bims-tumhet 2021-07-18 papers

bims-tumhet

Biomed News

on Tumor Heterogeneity

Issue of 2021‒07‒18
seven papers selected by
Sergio Marchini
Humanitas Research

Utility of Serial cfDNA NGS for Prospective Genomic Analysis of Patients on a Phase I Basket Study.
Promoter Methylation of the MGRN1 Gene Predicts Prognosis and Response to Chemotherapy of High-Grade Serous Ovarian Cancer Patients.
Tubo-Ovarian High-Grade Serous Carcinomas Commonly Express CA19.9.
The effectiveness of monotherapy with PI3K/AKT/mTOR pathway inhibitors in ovarian cancer: A meta-analysis.
Repositioning PARP inhibitors in the treatment of thoracic malignancies.
Clear cell carcinoma of the ovary: Epidemiology, pathological and biological features, treatment options and clinical outcomes.
Transcriptome-based stemness indices analysis reveals platinum-based chemo-theraputic response indicators in advanced-stage serous ovarian cancer.

JCO Precis Oncol. 2021 ;pii: PO.20.00184. [Epub ahead of print]5

Utility of Serial cfDNA NGS for Prospective Genomic Analysis of Patients on a Phase I Basket Study.

Lillian M Smyth, Jonathan B Reichel, Jiabin Tang, Juber Ahamad A Patel, Fanli Meng, Duygu S Selcuklu, Brian Houck-Loomis, Daoqi You, Aliaksandra Samoila, Gaia Schiavon, Bob T Li, Pedram Razavi, Salvatore Piscuoglio, Jorge S Reis-Filho, Barry S Taylor, José Baselga, David B Solit, David M Hyman, Michael F Berger, Sarat Chandarlapaty.

PURPOSE: Cell-free DNA (cfDNA) analysis offers a noninvasive means to access the tumor genome. Despite limited sensitivity of broad-panel sequencing for detecting low-frequency mutations in cfDNA, it may enable more comprehensive genomic characterization in patients with sufficiently high disease burden. We investigated the utility of large-panel cfDNA sequencing in patients enrolled to a Phase I AKT1-mutant solid tumor basket study.METHODS: Patients had AKT1 E17K-mutant solid tumors and were treated on the multicenter basket study (ClinicalTrials.gov identifier: NCT01226316) of capivasertib, an AKT inhibitor. Serial plasma samples were prospectively collected and sequenced using exon-capture next-generation sequencing (NGS) analysis of 410 genes (Memorial Sloan Kettering [MSK]-Integrated Molecular Profiling of Actionable Cancer Target [IMPACT]) and allele-specific droplet digital polymerase chain reaction (ddPCR) for AKT1 E17K. Tumor DNA (tDNA) NGS (MSK-IMPACT) was also performed on available pretreatment tissue biopsy specimens.
RESULTS: Among 25 patients, pretreatment plasma samples were sequenced to an average coverage of 504×. Somatic mutations were called in 20/25 (80%), with mutant allele fractions highly concordant with ddPCR of AKT1 E17K (r 2 = 0.976). Among 17 of 20 cfDNA-positive patients with available tDNA for comparison, mutational concordance was acceptable, with 82% of recurrent mutations shared between tissue and plasma. cfDNA NGS captured additional tumor heterogeneity, identifying mutations not observed in tDNA in 38% of patients, and revealed oncogenic mutations in patients without available baseline tDNA. Longitudinal cfDNA NGS (n = 98 samples) revealed distinct patterns of clonal dynamics in response to therapy.
CONCLUSION: Large gene panel cfDNA NGS is feasible for patients with high disease burden and is concordant with single-analyte approaches, providing a robust alternative to ddPCR with greater breadth. cfDNA NGS can identify heterogeneity and potentially biologically informative and clinically relevant alterations.

DOI: https://doi.org/10.1200/PO.20.00184
Front Oncol. 2021 ;11 659254

Promoter Methylation of the MGRN1 Gene Predicts Prognosis and Response to Chemotherapy of High-Grade Serous Ovarian Cancer Patients.

Xiao-Fei Li, Hai-Yan Sun, Tian Hua, Hai-Bo Zhang, Yun-Jie Tian, Yan Li, Shan Kang.

  Aberrant DNA methylation is considered to play a critical role in the chemoresistance of epithelial ovarian cancer (EOC). In this study, we explored the relationship between hypermethylation of the Mahogunin Ring Finger 1 (MGRN1) gene promoter and primary chemoresistance and clinical outcomes in high-grade serous ovarian cancer (HGSOC) patients. The MALDI-TOF mass spectrometry assays revealed a strong association between hypermethylation of the MGRN1 upstream region and platinum resistance in HGSOC patients. Spearman's correlation analysis revealed a significantly negative connection between the methylation level of MGRN1 and its expression in HGSOC. In vitro analysis demonstrated that knockdown of MGRN1 reduced the sensitivity of cells to cisplatin and that expression of EGR1 was significantly decreased in SKOV3 cells with low levels of MGRN1 expression. Similarly, EGR1 mRNA expression was lower in platinum-resistant HGSOC patients and was positively correlated with MGRN1 mRNA expression. Kaplan-Meier analyses showed that high methylation of the MGRN1 promoter region and low expression of MGRN1 were associated with worse survival of HGSOC patients. In multivariable models, low MGRN1 expression was an independent factor predicting poor outcome. Furthermore, low expression of EGR1 was also been confirmed to be significantly related to the poor prognosis of HGSOC patients by Kaplan-Meier. The hypermethylation of the MGRN1 promoter region and low expression of MGRN1 were associated with platinum resistance and poor outcomes in HGSOC patients, probably by altering EGR1 expression.

Keywords:  HGSOC; MGRN1; methylation; platinum resistance; prognosis

DOI:  https://doi.org/10.3389/fonc.2021.659254
Histopathology. 2021 Jul 16.

Tubo-Ovarian High-Grade Serous Carcinomas Commonly Express CA19.9.

Simon Rajendran, W Glenn McCluggage.

Tubo-ovarian high-grade serous carcinoma (HGSC) is one of the leading causes of cancer death in women worldwide and frequently presents at advanced stage (1). Many cases are unresectable at diagnosis due to extensive disease affecting multiple sites and in such cases when a disseminated tubo-ovarian HGSC is suspected, a percutaneous core biopsy is often undertaken prior to neoadjuvant chemotherapy being administered (2).

DOI: https://doi.org/10.1111/his.14453
Gynecol Oncol. 2021 Jul 10. pii: S0090-8258(21)00538-2. [Epub ahead of print]

The effectiveness of monotherapy with PI3K/AKT/mTOR pathway inhibitors in ovarian cancer: A meta-analysis.

Phyllis van der Ploeg, Aniek Uittenboogaard, Anna M J Thijs, Hans M Westgeest, Ingrid A Boere, Sandrina Lambrechts, Anja van de Stolpe, Ruud L M Bekkers, Jurgen M J Piek.

  OBJECTIVE: To determine the clinical benefit of monotherapy with PI3K/AKT/mTOR inhibitors in patients diagnosed with advanced or recurrent ovarian cancer and to investigate the predictive value of current PI3K/AKT/mTOR biomarkers on therapy response.METHODS: A systematic search was conducted in PubMed, Embase and the Cochrane Library for articles reporting on treatment with PI3K/AKT/mTOR inhibitors in ovarian cancer. The primary endpoint was defined as the clinical benefit rate (CBR), including the proportion of patients with complete (CR) and partial response (PR) and stable disease (SD). Secondary endpoints included the overall response rate (ORR, including CR and PR) and drug-related grade 3 and 4 adverse events.
RESULTS: We included 233 patients from 19 studies and observed a pooled CBR of 32% (95% CI 20-44%) and ORR of 3% (95% CI 0-6%) in advanced or recurrent ovarian cancer patients treated with PI3K/AKT/mTOR inhibitors. Subgroup analysis tended to favor the studies who selected patients based on current PI3K/AKT/mTOR biomarker criteria (e.g. genomic alterations or loss of PTEN protein expression), but the difference in CBR was not statistically significant from studies with unselected populations (respectively, CBR of 42% (95% CI 23-62%) and 27% (95% CI 14-42%), P = 0.217). To better reflect true patient benefit, we excluded SD <6 months as a beneficial outcome which resulted in a pooled CBR of 7% (95% CI 2-13%). The overall proportion of patients with drug-related grade 3 and 4 adverse events was 36%.
CONCLUSIONS: The efficacy of monotherapy with PI3K/AKT/mTOR inhibitors in advanced recurrent ovarian cancer patients is limited to a small subgroup and selection of patients with the use of current biomarkers did not improved the CBR significantly. Given the toxicity profile, we suggest that current treatment with PI3K/AKT/mTOR inhibitors should not be initiated unless in clinical trials. Furthermore, improved biomarkers to measure functional PI3K/AKT/mTOR pathway activity are needed to optimize patient selection.

Keywords:  Akt; Mammalian target of rapamycin; Ovarian cancer; Phosphatidylinositol-3-kinase; Signal transduction pathway; Targeted therapy

DOI:  https://doi.org/10.1016/j.ygyno.2021.07.008
Cancer Treat Rev. 2021 Jul 07. pii: S0305-7372(21)00104-3. [Epub ahead of print]99 102256

Repositioning PARP inhibitors in the treatment of thoracic malignancies.

Francesco Passiglia, Maria Lucia Reale, Valeria Cetoretta, Elena Parlagreco, Francesca Jacobs, Angela Listì, Luisella Righi, Paolo Bironzo, Silvia Novello, Giorgio Vittorio Scagliotti.

  The evaluation of the homologous recombination repair (HRR) status is emerging as a predictive tumor agnostic biomarker for poly (ADP-ribose) polymerase (PARP) inhibition across different tumor types and testing for HRR-signature is currently a developing area with promising therapeutic implications. Treatment with PARP inhibitors (PARPi) either as single agent or in combination with chemotherapy have shown so far limited activity in patients with thoracic malignancies. A deeper understanding of the biological background underlying HRR-deficient tumors, along with the recent advent of new effective targeted and immunotherapeutic agents, prompted the design of a new generation of clinical trials investigating novel PARPi-combinations in patients with lung cancer as well as malignant pleural mesothelioma. In this review we briefly summarize the biological basis of the DNA damage response pathway inhibition and provide an updated and detailed overview of clinical trials testing different PARPi-combinations strategies in patients with thoracic malignancies.

Keywords:  Homologous recombination repair; Malignant pleural mesothelioma; Non-small cell lung cancer; PARP; Small cell lung cancer

DOI:  https://doi.org/10.1016/j.ctrv.2021.102256
Gynecol Oncol. 2021 Jul 08. pii: S0090-8258(21)00529-1. [Epub ahead of print]

Clear cell carcinoma of the ovary: Epidemiology, pathological and biological features, treatment options and clinical outcomes.

Angiolo Gadducci, Francesco Multinu, Stefania Cosio, Silvestro Carinelli, Mariacristina Ghioni, Giovanni Damiano Aletti.

  Clear cell carcinoma of the ovary is a rare and distinct histotype of epithelial ovarian carcinomas. Women diagnosed with clear cell carcinomas are usually younger and diagnosed at earlier stages than those with the most common high-grade serous histology. Endometriosis is considered a main risk factor for the development of clear cell carcinoma of the ovary, and it can be considered a precursor of of this tumor, as it is identified in more than 50% of patients with clear cell carcinoma. Different molecular pathways and alterations heve been identified in ovarian clear cell carcinoma, including the most common mutations of AT-rich interaction domain 1A [ARID1A] and phosphatidylinositol-4,5-bisphosphate 3-kinase [PIK3] catalytic subunit alpha [PIK3CA]. The prognosis of patients at early stage is favorable, while patients with advanced or recurrent disease experience a poor oncologic outcomes. Despite a lower rate of responses due to an intrinsic chemoresistance, the treatment strategy for advanced disease resembles the treatment of high-grade serous carcinoma, which includes aggressive cytoreductive surgery and platinum-based chemotherapy. For this reason, the role of adjuvant chemotherapy in patients with stage I disease undergoing complete surgical staging is still under debate. Alternative treatments, including biological agents that target different pathways constitute the most promising treatment strategies, and well-designed, collaborative international trials should be designed in order to improve the oncologic outcomes and the quality of life of patients with this aggressive disease.

Keywords:  Clear cell carcinoma of the ovary; Molecular pathways; Pathology; Prognosis; Surgery; Targeted therapy

DOI:  https://doi.org/10.1016/j.ygyno.2021.06.033
Bioengineered. 2021 Dec;12(1): 3753-3771

Transcriptome-based stemness indices analysis reveals platinum-based chemo-theraputic response indicators in advanced-stage serous ovarian cancer.

Xinwei Sun, Qingyu Liu, Jie Huang, Ge Diao, Zhiqing Liang.

  Serous ovarian cancer (SOC) is a main histological subtype of ovarian cancer, in which cancer stem cells (CSC) are responsible for its chemoresistance. However, the underlying modulation mechanisms of chemoresistance led by cancer stemness are still undefined. We aimed to investigate potential drug-response indicators among stemness-associated biomarkers in advanced SOC samples. The mRNA expression-based stemness index (mRNAsi) of The Cancer Genome Atlas (TCGA) was evaluated and corrected by tumor purity. Weighted gene co-expression network analysis (WGCNA) was utilized to explore the gene modules and key genes involved in stemness characteristics. We found that mRNAsi and corrected mRNAsi scores were both greater in tumors of Grade 3 and 4 than that of Grade 1 and 2. Forty-two key genes were obtained from the most significant mRNAsi-related gene module. Functional annotation revealed that these key genes were mainly involved in the mitotic division. Thirteen potential platinum-response indicators were selected from the genes enriched to platinum-response associated pathways. Among them, we identified 11 genes with prognostic value of progression-free survival (PFS) in advanced SOC patients treated with platinum and 7 prognostic genes in patients treated with a combination of platinum and taxol. The expressions of the 13 key genes were also validated between platinum-resistant and -sensitive SOC samples of advanced stages in two Gene Expression Omnibus (GEO) datasets. The results revealed that CDC20 was a potential platinum-sensitivity indicator in advanced SOC. These findings may provide a new insight for chemotherapies in advanced SOC patients clinically.

Keywords:  SOC; TCGA; WGCNA; mRNAsi; platinum response; stemness

DOI:  https://doi.org/10.1080/21655979.2021.1939514