bims-ovdlit Biomed News
on Ovarian cancer: early diagnosis, liquid biopsy and therapy
Issue of 2021–11–21
four papers selected by
Lara Paracchini, Humanitas Research
  1. Therapeutic Actionability of Circulating Cell-Free DNA Alterations in Carcinoma of Unknown Primary.
  2. Genome-Scale Methylation Analysis of Circulating Cell-Free DNA in Gastric Cancer Patients.
  3. The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples.
  4. From bulk, single-cell to spatial RNA sequencing.
  1. JCO Precis Oncol. 2021 ;pii: PO.21.00011. [Epub ahead of print]5
    Therapeutic Actionability of Circulating Cell-Free DNA Alterations in Carcinoma of Unknown Primary.
    Shumei Kato, Caroline Weipert, Sophia Gumas, Ryosuke Okamura, Suzanna Lee, Jason K Sicklick, Jennifer Saam, Razelle Kurzrock.
      Cancer of unknown primary (CUP) is a metastatic disease with unidentifiable primary tumor. Somatic alterations can be assessed noninvasively via liquid biopsies interrogating cell-free DNA (cfDNA).
    METHODS: We evaluated 1,931 patients with CUP with a cfDNA next-generation sequencing panel (73-74 genes).
    RESULTS: Overall, 1,739 patients (90%) had ≥ 1 cfDNA alteration. We then explored alteration actionability (per the levels of evidence from the OncoKB database); 825 patients (47.4% of 1,739) had level 1, level 2, or resistance/R1 alterations. Among 40 clinically annotated patients with CUP who had cfDNA evaluated, higher degrees of matching treatment to alterations (Matching Score > 50% v ≤ 50%) was the only variable predicting improved outcome: longer median progression-free survival (10.4 v 2.5 months; P = .002), overall survival (13.4 v 5.7 months; P = .07, trend), and higher clinical benefit rate (stable disease ≥ 6 months/partial response/complete response; 83% v 25%; P = .003).
    CONCLUSION: In summary, cfDNA frequently reveals strong level-of-evidence actionable alterations in CUP, and high degrees of matching to therapy correlates with better outcomes.
    DOI:  https://doi.org/10.1200/PO.21.00011
  2. Clin Chem. 2021 Nov 15. pii: hvab204. [Epub ahead of print]
    Genome-Scale Methylation Analysis of Circulating Cell-Free DNA in Gastric Cancer Patients.
    Jie Ren, Ping Lu, Xin Zhou, Yuhan Liao, Xiaomeng Liu, Jingyi Li, Wendong Wang, Jilian Wang, Lu Wen, Wei Fu, Fuchou Tang.
       BACKGROUND: Aberrant DNA hypermethylation of CpG islands (CGIs) occurs frequently and is genome-wide in human gastric cancer (GC). A DNA methylation approach in plasma cell-free DNA (cfDNA) is attractive for the noninvasive detection of GC. Here, we performed genome-scale cfDNA methylation analysis in patients with GC.
    METHODS: We used MCTA-Seq, a genome-scale DNA methylation analysis method, on the plasma samples of patients with GC (n = 89) and control participants (n = 82), as well as 28 pairs of GC and adjacent noncancerous tissues. The capacity of the method for detecting GC and discriminating GC from colorectal cancer (CRC) and hepatocellular carcinoma (HCC) was assessed.
    RESULTS: We identified 153 cfDNA methylation biomarkers, including DOCK10, CABIN1, and KCNQ5, for detecting GC in blood. A panel of these biomarkers gave a sensitivity of 44%, 59%, 78%, and 100% for stage I, II, III, and IV tumors, respectively, at a specificity of 92%. CpG island methylation phenotype (CIMP) tumors and NON-CIMP tumors could be distinguished and detected effectively. We also identified several hundreds of cfDNA biomarkers differentially methylated between GC, CRC, and HCC, and showed that MCTA-Seq can discriminate early-stage GC, CRC, and HCC in blood by using a high specificity (approximately 100%) algorithm.
    CONCLUSIONS: Our comprehensive analyses provided valuable data on cfDNA methylation biomarkers of GC and showed the promise of cfDNA methylation for the blood-based noninvasive detection of GC.
    Keywords:  DNA methylation; circulating cell-free DNA; gastric cancer; next-generation sequencing; plasma
    DOI:  https://doi.org/10.1093/clinchem/hvab204
  3. Eur J Cancer. 2021 Nov 16. pii: S0959-8049(21)00613-4. [Epub ahead of print]
    The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples.
    Ruben Van Paemel, Charlotte Vandeputte, Lennart Raman, Jolien Van Thorre, Leen Willems, Jo Van Dorpe, Malaïka Van Der Linden, Jilke De Wilde, Andries De Koker, Björn Menten, Christine Devalck, Ales Vicha, Marek Grega, Gudrun Schleiermacher, Yasmine Iddir, Mathieu Chicard, Lieke van Zogchel, Janine Stutterheim, Nathalie S M Lak, G A M Tytgat, Geneviève Laureys, Frank Speleman, Bram De Wilde, Tim Lammens, Katleen De Preter, Nadine Van Roy.
       BACKGROUND: Paediatric tumours are often characterised by the presence of recurrent DNA copy number alterations (CNAs). These DNA copy number profiles, obtained from a tissue biopsy, can aid in the correct prognostic classification and therapeutic stratification of several paediatric cancer entities (e.g. MYCN amplification in neuroblastoma) and are part of the routine diagnostic practice. Liquid biopsies (LQBs) offer a potentially safer alternative for such invasive tumour tissue biopsies and can provide deeper insight into tumour heterogeneity.
    PROCEDURE: The robustness and reliability of LQB CNA analyses was evaluated. We performed retrospective CNA profiling using shallow whole-genome sequencing (sWGS) on paired plasma circulating cell-free DNA (cfDNA) and tissue DNA samples from routinely collected samples from paediatric patients (n = 128) representing different tumour entities, including osteosarcoma, Ewing sarcoma, rhabdomyosarcoma, Wilms tumour, brain tumours and neuroblastoma.
    RESULTS: Overall, we observed a good concordance between CNAs in tissue DNA and cfDNA. The main cause of CNA discordance was found to be low cfDNA sample quality (i.e. the ratio of cfDNA (<700 bp) and high molecular weight DNA (>700 bp)). Furthermore, CNAs were observed that were present in cfDNA and not in tissue DNA, or vice-versa. In neuroblastoma samples, no false-positives or false-negatives were identified for the detection of the prognostic marker MYCN amplification.
    CONCLUSION: In future prospective studies, CNA analysis on LQBs that are of sufficient quality can serve as a complementary assay for CNA analysis on tissue biopsies, as either cfDNA or tissue DNA can contain CNAs that cannot be identified in the other biomaterial.
    Keywords:  Biomarker; Copy number aberrations; Liquid biopsy; Shallow whole-genome sequencing; cfDNA
    DOI:  https://doi.org/10.1016/j.ejca.2021.09.022
  4. Int J Oral Sci. 2021 Nov 15. 13(1): 36
    From bulk, single-cell to spatial RNA sequencing.
    Xinmin Li, Cun-Yu Wang.
      RNA sequencing (RNAseq) can reveal gene fusions, splicing variants, mutations/indels in addition to differential gene expression, thus providing a more complete genetic picture than DNA sequencing. This most widely used technology in genomics tool box has evolved from classic bulk RNA sequencing (RNAseq), popular single cell RNA sequencing (scRNAseq) to newly emerged spatial RNA sequencing (spRNAseq). Bulk RNAseq studies average global gene expression, scRNAseq investigates single cell RNA biology up to 20,000 individual cells simultaneously, while spRNAseq has ability to dissect RNA activities spatially, representing next generation of RNA sequencing. This article highlights these technologies, characteristic features and suitable applications in precision oncology.
    DOI:  https://doi.org/10.1038/s41368-021-00146-0
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