bims-tumhet Biomed News
on Tumor Heterogeneity
Issue of 2021‒10‒31
nine papers selected by
Sergio Marchini
Humanitas Research
  1. Homologous recombination proficiency in ovarian and breast cancer patients.
  2. The role of patient-derived ovarian cancer organoids in the study of PARP inhibitors sensitivity and resistance: from genomic analysis to functional testing.
  3. Aberrant transcript usage is associated with homologous recombination deficiency and predicts therapeutic response.
  4. Targeting DNA Repair Response Promotes Immunotherapy in Ovarian Cancer: Rationale and Clinical Application.
  5. Maintenance olaparib for patients with newly diagnosed advanced ovarian cancer and a BRCA mutation (SOLO1/GOG 3004): 5-year follow-up of a randomised, double-blind, placebo-controlled, phase 3 trial.
  6. Repeatability of methylation measures using a QIAseq targeted methyl panel and comparison with the Illumina HumanMethylation450 assay.
  7. DNA Methylation Profiles of Ovarian Clear Cell Carcinoma.
  8. Genomic Instability Promotes the Progression of Clear Cell Renal Cell Carcinoma Through Influencing the Immune Microenvironment.
  9. Clinical significance of novel DNA methylation biomarkers for renal clear cell carcinoma.
  1. BMC Cancer. 2021 Oct 28. 21(1): 1154
    Homologous recombination proficiency in ovarian and breast cancer patients.
    Justin Fortune Creeden, Nisha S Nanavaty, Katelyn R Einloth, Cassidy E Gillman, Laura Stanbery, Danae M Hamouda, Lance Dworkin, John Nemunaitis.
      Homologous recombination and DNA repair are important for genome maintenance. Genetic variations in essential homologous recombination genes, including BRCA1 and BRCA2 results in homologous recombination deficiency (HRD) and can be a target for therapeutic strategies including poly (ADP-ribose) polymerase inhibitors (PARPi). However, response is limited in patients who are not HRD, highlighting the need for reliable and robust HRD testing. This manuscript will review BRCA1/2 function and homologous recombination proficiency in respect to breast and ovarian cancer. The current standard testing methods for HRD will be discussed as well as trials leading to approval of PARPi's. Finally, standard of care treatment and synthetic lethality will be reviewed.
    Keywords:  BRCA; Breast cancer; Homologous recombination; Homologous recombination deficient; Homologous recombination proficient; Ovarian cancer; PARP inhibitor
    DOI:  https://doi.org/10.1186/s12885-021-08863-9
  2. J Exp Clin Cancer Res. 2021 Oct 26. 40(1): 338
    The role of patient-derived ovarian cancer organoids in the study of PARP inhibitors sensitivity and resistance: from genomic analysis to functional testing.
    Mengyu Tao, Xia Wu.
      Epithelial ovarian cancer (EOC) harbors distinct genetic features such as homologous recombination repair (HRR) deficiency, and therefore may respond to poly ADP-ribose polymerase inhibitors (PARPi). Over the past few years, PARPi have been added to the standard of care for EOC patients in both front-line and recurrent settings. Next-generation sequencing (NGS) genomic analysis provides key information, allowing for the prediction of PARPi response in patients who are PARPi naïve. However, there are indeed some limitations in NGS analyses. A subset of patients can benefit from PARPi, despite the failed detection of the predictive biomarkers such as BRCA1/2 mutations or HRR deficiency. Moreover, in the recurrent setting, the sequencing of initial tumor does not allow for the detection of reversions or secondary mutations restoring proficient HRR and thus leading to PARPi resistance. Therefore, it becomes crucial to better screen patients who will likely benefit from PARPi treatment, especially those with prior receipt of maintenance PARPi therapy. Recently, patient-derived organoids (PDOs) have been regarded as a reliable preclinical platform with clonal heterogeneity and genetic features of original tumors. PDOs are found feasible for functional testing and interrogation of biomarkers for predicting response to PARPi in EOC. Hence, we review the strengths and limitations of various predictive biomarkers and highlight the role of patient-derived ovarian cancer organoids as functional assays in the study of PARPi response. It was found that a combination of NGS and functional assays using PDOs could enhance the efficient screening of EOC patients suitable for PARPi, thus prolonging their survival time.
    Keywords:  Functional test; Ovarian cancer; PARP inhibitor; Patient-derived organoid; Precise medicine; Predictive biomarker
    DOI:  https://doi.org/10.1186/s13046-021-02139-7
  3. Cancer Res. 2021 Oct 28. pii: canres.2023.2021. [Epub ahead of print]
    Aberrant transcript usage is associated with homologous recombination deficiency and predicts therapeutic response.
    Hyeon Gu Kang, Haeun Hwangbo, Myung Ji Kim, Sinae Kim, Eun Ji Lee, Min Ji Park, Jae-Weon Kim, Byoung-Gie Kim, Eun-Hae Cho, Suhwan Chang, Jung-Yun Lee, Jung Kyoon Choi.
      BRCA1/2 mutations account for only a small fraction of homologous recombination (HR) deficiency (HRD) cases. Recently developed genomic HRD (gHRD) tests suffer confounding factors that cause low precision in predicting samples that will respond to PARP inhibitors and DNA damaging agents. Here we present molecular and clinical evidence of transcriptional HRD (tHRD) that is based on aberrant transcript usage (TU) of minor isoforms. Specifically, increased TU of non-functional isoforms of DNA repair genes was prevalent in breast and ovarian cancer with gHRD. Functional assays validated the association of aberrant TU with impaired HR activity. Machine learning-based tHRD detection by the TU pattern of key genes was superior to directly screening for gHRD or BRCA1/2 mutations in accurately predicting responses of cell lines and cancer patients to PARP inhibitors and genotoxic drugs. This approach demonstrated the capability of tHRD status to reflect functional HR status, including in a cohort of olaparib treated ovarian cancer with acquired platinum resistance. Diagnostic tests based on tHRD are expected to broaden the clinical utility of PARP inhibitors.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-2023
  4. Front Immunol. 2021 ;12 661115
    Targeting DNA Repair Response Promotes Immunotherapy in Ovarian Cancer: Rationale and Clinical Application.
    Hongyu Xie, Wenjie Wang, Wencai Qi, Weilin Jin, Bairong Xia.
      Immune checkpoint inhibitors (ICI) have emerged as a powerful oncologic treatment modality for patients with different solid tumors. Unfortunately, the efficacy of ICI monotherapy in ovarian cancer is limited, and combination therapy provides a new opportunity for immunotherapy in ovarian cancer. DNA damage repair (DDR) pathways play central roles in the maintenance of genomic integrity and promote the progression of cancer. A deficiency in DDR genes can cause different degrees of DNA damage that enhance local antigen release, resulting in systemic antitumor immune responses. Thus, the combination of DDR inhibitors with ICI represents an attractive therapeutic strategy with the potential to improve the clinical outcomes of patients with ovarian cancer. In this review, we provide an overview of the interconnectivity between DDR pathway deficiency and immune response, summarize available clinical trials on the combination therapy in ovarian cancer, and discuss the potential predictive biomarkers that can be utilized to guide the use of combination therapy.
    Keywords:  DNA damage response; PARP inhibitors; combination therapy; immune checkpoint inhibitors (ICI); ovarian cancer
    DOI:  https://doi.org/10.3389/fimmu.2021.661115
  5. Lancet Oncol. 2021 Oct 26. pii: S1470-2045(21)00531-3. [Epub ahead of print]
    Maintenance olaparib for patients with newly diagnosed advanced ovarian cancer and a BRCA mutation (SOLO1/GOG 3004): 5-year follow-up of a randomised, double-blind, placebo-controlled, phase 3 trial.
    Susana Banerjee, Kathleen N Moore, Nicoletta Colombo, Giovanni Scambia, Byoung-Gie Kim, Ana Oaknin, Michael Friedlander, Alla Lisyanskaya, Anne Floquet, Alexandra Leary, Gabe S Sonke, Charlie Gourley, Amit Oza, Antonio González-Martín, Carol Aghajanian, William H Bradley, Eileen Holmes, Elizabeth S Lowe, Paul DiSilvestro.
      BACKGROUND: There is a high unmet need for treatment regimens that increase the chance of long-term remission and possibly cure for women with newly diagnosed advanced ovarian cancer. In the primary analysis of SOLO1/GOG 3004, the poly(ADP-ribose) polymerase (PARP) inhibitor olaparib significantly improved progression-free survival versus placebo in patients with a BRCA mutation; median progression-free survival was not reached. Here, we report an updated, post-hoc analysis of progression-free survival from SOLO1, after 5 years of follow-up.METHODS: SOLO1 was a randomised, double-blind, placebo-controlled, phase 3 trial, done across 118 centres in 15 countries, that enrolled patients aged 18 years or older with an Eastern Cooperative Oncology Group performance status of 0-1 and with BRCA-mutated, newly diagnosed, advanced, high-grade serous or endometrioid ovarian cancer with a complete or partial clinical response after platinum-based chemotherapy. Patients were randomly assigned (2:1) via a web-based or interactive voice-response system to receive olaparib (300 mg twice daily) or placebo tablets orally as maintenance monotherapy for up to 2 years; randomisation was by blocks and was stratified according to clinical response after platinum-based chemotherapy. Patients, treatment providers, and data assessors were masked to group assignment. The primary endpoint was investigator-assessed progression-free survival. Efficacy is reported in the intention-to-treat population and safety in patients who received at least one dose of treatment. The data cutoff for this updated, post-hoc analysis was March 5, 2020. This trial is registered with ClinicalTrials.gov (NCT01844986) and is ongoing but closed to new participants.
    FINDINGS: Between Sept 3, 2013, and March 6, 2015, 260 patients were randomly assigned to olaparib and 131 to placebo. The median treatment duration was 24·6 months (IQR 11·2-24·9) in the olaparib group and 13·9 months (8·0-24·8) in the placebo group; median follow-up was 4·8 years (2·8-5·3) in the olaparib group and 5·0 years (2·6-5·3) in the placebo group. In this post-hoc analysis, median progression-free survival was 56·0 months (95% CI 41·9-not reached) with olaparib versus 13·8 months (11·1-18·2) with placebo (hazard ratio 0·33 [95% CI 0·25-0·43]). The most common grade 3-4 adverse events were anaemia (57 [22%] of 260 patients receiving olaparib vs two [2%] of 130 receiving placebo) and neutropenia (22 [8%] vs six [5%]), and serious adverse events occurred in 55 (21%) of 260 patients in the olaparib group and 17 (13%) of 130 in the placebo group. No treatment-related adverse events that occurred during study treatment or up to 30 days after discontinuation were reported as leading to death. No additional cases of myelodysplastic syndrome or acute myeloid leukaemia were reported since the primary data cutoff, including after the 30-day safety follow-up period.
    INTERPRETATION: For patients with newly diagnosed advanced ovarian cancer and a BRCA mutation, after, to our knowledge, the longest follow-up for any randomised controlled trial of a PARP inhibitor in this setting, the benefit derived from 2 years' maintenance therapy with olaparib was sustained beyond the end of treatment, extending median progression-free survival past 4·5 years. These results support the use of maintenance olaparib as a standard of care in this setting.
    FUNDING: AstraZeneca; Merck Sharpe & Dohme, a subsidiary of Merck & Co, Kenilworth, NJ, USA.
    DOI:  https://doi.org/10.1016/S1470-2045(21)00531-3
  6. BMC Res Notes. 2021 Oct 24. 14(1): 394
    Repeatability of methylation measures using a QIAseq targeted methyl panel and comparison with the Illumina HumanMethylation450 assay.
    Chenglong Yu, Pierre-Antoine Dugué, James G Dowty, Fleur Hammet, JiHoon E Joo, Ee Ming Wong, Mahnaz Hosseinpour, Graham G Giles, John L Hopper, Tu Nguyen-Dumont, Robert J MacInnis, Melissa C Southey.
      OBJECTIVE: In previous studies using Illumina Infinium methylation arrays, we have identified DNA methylation marks associated with cancer predisposition and progression. In the present study, we have sought to find appropriate technology to both technically validate our data and expand our understanding of DNA methylation in these genomic regions. Here, we aimed to assess the repeatability of methylation measures made using QIAseq targeted methyl panel and to compare them with those obtained from the Illumina HumanMethylation450 (HM450K) assay. We included in the analysis high molecular weight DNA extracted from whole blood (WB) and DNA extracted from formalin-fixed paraffin-embedded tissues (FFPE).RESULTS: The repeatability of QIAseq-methylation measures was assessed at 40 CpGs, using the Intraclass Correlation Coefficient (ICC). The mean ICCs and 95% confidence intervals (CI) were 0.72 (0.62-0.81), 0.59 (0.47-0.71) and 0.80 (0.73-0.88) for WB, FFPE and both sample types combined, respectively. For technical replicates measured using QIAseq and HM450K, the mean ICCs (95% CI) were 0.53 (0.39-0.68), 0.43 (0.31-0.56) and 0.70 (0.59-0.80), respectively. Bland-Altman plots indicated good agreement between QIAseq and HM450K measurements. These results demonstrate that the QIAseq targeted methyl panel produces reliable and reproducible methylation measurements across the 40 CpGs that were examined.
    Keywords:  Bland–Altman plot; DNA methylation; Formalin-fixed paraffin-embedded; Illumina Infinium methylation arrays; Intraclass correlation coefficient; Targeted bisulphite sequencing; Whole blood
    DOI:  https://doi.org/10.1186/s13104-021-05809-z
  7. Cancer Epidemiol Biomarkers Prev. 2021 Oct 25. pii: cebp.0677.2021. [Epub ahead of print]
    DNA Methylation Profiles of Ovarian Clear Cell Carcinoma.
    Julie M Cunningham, Stacey J Winham, Chen Wang, Britta Weigelt, Zhuxuan Fu, Sebastian M Armasu, Bryan M McCauley, Alison H Brand, Yoke-Eng Chiew, Esther Elishaev, Charlie Gourley, Catherine J Kennedy, Angela Laslvic, Jenny Lester, Anna Piskorz, Magdalena Sekowska, James D Brenton, Michael Churchman, Anna DeFazio, Ronny Drapkin, Kevin M Elias, David G Huntsman, Beth Y Karlan, Martin Köbel, Jason Konner, Kate Lawrenson, Elli Papaemmanuil, Kelly L Bolton, Francesmary Modugno, Ellen L Goode.
      BACKGROUND: Ovarian clear cell carcinoma (OCCC) is a rare ovarian cancer histotype that tends to be resistant to standard platinum-based chemotherapeutics. We sought to better understand the role of DNA methylation in clinical and biological subclassification of OCCC.METHODS: We interrogated genome-wide methylation using DNA from fresh frozen tumors from 271 cases, applied non-smooth non-negative matrix factorization (nsNMF) clustering, and evaluated clinical associations and biological pathways.
    RESULTS: Two approximately equally sized clusters that associated with several clinical features were identified. Compared to Cluster 2 (N=137), Cluster 1 cases (N=134) presented at a more advanced stage, were less likely to be of Asian ancestry, and tended to have poorer outcomes including macroscopic residual disease following primary debulking surgery (p-values <0.10). Subset analyses of targeted tumor sequencing and immunohistochemical data revealed that Cluster 1 tumors showed TP53 mutation and abnormal p53 expression, and Cluster 2 tumors showed aneuploidy and ARID1A/PIK3CA mutation (p-values <0.05). Cluster-defining CpGs included 1,388 CpGs residing within 200 bp of the transcription start sites of 977 genes; 38% of these genes (N=369 genes) were differentially expressed across cluster in transcriptomic subset analysis (p-values <10-4). Differentially expressed genes were enriched for six immune-related pathways, including interferon alpha and gamma responses (p-values < 10-6).
    CONCLUSIONS: DNA methylation clusters in OCCC correlate with disease Impact: This work serves as a foundation for integrative analyses that better understand the complex biology of OCCC in an effort to improve potential for development of targeted therapeutics.
    DOI:  https://doi.org/10.1158/1055-9965.EPI-21-0677
  8. Front Genet. 2021 ;12 706661
    Genomic Instability Promotes the Progression of Clear Cell Renal Cell Carcinoma Through Influencing the Immune Microenvironment.
    Xiyi Wei, Yichun Wang, Chengjian Ji, Jiaocheng Luan, Liangyu Yao, Xi Zhang, Shuai Wang, Bing Yao, Chao Qin, Ninghong Song.
      Background: Long non-coding RNAs (lncRNAs) are now under discussion as novel promising biomarkers for clear cell renal cell carcinoma (ccRCC). However, the role of genomic instability-associated lncRNA signatures in tumors has not been thoroughly uncovered. The purpose of our study is to probe the role of genomic instability-derived lncRNA signature (GILncSig) and to further investigate the mechanism of genomic instability-mediated ccRCC progression. Methods: The transcriptome data and somatic mutation profiles of ccRCC as well as clinical characteristics used in this study were obtained from The Cancer Genome Atlas database and Gene Expression Omnibus database. Lasso regression analysis was performed to construct the GILncSig. Gene set enrichment analysis (GSEA) was performed to elucidate the biological functions and relative pathways. CIBERSORT and EPIC algorithm were applied to calculate the proportion of immune cells in ccRCC. ESTIMATE algorithm was utilized to compute the immune microenvironment scores. Results: In total, 148 novel genomic instability-derived lncRNAs in ccRCC were identified. Immediately, on the basis of univariate cox analysis and lasso analysis, a GILncSig was appraised, through which the patients were allocated into High-Risk and Low-Risk groups with significantly different characteristics and prognoses. In addition, we confirmed that the somatic mutation count, tumor mutation burden, and the expression of UBQLN4, which were ascertainably associated with genomic instability, were significantly correlated with the GILncSig, indicating its reliability as a measurement of the genomic instability. Furthermore, the efficiency of GILncSig in prognostic aspects was better than the single mutation gene in ccRCC. In addition, MNX1-AS1 was defined to be a potential biomarker characterized by strong correlation with clinical features. Moreover, GSEA results indicated that the IL6/JAK/STAT3/SIGNALING pathway could be considered as a potential mechanism of genomic instability to influence tumor progression. Besides, the immune microenvironment showed significant differences between the GS-like group and the GU-like group, which was specifically manifested as high expression of CTLA4, GITR, TNFSF14, and regulatory T cells (Tregs) as well as low expression of endothelial cells (ECs) in the GU-like group. Finally, the prognostic value and clinical relevance of GILncSig were verified in GEO datasets and other urinary tumors in TCGA dataset. Conclusion: In conclusion, our study provided a new perspective for the role of lncRNAs in genomic instability and revealed that genomic instability may mediate tumor progression by affecting immunity. Besides, MNX1-AS1 played critical roles in promoting the progression of ccRCC, which may be a potential therapeutic target. What is more, the immune atlas of genomic instability was characterized by high expression of CTLA4, GITR, TNFSF14, and Tregs, and low expression of ECs.
    Keywords:  MNX1-AS1; ccRCC; genomic instability; immune atlas; lncRNAs
    DOI:  https://doi.org/10.3389/fgene.2021.706661
  9. J Cancer Res Clin Oncol. 2021 Oct 23.
    Clinical significance of novel DNA methylation biomarkers for renal clear cell carcinoma.
    Raimonda Kubiliūtė, Kristina Žukauskaitė, Algirdas Žalimas, Albertas Ulys, Rasa Sabaliauskaitė, Arnas Bakavičius, Arūnas Želvys, Feliksas Jankevičius, Sonata Jarmalaitė.
      OBJECTIVE: Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney tumor characterized by the highest mortality rate of the genitourinary cancers, and, therefore, new diagnostic and/or prognostic biomarkers are urgently needed.METHODS: Based on genome-wide DNA methylation profiling in 11 pairs of ccRCC and non-cancerous renal tissues (NRT), the methylation at regulatory regions of ZNF677, FBN2, PCDH8, TFAP2B, TAC1, and FLRT2 was analyzed in 168 renal tissues and 307 urine samples using qualitative and quantitative methylation-specific PCR (MSP).
    RESULTS: Significantly higher methylation frequencies for all genes were found in ccRCC tissues compared to NRT (33-60% vs. 0-11%). The best diagnostic performance demonstrated a panel of ZNF677, FBN2, PCDH8, TFAP2B & TAC1 with 82% sensitivity and 96% specificity. Hypermethylation of ZNF677 and PCDH8 in the tissue samples was significantly related to numerous adverse clinicopathologic parameters. For the urine-based ccRCC detection, the highest diagnostic power (AUC = 0.78) was observed for a panel of ZNF677 & PCDH8 (with or without FBN2 or FLRT2) with 69-78% sensitivity and 69-80% specificity, albeit with lower values in the validation cohort. Besides, methylation of PCDH8 was significantly related to higher tumor stage and fat invasion in the study and validation cohorts. Moreover, PCDH8 was strongly predictive for OS (HR, 5.7; 95% CI 1.16-28.12), and its prognostic power considerably increased in combination with ZNF677 (HR, 12.5; 95% CI 1.47-105.58).
    CONCLUSION: In summary, our study revealed novel, potentially promising DNA methylation biomarkers of ccRCC with the possibility to be applied for non-invasive urine-based ccRCC detection and follow-up.
    Keywords:  Clear cell renal cell carcinoma; DNA methylation; Diagnostic biomarkers; Non-invasive biomarkers; Prognostic biomarkers
    DOI:  https://doi.org/10.1007/s00432-021-03837-7
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