comprehensive Review.
  3. Clinical applications and utility of cell-free DNA-based liquid biopsy analyses in cervical cancer and its precursor lesions.
  4. ctDNA guides omission of adjuvant chemotherapy for stage II CRC.
  5. The Homologous Recombination Deficiency Scar in Advanced Cancer: Agnostic Targeting of Damaged DNA Repair.
  6. Next-Generation Sequencing on Circulating Tumor DNA in Advanced Solid Cancer: Swiss Army Knife for the Molecular Tumor Board? A Review of the Literature Focused on FDA Approved Test.
  7. Genome-wide mapping of somatic mutation rates uncovers drivers of cancer.
  1. Sci Rep. 2022 Jun 21. 12(1): 10447
    Integrating chromatin accessibility states in the design of targeted sequencing panels for liquid biopsy.
    Pegah Taklifi, Fahimeh Palizban, Mahya Mehrmohamadi.
      Dying tumor cells shed DNA fragments into the circulation that are known as circulating tumor DNA (ctDNA). Liquid biopsy tests aim to detect cancer using known markers, including genetic alterations and epigenetic profiles of ctDNA. Despite various advantages, the major limitation remains the low fraction of tumor-originating DNA fragments in a high background of normal blood-cell originating fragments in the cell-free DNA (cfDNA) pool in plasma. Deep targeted sequencing of cfDNA allows for enrichment of fragments in known cancer marker-associated regions of the genome, thus increasing the chances of detecting the low fraction variant harboring fragments. Most targeted sequencing panels are designed to include known recurrent mutations or methylation markers of cancer. Here, we propose the integration of cancer-specific chromatin accessibility states into panel designs for liquid biopsy. Using machine learning approaches, we first identify accessible and inaccessible chromatin regions specific to each major human cancer type. We then introduce a score that quantifies local chromatin accessibility in tumor relative to blood cells and show that this metric can be useful for prioritizing marker regions with higher chances of being detected in cfDNA for inclusion in future panel designs.
    DOI:  https://doi.org/10.1038/s41598-022-14675-z
  2. Cancers (Basel). 2022 Jun 11. pii: 2885. [Epub ahead of print]14(12):
    Current and Emerging Methods for Ovarian Cancer Screening and Diagnostics: A Comprehensive Review.
    Juliane M Liberto, Sheng-Yin Chen, Ie-Ming Shih, Tza-Huei Wang, Tian-Li Wang, Thomas R Pisanic.
      With a 5-year survival rate of less than 50%, ovarian high-grade serous carcinoma (HGSC) is one of the most highly aggressive gynecological malignancies affecting women today. The high mortality rate of HGSC is largely attributable to delays in diagnosis, as most patients remain undiagnosed until the late stages of -disease. There are currently no recommended screening tests for ovarian cancer and there thus remains an urgent need for new diagnostic methods, particularly those that can detect the disease at early stages when clinical intervention remains effective. While diagnostics for ovarian cancer share many of the same technical hurdles as for other cancer types, the low prevalence of the disease in the general population, coupled with a notable lack of sensitive and specific biomarkers, have made the development of a clinically useful screening strategy particularly challenging. Here, we present a detailed review of the overall landscape of ovarian cancer diagnostics, with emphasis on emerging methods that employ novel protein, genetic, epigenetic and imaging-based biomarkers and/or advanced diagnostic technologies for the noninvasive detection of HGSC, particularly in women at high risk due to germline mutations such as BRCA1/2. Lastly, we discuss the translational potential of these approaches for achieving a clinically implementable solution for screening and diagnostics of early-stage ovarian cancer as a means of ultimately improving patient outcomes in both the general and high-risk populations.
    Keywords:  HGSC; biomarkers; diagnostic; emerging; ovarian cancer; screening
    DOI:  https://doi.org/10.3390/cancers14122885
  3. Br J Cancer. 2022 Jun 20.
    Clinical applications and utility of cell-free DNA-based liquid biopsy analyses in cervical cancer and its precursor lesions.
    Johanna Herbst, Klaus Pantel, Katharina Effenberger, Harriet Wikman.
      Human papilloma virus (HPV) is an infectious carcinogenic agent. Nearly all cervical cancers are positive for one of the high-risk HPV subtypes. Although the introduction of the HPV vaccines in many countries have shown tremendous positive effects on the incidence of both cervical intraepithelial lesions (CIN) and invasive cancer, the large majority of females worldwide are still not vaccinated. Patients with diagnosed high-grade CIN need a lifelong close monitoring of possible relapse or development of invasive cancer. Different blood-based liquid biopsy approaches have shown great promise as an easily obtainable minimally invasive tool for early detection and monitoring of disease. Among the different liquid biopsy approaches the clinical relevance of cell-free DNA (cfDNA) in cervical cancer has been best investigated. In cervical cancer, the DNA fragments can be of both, human as well as viral origin. Thus, the mutation and methylation status of genes related to carcinogenesis as well as the HPV status can be analysed in plasma from cervical cancer patients. This review describes recent advances in different cfDNA approaches for early detection and monitoring of cervical cancer and its precursor lesions.
    DOI:  https://doi.org/10.1038/s41416-022-01868-6
  4. Nat Rev Clin Oncol. 2022 Jun 24.
    ctDNA guides omission of adjuvant chemotherapy for stage II CRC.
    Diana Romero.
      
    DOI:  https://doi.org/10.1038/s41571-022-00657-7
  5. Cancers (Basel). 2022 Jun 15. pii: 2950. [Epub ahead of print]14(12):
    The Homologous Recombination Deficiency Scar in Advanced Cancer: Agnostic Targeting of Damaged DNA Repair.
    Vilma Pacheco-Barcia, Andrés Muñoz, Elena Castro, Ana Isabel Ballesteros, Gloria Marquina, Iván González-Díaz, Ramon Colomer, Nuria Romero-Laorden.
      BRCA1 and BRCA2 are the most recognized tumor-suppressor genes involved in double-strand DNA break repair through the homologous recombination (HR) system. Widely known for its role in hereditary cancer, HR deficiency (HRD) has turned out to be critical beyond breast and ovarian cancer: for prostate and pancreatic cancer also. The relevance for the identification of these patients exceeds diagnostic purposes, since results published from clinical trials with poly-ADP ribose polymerase (PARP) inhibitors (PARPi) have shown how this type of targeted therapy can modify the long-term evolution of patients with HRD. Somatic aberrations in other HRD pathway genes, but also indirect genomic instability as a sign of this DNA repair impairment (known as HRD scar), have been reported to be relevant events that lead to more frequently than expected HR loss of function in several tumor types, and should therefore be included in the current diagnostic and therapeutic algorithm. However, the optimal strategy to identify HRD and potential PARPi responders in cancer remains undefined. In this review, we summarize the role and prevalence of HRD across tumor types and the current treatment landscape to guide the agnostic targeting of damaged DNA repair. We also discuss the challenge of testing patients and provide a special insight for new strategies to select patients who benefit from PARPi due to HRD scarring.
    Keywords:  BRCA; HRD; PARP inhibitors; agnostic cancer; homologous recombination deficiency
    DOI:  https://doi.org/10.3390/cancers14122950
  6. Cells. 2022 Jun 11. pii: 1901. [Epub ahead of print]11(12):
    Next-Generation Sequencing on Circulating Tumor DNA in Advanced Solid Cancer: Swiss Army Knife for the Molecular Tumor Board? A Review of the Literature Focused on FDA Approved Test.
    Damien Vasseur, Hela Sassi, Arnaud Bayle, Marco Tagliamento, Benjamin Besse, Christophe Marzac, Ahmadreza Arbab, Nathalie Auger, Sophie Cotteret, Mihaela Aldea, Félix Blanc-Durand, Arthur Géraud, Anas Gazzah, Yohann Loriot, Antoine Hollebecque, Patricia Martín-Romano, Maud Ngo-Camus, Claudio Nicotra, Santiago Ponce, Madona Sakkal, Olivier Caron, Cristina Smolenschi, Jean-Baptiste Micol, Antoine Italiano, Etienne Rouleau, Ludovic Lacroix.
      FDA-approved next-generation sequencing assays based on cell-free DNA offers new opportunities in a molecular-tumor-board context thanks to the noninvasiveness of liquid biopsy, the diversity of analyzed parameters and the short turnaround time. It gives the opportunity to study the heterogeneity of the tumor, to elucidate complex resistance mechanisms and to adapt treatment strategies. However, lowering the limit of detection and increasing the panels' size raise new questions in terms of detection of incidental germline alterations, occult malignancies and clonal hematopoiesis of indeterminate potential mutations. In this review, after a technological discussion and description of the common problematics encountered, we establish recommendations in properly using these FDA-approved tests in a molecular-tumor-board context.
    Keywords:  FDA-approved; cfDNA; liquid biopsy; molecular tumor board; next-generation sequencing
    DOI:  https://doi.org/10.3390/cells11121901
  7. Nat Biotechnol. 2022 Jun 20.
    Genome-wide mapping of somatic mutation rates uncovers drivers of cancer.
    Maxwell A Sherman, Adam U Yaari, Oliver Priebe, Felix Dietlein, Po-Ru Loh, Bonnie Berger.
      Identification of cancer driver mutations that confer a proliferative advantage is central to understanding cancer; however, searches have often been limited to protein-coding sequences and specific non-coding elements (for example, promoters) because of the challenge of modeling the highly variable somatic mutation rates observed across tumor genomes. Here we present Dig, a method to search for driver elements and mutations anywhere in the genome. We use deep neural networks to map cancer-specific mutation rates genome-wide at kilobase-scale resolution. These estimates are then refined to search for evidence of driver mutations under positive selection throughout the genome by comparing observed to expected mutation counts. We mapped mutation rates for 37 cancer types and applied these maps to identify putative drivers within intronic cryptic splice regions, 5' untranslated regions and infrequently mutated genes. Our high-resolution mutation rate maps, available for web-based exploration, are a resource to enable driver discovery genome-wide.
    DOI:  https://doi.org/10.1038/s41587-022-01353-8
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