bims-tumhet Biomed News
on Tumor Heterogeneity
Issue of 2022‒01‒02
seven papers selected by
Sergio Marchini
Humanitas Research
  1. Immunotherapy in Ovarian Cancer: Thinking Beyond PD-1/PD-L1.
  2. Histopathologic features and molecular genetic landscape of HER2-amplified endometrial carcinomas.
  3. Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA.
  4. Correlation Between Clinical Outcomes and Serum CA-125 Levels After Standard Treatment for Epithelial Ovarian Cancer.
  5. Immuno-Oncology for Gynecologic Malignancies.
  6. Tumor Immune Microenvironment Related Gene-Based Model to Predict Prognosis and Response to Compounds in Ovarian Cancer.
  7. Trabectedin plus durvalumab in patients with advanced pretreated soft tissue sarcoma and ovarian carcinoma (TRAMUNE): an open-label, multicenter phase Ib study.
  1. Front Oncol. 2021 ;11 795547
    Immunotherapy in Ovarian Cancer: Thinking Beyond PD-1/PD-L1.
    Laure Chardin, Alexandra Leary.
      Ovarian cancer (OC) is the most lethal gynecologic malignancy, affecting approximately 1 in 70 women with only 45% surviving 5 years after diagnosis. This disease typically presents at an advanced stage, and optimal debulking with platinum-based chemotherapy remains the cornerstone of management. Although most ovarian cancer patients will respond effectively to current management, 70% of them will eventually develop recurrence and novel therapeutic strategies are needed. There is a rationale for immune-oncological treatments (IO) in the managements of patients with OC. Many OC tumors demonstrate tumor infiltrating lymphocytes (TILs) and the degree of TIL infiltration is strongly and reproducibly correlated with survival. Unfortunately, results to date have been disappointing in relapsed OC. Trials have reported very modest single activity with various antibodies targeting PD-1 or PD-L1 resulting in response rate ranging from 4% to 15%. This may be due to the highly immunosuppressive TME of the disease, a low tumor mutational burden and low PD-L1 expression. There is an urgent need to improve our understanding of the immune microenvironment in OC in order to develop effective therapies. This review will discuss immune subpopulations in OC microenvironment, current immunotherapy modalities targeting these immune subsets and data from clinical trials testing IO treatments in OC and its combination with other therapeutic agents.
    Keywords:  PD-L1; immunosuppression; immunotherapy; ovarian cancer; tumor microenvironment
    DOI:  https://doi.org/10.3389/fonc.2021.795547
  2. Mod Pathol. 2021 Dec 31.
    Histopathologic features and molecular genetic landscape of HER2-amplified endometrial carcinomas.
    Dara S Ross, Kelly A Devereaux, Cao Jin, David YunTe Lin, Yanming Zhang, Antonio Marra, Vicky Makker, Britta Weigelt, Lora H Ellenson, M Herman Chui.
      HER2 is an established therapeutic biomarker in advanced or recurrent endometrial serous carcinoma. Current clinical guidelines recommend HER2 testing exclusively in this endometrial carcinoma (EC) subtype; however, the full spectrum of ECs harboring HER2 amplification remains ill-defined. The present study characterizes the clinicopathologic and molecular features of HER2-amplified ECs across all histologic subtypes. Retrospective analysis of our institutional cohort of 2,042 ECs subjected to targeted clinical massively parallel sequencing identified 77 (3.8%) cases with HER2 amplification, a group comprised of serous (n = 29), endometrioid (low-grade, n = 2, high-grade, n = 1) and clear cell (n = 4) carcinomas, carcinosarcomas (n = 18) and high-grade ECs with ambiguous features (HGEC, n = 23). A co-existing TP53 mutation was identified in 94% (72/77) of HER2-amplified ECs. Other recurrent genetic alterations included amplification of CCNE1 (22%) and ERBB3 (10%), FBXW7 mutations or deletions (13%), and mutations in PIK3CA (40%) and PPP2R1A (13%). The HER2 immunohistochemistry score was 2+ or 3+ for all evaluable cases (n = 61). Apart from carcinosarcomas, which often showed lower HER2 expression, particularly in the sarcomatous component, HER2 immunohistochemical staining pattern and intensity were similar across EC subtypes. Intratumor heterogeneity in HER2 expression was common and correlated with genetic heterogeneity as detected by fluorescence in-situ hybridization. These results demonstrate the frequent co-occurrence of HER2 amplification with TP53 mutation and high-grade histology, rather than being specific to serous carcinoma, per se. Overall, these findings suggest that HER2 targeted therapy may be more broadly applicable to all high-grade EC histotypes and consideration should be given to expanding therapeutic eligibility.
    DOI:  https://doi.org/10.1038/s41379-021-00997-2
  3. Epigenomes. 2021 Feb 19. pii: 6. [Epub ahead of print]5(1):
    Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA.
    Celina Whalley, Karl Payne, Enric Domingo, Andrew Blake, Susan Richman, Jill Brooks, Nikolaos Batis, Rachel Spruce, S-Cort Consortium, Hisham Mehanna, Paul Nankivell, Andrew D Beggs.
      BACKGROUND: Abnormal CpG methylation in cancer is ubiquitous and generally detected in tumour specimens using a variety of techniques at a resolution encompassing single CpG loci to genome wide coverage. Analysis of samples with very low DNA inputs, such as formalin fixed (FFPE) biopsy specimens from clinical trials or circulating tumour DNA is challenging at the genome-wide level because of lack of available input. We present the results of low input experiments into the Illumina Infinium HD methylation assay on FFPE specimens and ctDNA samples.METHODS: For all experiments, the Infinium HD assay for methylation was used. In total, forty-eight FFPE specimens were used at varying concentrations (lowest input 50 ng); eighteen blood derived specimens (lowest input 10 ng) and six matched ctDNA input (lowest input 10 ng)/fresh tumour specimens (lowest input 250 ng) were processed. Downstream analysis was performed in R/Bioconductor for quality control metrics and differential methylation analysis as well as copy number calls.
    RESULTS: Correlation coefficients for CpG methylation were high at the probe level averaged R2 = 0.99 for blood derived samples and R2 > 0.96 for the FFPE samples. When matched ctDNA/fresh tumour samples were compared, R2 > 0.91 between the two. Results of differential methylation analysis did not vary significantly by DNA input in either the blood or FFPE groups. There were differences seen in the ctDNA group as compared to their paired tumour sample, possibly because of enrichment for tumour material without contaminating normal. Copy number variants observed in the tumour were generally also seen in the paired ctDNA sample with good concordance via DQ plot.
    CONCLUSIONS: The Illumina Infinium HD methylation assay can robustly detect methylation across a range of sample types, including ctDNA, down to an input of 10 ng. It can also reliably detect oncogenic methylation changes and copy number variants in ctDNA. These findings demonstrate that these samples can now be accessed by methylation array technology, allowing analysis of these important sample types.
    Keywords:  circulating tumour DNA; epigenome; formalin fixed paraffin embedded
    DOI:  https://doi.org/10.3390/epigenomes5010006
  4. Anticancer Res. 2022 Jan;42(1): 349-353
    Correlation Between Clinical Outcomes and Serum CA-125 Levels After Standard Treatment for Epithelial Ovarian Cancer.
    Juhun Lee, Jong Mi Kim, Yoon Hee Lee, Gun Oh Chong, Dae Gy Hong.
      BACKGROUND/AIM: To analyze the relationship between clinical outcomes for epithelial ovarian cancer and serum CA-125 levels after chemotherapy in Korean women.PATIENTS AND METHODS: This study included 183 patients who underwent the standard treatment regimen for epithelial ovarian cancer. They were divided into early- (I, II) and advanced-stage (III, IV) groups. Serum CA-125 level after adjuvant chemotherapy completion (post-chemotherapy; PC-CA-125) was measured. Overall survival (OS), progression-free survival (PFS), platinum-free interval (PFI), and platinum resistance were evaluated.
    RESULTS: In advanced-stage group, OS, PFS, PFI, and platinum resistance were significantly correlated with PC-CA-125. In early-stage group, PFS and platinum resistance differed significantly. Cutoff value for platinum resistance was 10.45 U/ml, 10.40 U/ml, and 15.80 U/ml for study population, early stage, and advanced groups, respectively. Accuracy was 71.1%-77.1%.
    CONCLUSION: PC-CA-125 is correlated with clinical outcomes in ovarian cancer. Thus, CA-125 can be used to predict platinum resistance in ovarian cancer treatment.
    Keywords:  CA-125; Ovarian cancer; chemotherapy; clinical outcomes; overall survival; platinum resistance; platinum-free interval; progression-free survival
    DOI:  https://doi.org/10.21873/anticanres.15492
  5. Adv Exp Med Biol. 2021 ;1342 193-232
    Immuno-Oncology for Gynecologic Malignancies.
    Jeffrey A How, Ami Patel, Amir A Jazaeri.
      Patients with advanced and/or recurrent gynecologic cancers derive limited benefit from currently available cytotoxic and targeted therapies. Successes of immunotherapy in other difficult-to-treat malignancies such as metastatic melanoma and advanced lung cancer have led to intense interest in clinical testing of these treatments in patients with gynecologic cancers. Currently, in the realm of gynecologic oncology, the FDA-approved use of immune checkpoint inhibitors is limited to microsatellite instability-high cancers, cancers with high tumor mutational burden, and PD-L1-positive cervical cancer. However, there has been an exponential growth of clinical trials testing immunotherapy approaches both alone and in combination with chemotherapy and/or targeted agents in patients with gynecologic cancers. This chapter will review some of the major reported and ongoing immunotherapy clinical trials in patients with endometrial, cervical, and epithelial ovarian cancer.
    Keywords:  Adoptive cell transfer; Cancer vaccines; Cervical cancer; Endometrial cancer; Immune checkpoint inhibitors; Immunotherapy; Ovarian cancer
    DOI:  https://doi.org/10.1007/978-3-030-79308-1_6
  6. Front Oncol. 2021 ;11 807410
    Tumor Immune Microenvironment Related Gene-Based Model to Predict Prognosis and Response to Compounds in Ovarian Cancer.
    Jiang Yang, Shasha Hong, Xiaoyi Zhang, Jingchun Liu, Ying Wang, Zhi Wang, Likun Gao, Li Hong.
      Background: The tumor immune microenvironment (TIME) has been recognized to be an imperative factor facilitating the acquisition of many cancer-related hallmarks and is a critical target for targeted biological therapy. This research intended to construct a risk score model premised on TIME-associated genes for prediction of survival and identification of potential drugs for ovarian cancer (OC) patients.Methods and Results: The stromal and immune scores were computed utilizing the ESTIMATE algorithm in OC patient samples from The Cancer Genome Atlas (TCGA) database. Weighted gene co-expression network and differentially expressed genes analyses were utilized to detect stromal-and immune-related genes. The Least Absolute Shrinkage and Selection Operator (LASSO)-Cox regression was utilized for additional gene selection. The genes that were selected were utilized as the input for a stepwise regression to construct a TIME-related risk score (TIMErisk), which was then validated in Gene Expression Omnibus (GEO) database. For the evaluation of the protein expression levels of TIME regulators, the Human Protein Atlas (HPA) dataset was utilized, and for their biological functions, the TIMER and CIBERSORT algorithm, immunoreactivity, and Immune Cell Abundance Identifier (ImmuCellAI) were used. Possible OC medications were forecasted utilizing the Genomics of Drug Sensitivity in Cancer (GDSC) database and connectivity map (CMap). TIMErisk was developed based on ALPK2, CPA3, PTGER3, CTHRC1, PLA2G2D, CXCL11, and ZNF683. High TIMErisk was recognized as a poor factor for survival in the GEO and TCGA databases; subgroup analysis with FIGO stage, grade, lymphatic and venous invasion, debulking, and tumor site also indicated similar results. Functional immune cells corresponded to more incisive immune reactions, including secretion of chemokines and interleukins, natural killer cell cytotoxicity, TNF signaling pathway, and infiltration of activated NK cells, eosinophils, and neutrophils in patients with low TIMErisk. Several small molecular medications which may enhance the prognosis of patients in the TIMErisk subgroup were identified. Lastly, an enhanced predictive performance nomogram was constructed by compounding TIMErisk with the FIGO stage and debulking.
    Conclusion: These findings may offer a valuable indicator for clinical stratification management and personalized therapeutic options for OC patients and may be a foundation for future mechanistic research of their association.
    Keywords:  TIMErisk; ovarian cancer; potential compound; prognosis; the tumor immune microenvironment
    DOI:  https://doi.org/10.3389/fonc.2021.807410
  7. Clin Cancer Res. 2021 Dec 29. pii: clincanres.2258.2021. [Epub ahead of print]
    Trabectedin plus durvalumab in patients with advanced pretreated soft tissue sarcoma and ovarian carcinoma (TRAMUNE): an open-label, multicenter phase Ib study.
    Maud Toulmonde, Mehdi Brahmi, Antoine Giraud, Camille Chakiba, Alban Bessede, Michèle Kind, Emilie Toulza, Marina Pulido, Sabrina Albert, Jean-Philippe Guégan, Sophie Cousin, Simone Mathoulin-Pélissier, Raul Perret, Sabrina Croce, Jean-Yves Blay, Isabelle Ray-Coquard, Anne Floquet, Antoine Italiano.
      PURPOSE: Trabectedin has shown pre-clinical synergy with immune-checkpoint inhibitors in pre-clinical models.EXPERIMENTAL DESIGN: TRAMUNE is a phase Ib study investigating trabectedin combined with durvalumab trough a dose-escalation phase and two expansion cohorts (soft tissue sarcoma and ovarian carcinoma). Trabectedin was given at three dose levels (1 mg/m2, 1.2 mg/m2 and 1.5 mg/m2) on day 1, in combination with durvalumab, 1120 mg on day 2, every 3 weeks. The primary endpoints were the recommended phase II dose (RP2D) of trabectedin combined with durvalumab and the objective response rate (ORR) as per RECIST 1.1. The secondary endpoints included safety, 6-month progression-free rate (PFR), progression-free survival (PFS), overall survival, and biomarker analyses.
    RESULTS: 40 patients were included (dose escalation: n=9; STS cohort: n=16; ovarian cohort: n=15, 80% platinum resistant/refractory). The most frequent toxicities were grade 1-2 fatigue, nausea, neutropenia, and alanine/aspartate aminotransferase increase. One patient experienced a dose-limiting toxicity at dose level 2. Trabectedin at 1.2 mg/m2 was selected as the RP2D. In the STS cohort, 43% of patients experienced tumor shrinkage, the ORR was 7% (95% CI 0.2 - 33.9) and the 6-month PFR 28.6% (95% CI 8.4-58.1). In the ovarian carcinoma cohort, 43% of patients experienced tumor shrinkage, the ORR was 21.4% (95% CI 4.7 - 50.8) and the 6-month PFR 42.9% (95% CI 17.7 - 71.1). Baseline levels of PD-L1 expression and CD8-positive T-cell infiltrates were associated with PFS in ovarian carcinoma patients.
    CONCLUSIONS: Combining trabectedin and durvalumab is manageable. Promising activity is observed in platinum-refractory ovarian carcinoma patients.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-21-2258
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