bims-tumhet Biomed News
on Tumor Heterogeneity
Issue of 2021–11–28
ten papers selected by
Sergio Marchini, Humanitas Research
  1. Maintenance Treatment of Newly Diagnosed Advanced Ovarian Cancer: Time for a Paradigm Shift?
  2. The Protein Landscape of Mucinous Ovarian Cancer: Towards a Theranostic.
  3. Liquid Biopsies beyond Mutation Calling: Genomic and Epigenomic Features of Cell-Free DNA in Cancer.
  4. The Prognostic Value of Circulating Tumor DNA in Ovarian Cancer: A Meta-Analysis.
  5. Genomic instability, inflammatory signaling and response to cancer immunotherapy.
  6. A state-of the-art review of stratified medicine in cancer: towards a future precision medicine strategy in cancer.
  7. Targeting the DNA damage response: PARP inhibitors and new perspectives in the landscape of cancer treatment.
  8. DNA Methylation and Immune Memory Response.
  9. Current and future clinical applications of ctDNA in immuno-oncology.
  10. Immune Cell Infiltration Landscape of Ovarian Cancer to Identify Prognosis and Immunotherapy-Related Genes to Aid Immunotherapy.
  1. Cancers (Basel). 2021 Nov 17. pii: 5756. [Epub ahead of print]13(22):
    Maintenance Treatment of Newly Diagnosed Advanced Ovarian Cancer: Time for a Paradigm Shift?
    Paul DiSilvestro, Nicoletta Colombo, Philipp Harter, Antonio González-Martín, Isabelle Ray-Coquard, Robert L Coleman.
      Recent data have demonstrated substantial efficacy with poly (ADP-ribose) polymerase (PARP) inhibitors as treatment and/or maintenance therapy in patients with newly diagnosed advanced epithelial ovarian cancer (EOC). Here, we review efficacy and safety results from four recent Phase III trials in newly diagnosed EOC: SOLO1 (olaparib), PAOLA-1 (olaparib in combination with bevacizumab), PRIMA (niraparib), and VELIA (veliparib). The implications of these data for current clinical practice and areas for future research are discussed, including ongoing studies of targeted agents in the newly diagnosed setting. Data from SOLO1, PAOLA-1, PRIMA, and VELIA confirm the benefit of PARP inhibitors (olaparib, niraparib, veliparib) for women with newly diagnosed EOC. The greatest benefit was seen in patients with a BRCA1 and/or BRCA2 mutation or in the homologous recombination deficiency (HRD)-test positive subgroup. These four well-conducted studies have generated practice-changing data. However, deciding how to apply these results in clinical practice is challenging, and substantial differences in trial design impede cross-trial comparisons. Recent PARP inhibitor approvals (olaparib, niraparib) in the newly diagnosed EOC setting have provided new maintenance treatment options for a broader patient population. The results of these studies call for personalized medicine based on biomarker profile and other factors, including tolerability, cost considerations, and physician and patient preference. Important areas for future research include appropriate use of both BRCA mutation and HRD testing to inform magnitude of PARP inhibitor benefit as well as exploring further options for patients who are HRD-test negative and for those who become PARP inhibitor resistant.
    Keywords:  BRCA mutation; PARP inhibitor; homologous recombination deficiency; ovarian cancer
    DOI:  https://doi.org/10.3390/cancers13225756
  2. Cancers (Basel). 2021 Nov 09. pii: 5596. [Epub ahead of print]13(22):
    The Protein Landscape of Mucinous Ovarian Cancer: Towards a Theranostic.
    Arkan Youssef, Mohammad B Haskali, Kylie L Gorringe.
      MOC is a rare histotype of epithelial ovarian cancer, and current management options are inadequate for the treatment of late stage or recurrent disease. A shift towards personalised medicines in ovarian cancer is being observed, with trials targeting specific molecular pathways, however, MOC lags due to its rarity. Theranostics is a rapidly evolving category of personalised medicine, encompassing both a diagnostic and therapeutic approach by recognising targets that are expressed highly in tumour tissue in order to deliver a therapeutic payload. The present review evaluates the protein landscape of MOC in recent immunohistochemical- and proteomic-based research, aiming to identify potential candidates for theranostic application. Fourteen proteins were selected based on cell membrane localisation: HER2, EGFR, FOLR1, RAC1, GPR158, CEACAM6, MUC16, PD-L1, NHE1, CEACAM5, MUC1, ACE2, GP2, and PTPRH. Optimal proteins to target using theranostic agents must exhibit high membrane expression on cancerous tissue with low expression on healthy tissue to afford improved disease outcomes with minimal off-target effects and toxicities. We provide guidelines to consider in the selection of a theranostic target for MOC and suggest future directions in evaluating the results of this review.
    Keywords:  mucinous ovarian cancer; personalised medicine; targeted therapy; theranostics
    DOI:  https://doi.org/10.3390/cancers13225596
  3. Cancers (Basel). 2021 Nov 10. pii: 5615. [Epub ahead of print]13(22):
    Liquid Biopsies beyond Mutation Calling: Genomic and Epigenomic Features of Cell-Free DNA in Cancer.
    Arlou Kristina Angeles, Florian Janke, Simone Bauer, Petros Christopoulos, Anja Lisa Riediger, Holger Sültmann.
      Cell-free DNA (cfDNA) analysis using liquid biopsies is a non-invasive method to gain insights into the biology, therapy response, mechanisms of acquired resistance and therapy escape of various tumors. While it is well established that individual cancer treatment options can be adjusted by panel next-generation sequencing (NGS)-based evaluation of driver mutations in cfDNA, emerging research additionally explores the value of deep characterization of tumor cfDNA genomics and fragmentomics as well as nucleosome modifications (chromatin structure), and methylation patterns (epigenomics) for comprehensive and multi-modal assessment of cfDNA. These tools have the potential to improve disease monitoring, increase the sensitivity of minimal residual disease identification, and detection of cancers at earlier stages. Recent progress in emerging technologies of cfDNA analysis is summarized, the added potential clinical value is highlighted, strengths and limitations are identified and compared with conventional targeted NGS analysis, and current challenges and future directions are discussed.
    Keywords:  DNA hydroxymethylation; DNA methylation; cell-free DNA; epigenomics; fragmentomics; histone modification; liquid biopsy; nucleosome positioning; precision medicine
    DOI:  https://doi.org/10.3390/cancers13225615
  4. Technol Cancer Res Treat. 2021 Jan-Dec;20:20 15330338211043784
    The Prognostic Value of Circulating Tumor DNA in Ovarian Cancer: A Meta-Analysis.
    Yuanyuan Lu, Li Li.
      Background: Studies have shown that circulating tumor DNA (ctDNA) indicates a poor prognosis in ovarian cancer. In this study, meta-analysis was used to assess the relationship between ctDNA and the prognosis of patients with epithelial ovarian cancer. Methods: The clinical trials included in this study were obtained via a search of PubMed, the Cochrane Library, the Web of Science and Embase between the period of establishment and March 2020. We selected clinical studies using qualitative or quantitative ctDNA methods to analyse the prognosis of ovarian epithelial cancer, screened the studies according to the determined inclusion and exclusion criteria, and used the modified JADAD score scale and NOS scale for evaluation, with OS (overall survival) and PFS (progression-free survival) as end events. The Cochrane Evaluation Tool was used to evaluate the quality of the randomized controlled trials. Stata 15.0 software was used to combine the effect ratio (hazard ratio, HR) and its 95% confidence interval (CI). In addition, a source analysis of ctDNA specimens, an analysis of ctDNA detection methods and a subgroup and sensitivity analysis of FIGO staging were performed. Results: A total of 8 studies were included in this meta-analysis, and ctDNA was found to be an independent risk factor for patients with epithelial ovarian cancer (OS: HR = 2.36, 95% CI [1.76,3.17], P < .001; PFS: HR = 2.51, 95% CI [1.83,3.45]). Conclusions: The results of our analysis suggested that ctDNA is a potential biomarker that can be used to evaluate the prognosis of patients with ovarian cancer.
    Keywords:  circulating tumor DNA; meta-analysis; ovarian cancer; prognosis
    DOI:  https://doi.org/10.1177/15330338211043784
  5. Biochim Biophys Acta Rev Cancer. 2021 Nov 17. pii: S0304-419X(21)00159-1. [Epub ahead of print] 188661
    Genomic instability, inflammatory signaling and response to cancer immunotherapy.
    Mengting Chen, Renske Linstra, Marcel A T M Van Vugt.
      Genomic and chromosomal instability are hallmarks of cancer and shape the genomic composition of cancer cells, thereby determining their behavior and response to treatment. Various genetic and epigenetic alterations in cancer have been linked to genomic instability, including DNA repair defects, oncogene-induced replication stress, and spindle assembly checkpoint malfunction. A consequence of genomic and chromosomal instability is the leakage of DNA from the nucleus into the cytoplasm, either directly or through the formation and subsequent rupture of micronuclei. Cytoplasmic DNA subsequently activates cytoplasmic DNA sensors, triggering downstream pathways, including a type I interferon response. This inflammatory signaling has pleiotropic effects, including enhanced anti-tumor immunity and potentially results in sensitization of cancer cells to immune checkpoint inhibitors. However, cancers frequently evolve mechanisms to avoid immune clearance, including suppression of inflammatory signaling. In this review, we summarize inflammatory signaling pathways induced by various sources of genomic instability, adaptation mechanisms that suppress inflammatory signaling, and implications for cancer immunotherapy.
    Keywords:  Chromosomal instability; DNA damage repair; Homologous recombination; Immune checkpoint inhibition; Type I interferon; cGAS/STING pathway
    DOI:  https://doi.org/10.1016/j.bbcan.2021.188661
  6. Ann Oncol. 2021 Nov 19. pii: S0923-7534(21)04785-2. [Epub ahead of print]
    A state-of the-art review of stratified medicine in cancer: towards a future precision medicine strategy in cancer.
    G W Middleton, H L Robbins, F Andre, C Swanton.
       BACKGROUND: Building on the success of targeted therapy in certain well-defined cancer genotypes, three platform studies - NCI-MATCH, LUNG-MAP and The National Lung Matrix Trial (NLMT) have attempted to discover new genotype-matched therapies for people with cancer.
    PATIENTS AND METHODS: We review the outputs from these platform studies. This review led us to propose a series of recommendations and considerations that we hope will inform future precision medicine programmes in cancer RESULTS: The three studies collectively screened over 13,000 patients. Across 37 genotype matched cohorts there have been 66/875 responders, an overall response rate of 7.5%. Targeting copy number gain yielded 5/199 responses across 9 biomarker:drug matched cohorts, a response rate of 2.5%.
    CONCLUSIONS: The majority of these studies used single-agent targeted therapies. Whilst pre-clinical data can suggest rational combination treatment to reverse adaptive resistance or block parallel activated pathways there is an essential need for accurate modelling of the toxicity:activity trade-off of combinations. Agent selection is often sub-optimal; dose expansion should only be performed with agents with clear clinical proof of mechanism and the high target selectivity. Targeting copy number change has been disappointing; it is crucial to define the drivers on shared amplicons that include the targeted aberration. Maximising outcomes with currently available targeted therapies requires moving towards a more contextualised stratified medicine acknowledging the criticality of the genomic, transcriptional and immunological context on which the targeted aberration is inscribed. Genomic complexity and instability is likely to be a leading cause of targeted therapy failure in genomically complex cancers. Pre-clinical models must be developed that more accurately capture the genomic complexity of human disease. The degree of attrition of studies performed after standard of care therapy suggest that serious efforts be made to develop a suite of precision medicine studies in the minimal residual disease setting.
    Keywords:  Targeted therapy; genotype-matching; platform trials; precision medicine
    DOI:  https://doi.org/10.1016/j.annonc.2021.11.004
  7. Crit Rev Oncol Hematol. 2021 Nov 17. pii: S1040-8428(21)00326-7. [Epub ahead of print] 103539
    Targeting the DNA damage response: PARP inhibitors and new perspectives in the landscape of cancer treatment.
    Sofia Genta, Federica Martorana, Anastasios Stathis, Ilaria Colombo.
      Cancer derives from alterations of pathways responsible for cell survival, differentiation and proliferation. Dysfunctions of mechanisms protecting genome integrity can promote oncogenesis but can also be exploited as therapeutic target. Poly-ADP-Ribose-Polymerase (PARP)-inhibitors, the first approved targeted agents able to tackle DNA damage response (DDR), have demonstrated antitumor activity, particularly when homologous recombination impairment is present. Despite the relevant results achieved, a large proportion of patients fail to obtain durable responses. The development of innovative treatments, able to overcome resistance and ensure long-lasting benefit for a wider population is still an unmet need. Moreover, improvement in biomarker assays is necessary to properly identify patients who can benefit from DDR targeting agents. Here we summarize the main DDR pathways, explain the current role of PARP inhibitors in cancer therapy and illustrate new therapeutic strategies targeting the DDR, focusing on the combinations of PARP inhibitors with other agents and on cell-cycle checkpoint inhibitors.
    Keywords:  DNA damage response; PARP inhibitors; PARP inhibitors resistance; cell-cycle checkpoint inhibitors; homologous recombination
    DOI:  https://doi.org/10.1016/j.critrevonc.2021.103539
  8. Cells. 2021 Oct 29. pii: 2943. [Epub ahead of print]10(11):
    DNA Methylation and Immune Memory Response.
    Nathalia Noschang Mittelstaedt, André Luiz Becker, Deise Nascimento de Freitas, Rafael F Zanin, Renato T Stein, Ana Paula Duarte de Souza.
      The generation of memory is a cardinal feature of the adaptive immune response, involving different factors in a complex process of cellular differentiation. This process is essential for protecting the second encounter with pathogens and is the mechanism by which vaccines work. Epigenetic changes play important roles in the regulation of cell differentiation events. There are three types of epigenetic regulation: DNA methylation, histone modification, and microRNA expression. One of these epigenetic changes, DNA methylation, occurs in cytosine residues, mainly in CpG dinucleotides. This brief review aimed to analyse the literature to verify the involvement of DNA methylation during memory T and B cell development. Several studies have highlighted the importance of the DNA methyltransferases, enzymes that catalyse the methylation of DNA, during memory differentiation, maintenance, and function. The methylation profile within different subsets of naïve activated and memory cells could be an interesting tool to help monitor immune memory response.
    Keywords:  B cells; DNA methylation; T cells; epigenetic; memory response
    DOI:  https://doi.org/10.3390/cells10112943
  9. Cancer Res. 2021 Nov 23. pii: canres.1718.2021. [Epub ahead of print]
    Current and future clinical applications of ctDNA in immuno-oncology.
    Julia Christina Stadler, Yassine Belloum, Benjamin Deitert, Mark Sementsov, Isabel Heidrich, Christoffer Gebhardt, Laura Keller, Klaus Pantel.
      Testing peripheral blood for circulating tumor DNA (ctDNA) offers a minimally invasive opportunity to diagnose, characterize, and monitor the disease in individual cancer patients. ctDNA can reflect the actual tumor burden and specific genomic state of disease and thus might serve as a prognostic and predictive biomarker for immune checkpoint inhibitor (ICI) therapy. Recent studies in various cancer entities (e.g., melanoma, non-small cell lung cancer, colon cancer, and urothelial cancer) have shown that sequential ctDNA analyses allow for the identification of responders to ICI therapy with a significant lead time to imaging. ctDNA assessment may also help distinguish pseudo-progression under ICI therapy from real progression. Developing dynamic changes in ctDNA concentrations as a potential surrogate endpoint of clinical efficacy in patients undergoing adjuvant immunotherapy is ongoing. Besides overall ctDNA burden, further ctDNA characterization can help uncover tumor-specific determinants (e.g., tumor mutational burden, microsatellite instability) of responses or resistance to immunotherapy. In future studies, standardized ctDNA assessments need to be included in interventional clinical trials across cancer entities to demonstrate the clinical utility of ctDNA as a biomarker for personalized cancer immunotherapy.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-1718
  10. Front Cell Dev Biol. 2021 ;9 749157
    Immune Cell Infiltration Landscape of Ovarian Cancer to Identify Prognosis and Immunotherapy-Related Genes to Aid Immunotherapy.
    Xiushen Li, Weizheng Liang, Huanyi Zhao, Zheng Jin, Guoqi Shi, Wanhua Xie, Hao Wang, Xueqing Wu.
      Ovarian cancer (OC) is the second leading cause of death in gynecological cancer. Multiple study have shown that the efficacy of tumor immunotherapy is related to tumor immune cell infiltration (ICI). However, so far, the Immune infiltration landscape of tumor microenvironment (TME) in OC has not been elucidated. In this study, We organized the transcriptome data of OC in the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, evaluated the patient's TME information, and constructed the ICI scores to predict the clinical benefits of patients undergoing immunotherapy. Immune-related genes were further used to construct the prognostic model. After clustering analysis of ICI genes, we found that patients in ICI gene cluster C had the best prognosis, and their tumor microenvironment had the highest proportion of macrophage M1 and T cell follicular helper cells. This result was consistent with that of multivariate cox (multi-cox) analysis. The prognostic model constructed by immune-related genes had good predictive performance. By estimating Tumor mutation burden (TMB), we also found that there were multiple genes with statistically different mutation frequencies in the high and low ICI score groups. The model based on the ICI score may help to screen out patients who would benefit from immunotherapy. The immune-related genes screened may be used as biomarkers and therapeutic targets.
    Keywords:  immune cell infiltration; immunotherapy; ovarian cancer; prognosis; tumor mutation burden
    DOI:  https://doi.org/10.3389/fcell.2021.749157
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