bims-ovdlit 2021-08-08 papers

bims-ovdlit

Biomed News

on Ovarian cancer: early diagnosis, liquid biopsy and therapy

Issue of 2021–08–08
twelve papers selected by
Lara Paracchini, Humanitas Research

Single-Cell RNA Sequencing of Ovarian Cancer: Promises and Challenges.
The relevance of liquid biopsy in surgical oncology: The application of perioperative circulating nucleic acid dynamics in improving patient outcomes.
PARP-inhibitors in epithelial ovarian cancer: Actual positioning and future expectations.
PAX8, an Emerging Player in Ovarian Cancer.
Quantitative Assessment and Prognostic Associations of the Immune Landscape in Ovarian Clear Cell Carcinoma.
Classification of High-Grade Serous Ovarian Carcinoma by Epithelial-to-Mesenchymal Transition Signature and Homologous Recombination Repair Genes.
Single-cell spatial sequencing.
Microbiome-targeted diets that alter immune status.
Bilateral salpingo-oophorectomy and breast cancer risk for BRCA1 and BRCA2 mutation carriers: Assessing the evidence.
Spatial omics and multiplexed imaging to explore cancer biology.
Introduction to Single-Cell DNA Methylation Profiling Methods.
The use of a next-generation sequencing-derived machine-learning risk-prediction model (OncoCast-MPM) for malignant pleural mesothelioma: a retrospective study.

Adv Exp Med Biol. 2021 ;1330 113-123

Single-Cell RNA Sequencing of Ovarian Cancer: Promises and Challenges.

Shobhana Talukdar, Zenas Chang, Boris Winterhoff, Timothy K Starr.

  Ovarian cancer remains the leading cause of death from gynecologic malignancy in the Western world. Tumors are comprised of heterogeneous populations of various cancer, immune, and stromal cells; it is hypothesized that rare cancer stem cells within these subpopulations lead to disease recurrence and treatment resistance. Technological advances now allow for the analysis of tumor genomes and transcriptomes at the single-cell level, which provides the resolution to potentially identify these rare cancer stem cells within the larger tumor.In this chapter, we review the evolution of next-generation RNA sequencing techniques, the methodology of single-cell isolation and sequencing, sequencing data analysis, and the potential applications in ovarian cancer. We also summarize the current published work using single-cell sequencing in ovarian cancer.By utilizing this novel technique to characterize the gene expression of rare subpopulations, new targets and treatment pathways may be identified in ovarian cancer to change treatment paradigms.

Keywords:  Gene expression; Next generation RNA sequencing; Ovarian cancer; Rare cancer stem cells; Rare cancer subpopulations; Single cell isolation; Single cell sequencing; Treatment

DOI:  https://doi.org/10.1007/978-3-030-73359-9_7
Surgeon. 2021 Aug 03. pii: S1479-666X(21)00125-6. [Epub ahead of print]

The relevance of liquid biopsy in surgical oncology: The application of perioperative circulating nucleic acid dynamics in improving patient outcomes.

Patrick R Jordan, Donal Peter O'Leary, Cristina A Fleming, Jianghuai Wang, Henry Paul Redmond.

   BACKGROUND: Liquid biopsy is gaining increasing clinical utility in the management of cancer patients. The main components of a liquid biopsy are circulating nucleic acids, circulating tumour cells and extracellular vesicles such as exosomes. Circulating nucleic acids including cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) in particular have been the focus of recent attention as they have demonstrated excellent potential in cancer screening, provision of prognostic information and in genomic profiling of a tumour without the need for repeated tissue biopsies. The aim of this review was to explore the current evidence in relation to the use of liquid biopsy in the perioperative setting and identify ways in which liquid biopsy may be applied in the future.
METHODS: This narrative review is based on a comprehensive literature search up to the 1st of June 2020 for papers relevant to the application of liquid biopsy in surgical oncology, focusing particularly on the perioperative period.
RESULTS: Recent evidence has demonstrated that perioperative liquid biopsy can accurately stratify patients' risk of recurrence compared to conventional biomarkers. Attention to the perioperative dynamics of liquid biopsy components can potentially provide new understanding of the complex relationship between surgery and cancer outcome. In addition, careful evaluation of liquid biopsy components in the perioperative window may provide important diagnostic and therapeutic information for cancer patients.
CONCLUSION: The rapidly evolving concept of the liquid biopsy has the potential to become the cornerstone for decision making around surveillance and adjuvant therapies the era of personalised medicine.

Keywords:  Cell-free DNA; Circulating tumour DNA; Liquid biopsy; Perioperative; Surgery

DOI:  https://doi.org/10.1016/j.surge.2021.06.006
Cancer Treat Rev. 2021 Jul 15. pii: S0305-7372(21)00103-1. [Epub ahead of print]99 102255

PARP-inhibitors in epithelial ovarian cancer: Actual positioning and future expectations.

Hélène Vanacker, Philipp Harter, Sana Intidhar Labidi-Galy, Susana Banerjee, Ana Oaknin, Domenica Lorusso, Isabelle Ray-Coquard.

  Poly-(ADP)-ribose polymerase inhibitors (PARPi) are a class of oral anticancer drugs first developed as "synthetically lethal" in cancers harboring BRCA1/BRCA2 inactivating mutations. In high-grade serous or endometrioid ovarian cancers (HGOC), PARPi demonstrated benefit as maintenance therapy in relapsing BRCA-mutated and non-mutated tumors. Recently, they extended their indications to frontline maintenance therapy. This review summarizes the current place of PARPi (i) as maintenance or single agent in recurrent disease and (ii) frontline maintenance with different settings. We reviewed the course of biomarker identification, the challenge of overcoming resistance to PARPi and future combinations with targeted therapies, including anti-angiogenic, immune checkpoint inhibitors and DNA damage response inhibitors.

Keywords:  BRCA; HRD; Niraparib; Olaparib; Ovarian cancer; PARP inhibitor; Rucaparib, Veliparib

DOI:  https://doi.org/10.1016/j.ctrv.2021.102255
Adv Exp Med Biol. 2021 ;1330 95-112

PAX8, an Emerging Player in Ovarian Cancer.

Priyanka Gokulnath, Amata Amy Soriano, Tiziana de Cristofaro, Tina Di Palma, Mariastella Zannini.

  Ovarian Cancer is one of the most lethal and widespread gynecological malignancies. It is the seventh leading cause of all cancer deaths worldwide. High-Grade Serous Cancer (HGSC), the most commonly occurring subtype, alone contributes to 70% of all ovarian cancer deaths. This is mainly attributed to the complete lack of symptoms during the early stages of the disease and absence of an early diagnostic marker.PAX8 is emerging as an important histological marker for most of the epithelial ovarian cancers, as it is expressed in about 90% of malignant ovarian cancers, specifically in HGSC. PAX8 is a member of the Paired-Box gene family (PAX1-9) of transcription factors whose expression is tightly controlled temporally and spatially. The PAX genes are well known for their role in embryonic development and their expression continues to persist in some adult tissues. PAX8 is required for the normal development of Müllerian duct that includes Fallopian tube, uterus, cervix, and upper part of vagina. In adults, it is expressed in the Fallopian tube and uterine epithelium and not in the ovarian epithelium. Considering the recent studies that predict the events preceding the tumorigenesis of HGSC from the Fallopian tube, PAX8 appears to have an important role in the development of ovarian cancer.In this chapter, we review some of the published findings to highlight the significance of PAX8 as an important marker and an emerging player in the pathogenesis of ovarian cancer. We also discuss regarding the future perspectives of PAX8 wherein it could contribute to the betterment of ovarian cancer diagnosis and treatment.

Keywords:  Biomarkers; Cancer tissues; Metastasis; Ovarian cancers; PAX genes; Transcription factors

DOI:  https://doi.org/10.1007/978-3-030-73359-9_6
Cancers (Basel). 2021 Jul 30. pii: 3854. [Epub ahead of print]13(15):

Quantitative Assessment and Prognostic Associations of the Immune Landscape in Ovarian Clear Cell Carcinoma.

Saira Khalique, Sarah Nash, David Mansfield, Julian Wampfler, Ayoma Attygale, Katherine Vroobel, Harriet Kemp, Richard Buus, Hannah Cottom, Ioannis Roxanis, Thomas Jones, Katharina von Loga, Dipa Begum, Naomi Guppy, Pradeep Ramagiri, Kerry Fenwick, Nik Matthews, Michael J F Hubank, Christopher J Lord, Syed Haider, Alan Melcher, Susana Banerjee, Rachael Natrajan.

  Ovarian clear cell carcinoma (OCCC) is a rare subtype of epithelial ovarian cancer characterised by a high frequency of loss-of-function ARID1A mutations and a poor response to chemotherapy. Despite their generally low mutational burden, an intratumoural T cell response has been reported in a subset of OCCC, with ARID1A purported to be a biomarker for the response to the immune checkpoint blockade independent of micro-satellite instability (MSI). However, assessment of the different immune cell types and spatial distribution specifically within OCCC patients has not been described to date. Here, we characterised the immune landscape of OCCC by profiling a cohort of 33 microsatellite stable OCCCs at the genomic, gene expression and histological level using targeted sequencing, gene expression profiling using the NanoString targeted immune panel, and multiplex immunofluorescence to assess the spatial distribution and abundance of immune cell populations at the protein level. Analysis of these tumours and subsequent independent validation identified an immune-related gene expression signature associated with risk of recurrence of OCCC. Whilst histological quantification of tumour-infiltrating lymphocytes (TIL, Salgado scoring) showed no association with the risk of recurrence or ARID1A mutational status, the characterisation of TILs via multiplexed immunofluorescence identified spatial differences in immunosuppressive cell populations in OCCC. Tumour-associated macrophages (TAM) and regulatory T cells were excluded from the vicinity of tumour cells in low-risk patients, suggesting that high-risk patients have a more immunosuppressive microenvironment. We also found that TAMs and cytotoxic T cells were also excluded from the vicinity of tumour cells in ARID1A-mutated OCCCs compared to ARID1A wild-type tumours, suggesting that the exclusion of these immune effectors could determine the host response of ARID1A-mutant OCCCs to therapy. Overall, our study has provided new insights into the immune landscape and prognostic associations in OCCC and suggest that tailored immunotherapeutic approaches may be warranted for different subgroups of OCCC patients.

Keywords:  ARID1A; biomarker; clear cell ovarian cancer; immune microenvironment; next generation sequencing

DOI:  https://doi.org/10.3390/cancers13153854
Genes (Basel). 2021 Jul 20. pii: 1103. [Epub ahead of print]12(7):

Classification of High-Grade Serous Ovarian Carcinoma by Epithelial-to-Mesenchymal Transition Signature and Homologous Recombination Repair Genes.

Min-Hwan Sohn, Se Ik Kim, Jong-Yeon Shin, Hee Seung Kim, Hyun Hoon Chung, Jae-Weon Kim, Maria Lee, Jeong-Sun Seo.

  High-grade serous ovarian cancer (HGSOC) is one of the deadliest cancers that can occur in women. This study aimed to investigate the molecular characteristics of HGSOC through integrative analysis of multi-omics data. We used fresh-frozen, chemotherapy-naïve primary ovarian cancer tissues and matched blood samples of HGSOC patients and conducted next-generation whole-exome sequencing (WES) and RNA sequencing (RNA-seq). Genomic and transcriptomic profiles were comprehensively compared between patients with germline BRCA1/2 mutations and others with wild-type BRCA1/2. HGSOC samples initially divided into two groups by the presence of germline BRCA1/2 mutations showed mutually exclusive somatic mutation patterns, yet the implementation of high-dimensional analysis of RNA-seq and application of epithelial-to-mesenchymal (EMT) index onto the HGSOC samples revealed that they can be divided into two subtypes; homologous recombination repair (HRR)-activated type and mesenchymal type. Patients with mesenchymal HGSOC, characterized by the activation of the EMT transcriptional program, low genomic alteration and diverse cell-type compositions, exhibited significantly worse overall survival than did those with HRR-activated HGSOC (p = 0.002). In validation with The Cancer Genome Atlas (TCGA) HGSOC data, patients with a high EMT index (≥the median) showed significantly worse overall survival than did those with a low EMT index (<the median) (p = 0.030). In conclusion, through a comprehensive multi-omics approach towards our HGSOC cohorts, two distinctive types of HGSOC (HRR-activated and mesenchymal) were identified. Our novel EMT index seems to be a potential prognostic biomarker for HGSOC.

Keywords:  epithelial-to-mesenchymal transition; gene signature; high-grade serous carcinoma; homologous recombination repair; ovarian cancer

DOI:  https://doi.org/10.3390/genes12071103
Nat Genet. 2021 Aug;53(8): 1119

Single-cell spatial sequencing.

Ornob Alam.

DOI: https://doi.org/10.1038/s41588-021-00919-7
Nat Rev Gastroenterol Hepatol. 2021 Aug 05.

Microbiome-targeted diets that alter immune status.

Caroline Barranco.

DOI: https://doi.org/10.1038/s41575-021-00509-2
Cancer Prev Res (Phila). 2021 Aug 04. pii: canprevres.0141.2021. [Epub ahead of print]

Bilateral salpingo-oophorectomy and breast cancer risk for BRCA1 and BRCA2 mutation carriers: Assessing the evidence.

Ciara Conduit, Roger L Milne, Michael L Friedlander, Kelly-Anne Phillips.

Without preventive interventions, women with germline pathogenic variants in BRCA1 or BRCA2 have high lifetime risks for breast cancer (BC) and tubo-ovarian cancer. The increased risk for BC starts at a considerably younger age than that for tubo-ovarian cancer. Risk-reducing bilateral salpingo-oophorectomy (rrBSO) is effective in reducing tubo-ovarian cancer risk for BRCA1 and BRCA2 mutation carriers, but whether it reduces BC risk is less clear. All studies of rrBSO and BC risk are observational in nature, and subject to various forms of bias and confounding, thus limiting conclusions that can be drawn about causation. Early studies supported a statistically significant protective association for rrBSO on BC risk, which is reflected by several international guidelines that recommend consideration of pre-menopausal rrBSO for BC risk reduction. However, these historical studies were hampered by the presence of several important biases, including immortal person-time bias, confounding by indication, informative censoring, and confounding by other risk factors, which may have led to over-estimation of any protective benefit. Contemporary studies, specifically designed to reduce some of these biases, have yielded contradictory results. Taken together, there is no clear and consistent evidence for a role of pre-menopausal rrBSO in reducing BC risk in BRCA1 or BRCA2 mutation carriers.

DOI: https://doi.org/10.1158/1940-6207.CAPR-21-0141
Nat Methods. 2021 Aug 02.

Spatial omics and multiplexed imaging to explore cancer biology.

Sabrina M Lewis, Marie-Liesse Asselin-Labat, Quan Nguyen, Jean Berthelet, Xiao Tan, Verena C Wimmer, Delphine Merino, Kelly L Rogers, Shalin H Naik.

Understanding intratumoral heterogeneity-the molecular variation among cells within a tumor-promises to address outstanding questions in cancer biology and improve the diagnosis and treatment of specific cancer subtypes. Single-cell analyses, especially RNA sequencing and other genomics modalities, have been transformative in revealing novel biomarkers and molecular regulators associated with tumor growth, metastasis and drug resistance. However, these approaches fail to provide a complete picture of tumor biology, as information on cellular location within the tumor microenvironment is lost. New technologies leveraging multiplexed fluorescence, DNA, RNA and isotope labeling enable the detection of tens to thousands of cancer subclones or molecular biomarkers within their native spatial context. The expeditious growth in these techniques, along with methods for multiomics data integration, promises to yield a more comprehensive understanding of cell-to-cell variation within and between individual tumors. Here we provide the current state and future perspectives on the spatial technologies expected to drive the next generation of research and diagnostic and therapeutic strategies for cancer.

DOI: https://doi.org/10.1038/s41592-021-01203-6
Biomolecules. 2021 Jul 10. pii: 1013. [Epub ahead of print]11(7):

Introduction to Single-Cell DNA Methylation Profiling Methods.

Jongseong Ahn, Sunghoon Heo, Jihyun Lee, Duhee Bang.

  DNA methylation is an epigenetic mechanism that is related to mammalian cellular differentiation, gene expression regulation, and disease. In several studies, DNA methylation has been identified as an effective marker to identify differences between cells. In this review, we introduce single-cell DNA-methylation profiling methods, including experimental strategies and approaches to computational data analysis. Furthermore, the blind spots of the basic analysis and recent alternatives are briefly described. In addition, we introduce well-known applications and discuss future development.

Keywords:  DNA methylation; bioinformatics; single cell

DOI:  https://doi.org/10.3390/biom11071013
Lancet Digit Health. 2021 Jul 28. pii: S2589-7500(21)00104-7. [Epub ahead of print]

The use of a next-generation sequencing-derived machine-learning risk-prediction model (OncoCast-MPM) for malignant pleural mesothelioma: a retrospective study.

Marjorie G Zauderer, Axel Martin, Jacklynn Egger, Hira Rizvi, Michael Offin, Andreas Rimner, Prasad S Adusumilli, Valerie W Rusch, Mark G Kris, Jennifer L Sauter, Marc Ladanyi, Ronglai Shen.

BACKGROUND: Current risk stratification for patients with malignant pleural mesothelioma based on disease stage and histology is inadequate. For some individuals with early-stage epithelioid tumours, a good prognosis by current guidelines can progress rapidly; for others with advanced sarcomatoid cancers, a poor prognosis can progress slowly. Therefore, we aimed to develop and validate a machine-learning tool-known as OncoCast-MPM-that could create a model for patient prognosis.
METHODS: We did a retrospective study looking at malignant pleural mesothelioma tumours using next-generation sequencing from the Memorial Sloan Kettering Cancer Center-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT). We collected clinical, pathological, and routine next-generation sequencing data from consecutive patients with malignant pleural mesothelioma treated at the Memorial Sloan Kettering Cancer Center (New York, NY, USA), as well as the MSK-IMPACT data. Together, these data comprised the MSK-IMPACT cohort. Using OncoCast-MPM, an open-source, web-accessible, machine-learning risk-prediction model, we integrated available data to create risk scores that stratified patients into low-risk and high-risk groups. Risk stratification of the MSK-IMPACT cohort was then validated using publicly available malignant pleural mesothelioma data from The Cancer Genome Atlas (ie, the TCGA cohort).
FINDINGS: Between Feb 15, 2014, and Jan 28, 2019, we collected MSK-IMPACT data from the tumour tissue of 194 patients in the MSK-IMPACT cohort. The median overall survival was higher in the low-risk group than in the high-risk group as determined by OncoCast-MPM (30·8 months [95% CI 22·7-36·2] vs 13·9 months [10·7-18·0]; hazard ratio [HR] 3·0 [95% CI 2·0-4·5]; p<0·0001). No single factor or gene alteration drove risk differentiation. OncoCast-MPM was validated against the TCGA cohort, which consisted of 74 patients. The median overall survival was higher in the low-risk group than in the high-risk group (23·6 months [95% CI 15·1-28·4] vs 13·6 months [9·8-17·9]; HR 2·3 [95% CI 1·3-3·8]; p=0·0019). Although stage-based risk stratification was unable to differentiate survival among risk groups at 3 years in the MSK-IMPACT cohort (31% for early-stage disease vs 30% for advanced-stage disease; p=0·90), the OncoCast-MPM-derived 3-year survival was significantly higher in the low-risk group than in the high-risk group (40% vs 7%; p=0·0052).
INTERPRETATION: OncoCast-MPM generated accurate, individual patient-level risk assessment scores. After prospective validation with the TCGA cohort, OncoCast-MPM might offer new opportunities for enhanced risk stratification of patients with malignant pleural mesothelioma in clinical trials and drug development.
FUNDING: US National Institutes of Health/National Cancer Institute.

DOI: https://doi.org/10.1016/S2589-7500(21)00104-7