bims-tumhet Biomed News
on Tumor Heterogeneity
Issue of 2022‒05‒15
ten papers selected by
Sergio Marchini
Humanitas Research
  1. Dynamics of the Tumor Immune Microenvironment during Neoadjuvant Chemotherapy of High-Grade Serous Ovarian Cancer.
  2. Copy Number Alterations as Novel Biomarkers and Therapeutic Targets in Colorectal Cancer.
  3. Potential clinical utility of liquid biopsies in ovarian cancer.
  4. Epigenetics: A Gatekeeper to DNA Amplification and Replication Control.
  5. Cell type identification in spatial transcriptomics data can be improved by leveraging cell-type-informative paired tissue images using a Bayesian probabilistic model.
  6. Circulating Tumor DNA Is Associated with Response and Survival in Patients with Advanced Leiomyosarcoma.
  7. Chromosomal instability as a source of genomic plasticity.
  8. DNA methylation analysis of tumor suppressor genes in liquid biopsy components of early stage NSCLC: a promising tool for early detection.
  9. Spatial Transcriptomics Reveal Potential Sex Differences in Gene Expression of the Supraoptic Nucleus.
  10. Tumour driver mutations compromise between cancer growth and immune responses.
  1. Cancers (Basel). 2022 May 06. pii: 2308. [Epub ahead of print]14(9):
    Dynamics of the Tumor Immune Microenvironment during Neoadjuvant Chemotherapy of High-Grade Serous Ovarian Cancer.
    Yong Jae Lee, Ha Young Woo, Yoo-Na Kim, Junsik Park, Eun Ji Nam, Sang Wun Kim, Sunghoon Kim, Young Tae Kim, Eunhyang Park, Je-Gun Joung, Jung-Yun Lee.
      The dynamic changes in the tumor immune microenvironment (TIME) triggered by neoadjuvant chemotherapy (NAC) have not been clearly defined in advanced-stage ovarian cancer. We analyzed the immunologic changes induced by NAC to correlate them with clinical outcomes. We compared the changes in the immune infiltration of high-grade serous carcinoma biopsies before and after NAC via immunohistochemistry (147 paired samples) and whole transcriptome sequencing (35 paired samples). Immunohistochemistry showed significantly increased PD-L1 levels and TIL levels after NAC. Whole transcriptome sequencing revealed that the stromal score, immune score, and cytolytic activity score significantly increased after NAC. An increased tumor-infiltrating lymphocyte (TIL) level in response to NAC was associated with shorter progression-free survival compared with decreased TIL level after NAC. In tumors with increased TIL levels after NAC, the relative fraction of CD8 T cells and regulatory T cells significantly increased with immunohistochemistry. Post-NAC tumors were enriched in gene sets associated with immune signaling pathways, such as regulatory T cell and JAK/STAT signaling pathways. NAC induced dynamic changes in the TIME that increased TIL levels, but their high abundance did not impart any survival benefit. Our data may provide therapeutic strategies to improve the survival benefit from immunotherapies in ovarian cancer.
    Keywords:  high grade serous ovarian cancer; immune checkpoint inhibitors; neoadjuvant chemotherapy; tumor immune microenvironment; tumor-infiltrating lymphocytes
    DOI:  https://doi.org/10.3390/cancers14092308
  2. Cancers (Basel). 2022 Apr 29. pii: 2223. [Epub ahead of print]14(9):
    Copy Number Alterations as Novel Biomarkers and Therapeutic Targets in Colorectal Cancer.
    Elaine S Tan, Todd C Knepper, Xuefeng Wang, Jennifer B Permuth, Liang Wang, Jason B Fleming, Hao Xie.
      In colorectal cancer, somatic mutations have played an important role as prognostic and predictive biomarkers, with some also functioning as therapeutic targets. Another genetic aberration that has shown significance in colorectal cancer is copy number alterations (CNAs). CNAs occur when a change to the DNA structure propagates gain/amplification or loss/deletion in sections of DNA, which can often lead to changes in protein expression. Multiple techniques have been developed to detect CNAs, including comparative genomic hybridization with microarray, low pass whole genome sequencing, and digital droplet PCR. In this review, we summarize key findings in the literature regarding the role of CNAs in the pathogenesis of colorectal cancer, from adenoma to carcinoma to distant metastasis, and discuss the roles of CNAs as prognostic and predictive biomarkers in colorectal cancer.
    Keywords:  biomarkers; colorectal cancer; copy number alteration
    DOI:  https://doi.org/10.3390/cancers14092223
  3. Mol Cancer. 2022 May 11. 21(1): 114
    Potential clinical utility of liquid biopsies in ovarian cancer.
    Jie Wei Zhu, Parsa Charkhchi, Mohammad R Akbari.
      BACKGROUND: Ovarian cancer (OC) is the most lethal gynecologic malignancy worldwide. One of the main challenges in the management of OC is the late clinical presentation of disease that results in poor survival. Conventional tissue biopsy methods and serological biomarkers such as CA-125 have limited clinical applications. Liquid biopsy is a novel sampling method that analyzes distinctive tumour components released into the peripheral circulation, including circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), cell-free RNA (cfRNA), tumour-educated platelets (TEPs) and exosomes. Increasing evidence suggests that liquid biopsy could enhance the clinical management of OC by improving early diagnosis, predicting prognosis, detecting recurrence, and monitoring response to treatment. Capturing the unique tumour genetic landscape can also guide treatment decisions and the selection of appropriate targeted therapies. Key advantages of liquid biopsy include its non-invasive nature and feasibility, which allow for serial sampling and longitudinal monitoring of dynamic tumour changes over time. In this review, we outline the evidence for the clinical utility of each liquid biopsy component and review the advantages and current limitations of applying liquid biopsy in managing ovarian cancer. We also highlight future directions considering the current challenges and explore areas where more studies are warranted to elucidate its emerging clinical potential.
    DOI:  https://doi.org/10.1186/s12943-022-01588-8
  4. FASEB J. 2022 May;36 Suppl 1
    Epigenetics: A Gatekeeper to DNA Amplification and Replication Control.
    Johnathan R Whetstine.
      DNA amplification is associated with pathological states such as neurological disorders, cardiac disease and cancer. At least 50% of the amplifications in cancer are transient extrachromosomal DNA (ecDNA). The transient behavior contributes to copy number plasticity, results in heterogeneous oncogene expression and alters therapeutic response. The unanswered question remains as to whether distinct mechanisms control ecDNA copy gains within cells and how they impact copy gain events associated with disease. Our laboratory aims to define the principles regulating selective DNA amplification and the associated plasticity, so we may control these events in disease. By resolving general mechanisms governing selective DNA amplifications, we will build a framework to further understand the molecular basis by which copy gains occur in neoplasia and other diseases. Recent studies have begun to uncover the importance of epigenetic states and histone lysine methyltransferases (KMTs) and demethylases (KDMs) in regulating extrachromosomal transient site-specific DNA copy number gains (TSSGs). In fact, our laboratory discovered the first chromatin factor promoting TSSGs in the human genome. We have revealed a critical interplay between a myriad of KMTs and KDMs in modulating methylation balance in order to control rereplication and extrachromosomal amplification events. The methyl-lysine modifier networks that control site-specific DNA amplification were resolved through genetic and chemical treatments coupled to cytological approaches, epigenomic profiling and 3D genome organizational analyses. While interrogating their role in controlling DNA amplification, we have also begun to appreciate their impact on chromatin modification dynamics and global DNA replication timing. We have established that enhancers coupled to methylation changes in broad methylation domains strongly predicts replication timing changes when perturbed by specific lysine modifiers. Taken together, we have established that methyl-lysine modifiers are key regulators promoting or preventing DNA amplification and play instrumental roles in regulating replication timing control through the combined regulation of methylation states. The most recent studies addressing these observations will be presented at the meeting.
    DOI:  https://doi.org/10.1096/fasebj.2022.36.S1.L7417
  5. Nucleic Acids Res. 2022 May 10. pii: gkac320. [Epub ahead of print]
    Cell type identification in spatial transcriptomics data can be improved by leveraging cell-type-informative paired tissue images using a Bayesian probabilistic model.
    Asif Zubair, Richard H Chapple, Sivaraman Natarajan, William C Wright, Min Pan, Hyeong-Min Lee, Heather Tillman, John Easton, Paul Geeleher.
      Spatial transcriptomics technologies have recently emerged as a powerful tool for measuring spatially resolved gene expression directly in tissues sections, revealing cell types and their dysfunction in unprecedented detail. However, spatial transcriptomics technologies are limited in their ability to separate transcriptionally similar cell types and can suffer further difficulties identifying cell types in slide regions where transcript capture is low. Here, we describe a conceptually novel methodology that can computationally integrate spatial transcriptomics data with cell-type-informative paired tissue images, obtained from, for example, the reverse side of the same tissue section, to improve inferences of tissue cell type composition in spatial transcriptomics data. The underlying statistical approach is generalizable to any spatial transcriptomics protocol where informative paired tissue images can be obtained. We demonstrate a use case leveraging cell-type-specific immunofluorescence markers obtained on mouse brain tissue sections and a use case for leveraging the output of AI annotated H&E tissue images, which we used to markedly improve the identification of clinically relevant immune cell infiltration in breast cancer tissue. Thus, combining spatial transcriptomics data with paired tissue images has the potential to improve the identification of cell types and hence to improve the applications of spatial transcriptomics that rely on accurate cell type identification.
    DOI:  https://doi.org/10.1093/nar/gkac320
  6. Clin Cancer Res. 2022 Feb 21. OF1-OF8
    Circulating Tumor DNA Is Associated with Response and Survival in Patients with Advanced Leiomyosarcoma.
    Laura M Madanat-Harjuoja, Kelly Klega, Yao Lu, David S Shulman, Aaron R Thorner, Anwesha Nag, William D Tap, Denise K Reinke, Lisa Diller, Karla V Ballman, Suzanne George, Brian D Crompton.
      PURPOSE: We sought to determine whether the detection of circulating tumor DNA (ctDNA) in samples of patients undergoing chemotherapy for advanced leiomyosarcoma (LMS) is associated with objective response or survival.METHODS: Using ultra-low-passage whole-genome sequencing (ULP-WGS) of plasma cell-free DNA from patients treated on a prospective clinical trial, we tested whether detection of ctDNA evaluated prior to the start of therapy and after two cycles of chemotherapy was associated with treatment response and outcome. Associations between detection of ctDNA and pathologic measures of disease burden were evaluated.
    RESULTS: We found that ctDNA was detectable by ULP-WGS in 49% patients prior to treatment and in 24.6% patients after two cycles of chemotherapy. Detection of pretreatment ctDNA was significantly associated with a lower overall survival [HR, 1.55; 95% confidence interval (CI), 1.03-2.31; P = 0.03] and a significantly lower likelihood of objective response [odds ratio (OR), 0.21; 95% CI, 0.06-0.59; P = 0.005]. After two cycles of chemotherapy, patients who continued to have detectable levels of ctDNA experienced a significantly worse overall survival (HR, 1.77; 95% CI, 1-3.14; P = 0.05) and were unlikely to experience an objective response (OR, 0.05; 95% CI, 0-0.39; P = 0.001).
    CONCLUSIONS: Our results demonstrate that detection of ctDNA is associated with outcome and objective response to chemotherapy in patients with advanced LMS. These results suggest that liquid biopsy assays could be used to inform treatment decisions by recognizing patients who are likely and unlikely to benefit from chemotherapy.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-21-3951
  7. Curr Opin Genet Dev. 2022 May 05. pii: S0959-437X(22)00022-3. [Epub ahead of print]74 101913
    Chromosomal instability as a source of genomic plasticity.
    Duaa H Al-Rawi, Samuel F Bakhoum.
      Chromosomal instability (CIN) is a hallmark of the most aggressive malignancies. Features of these tumors include complex genomic rearrangements, the presence of mis-segregated chromosomes in micronuclei, and extrachromosomal DNA (ecDNA) formation. Here, we review the development of CIN, and examine CIN in the context of cancer evolution, tumor genomic evolution, and therapeutic resistance. We also discuss the role of whole-genome duplications, breakage-fusion-bridge cycles, ecDNA or double minutes in gene amplification promoting tumor evolution.
    Keywords:  Cancer Evolution; Chromosomal Instability; Micronuclei; ecDNA
    DOI:  https://doi.org/10.1016/j.gde.2022.101913
  8. Clin Epigenetics. 2022 May 10. 14(1): 61
    DNA methylation analysis of tumor suppressor genes in liquid biopsy components of early stage NSCLC: a promising tool for early detection.
    Α Markou, D Londra, V Tserpeli, Ι Kollias, E Tsaroucha, I Vamvakaris, K Potaris, I Pateras, Α Kotsakis, V Georgoulias, Ε Lianidou.
      PURPOSE: Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) analysis represents a liquid biopsy approach for real-time monitoring of tumor evolution. DNA methylation is considered to be an early event in the process of cancer development and progression. The aim of the present study was to evaluate whether detection of DNA methylation of selected tumor suppressor genes in CTC and matched ctDNA provides prognostic information in early stage NSCLC.EXPERIMENTAL DESIGN: The methylation status of five selected gene promoters (APC, RASSFIA1, FOXA1, SLFN11, SHOX2) was examined by highly specific and sensitive real-time methylation specific PCR assays in: (a) a training group of 35 primary tumors and their corresponding adjacent non-cancerous tissues of early stage NSCLC patients, (b) a validation group of 22 primary tumor tissues (FFPEs) and 42 peripheral blood samples of early stage NSCLC patients. gDNA was isolated from FFPEs, CTCs (size-based enriched by Parsortix; Angle and plasma, and (c) a control group of healthy blood donors (n = 12).
    RESULTS: All five gene promoters tested were highly methylated in the training group; methylation of SHOX2 promoter in primary tumors was associated with unfavorable outcome. RASSFIA and APC were found methylated in plasma-cfDNA samples at 14.3% and 11.9%, respectively, whereas in the corresponding CTCs SLFN11 and APC promoters were methylated in 7.1%. The incidence of relapses was higher in patients with a) promoter methylation of APC and SLFN11 in plasma-cfDNA (P = 0.037 and P = 0.042 respectively) and b) at least one detected methylated gene promoter in CTC or plasma-cfDNA (P = 0.015).
    CONCLUSIONS: DNA methylation of these five gene promoters was significantly lower in CTCs and plasma-cfDNA than in the primary tumors. Combination of DNA methylation analysis in CTC and plasma-cfDNA was associated with worse DFI of NSCLC patients. Additional studies are required to validate our findings in a large cohort of early stage NSCLC patients.
    Keywords:  Biomarkers; CTCs; DNA methylation; Liquid biopsy; NSCLC; Tumor suppressor genes; cfDNA
    DOI:  https://doi.org/10.1186/s13148-022-01283-x
  9. FASEB J. 2022 May;36 Suppl 1
    Spatial Transcriptomics Reveal Potential Sex Differences in Gene Expression of the Supraoptic Nucleus.
    Dianna H-T Nguyen, Nicole Phillips, J T Cunningham.
      The supraoptic nucleus (SON) of the hypothalamus contains magnocellular neurosecretory cells that play a key role in the regulation of fluid and electrolyte homeostasis. Although there are many well-known sexually dimorphic regions of the hypothalamus, little is known about whether this is also true for the SON and whether there are sex differences in SON gene expression. Our study aims to address this knowledge gap by leveraging spatially-resolved transcriptomics to better visualize gene expression profiles of cells in the SON of male and female rats and gain insight on their physiological functions without sacrificing morphological context. Visium Spatial Gene Expression (10x Genomics) was used to obtain spatially-resolved gene expression data for the SON of adult male (n=3) and female (n=3) Sprague-Dawley rats. Briefly, each brain was sectioned at 10μm thickness to collect coronal sections (~4x4mm) containing the SON and other brain structures. Each section was then mounted on the capture areas of Visium slides containing probes that bind mRNA. Next, the sections underwent the workflow as follows: 1) sample staining and imaging, 2) cDNA library preparation, 3) sequencing, and 4) analysis/data visualization. Data were analyzed using 10x Genomics' Space Ranger and Loupe Browser applications to overlay spatial gene expression data with reference images. Results show that gene cluster analysis successfully differentiated myelinated fiber tracts from nuclei and identified several distinct neuronal populations in the coronal brain sections from both male and female rats. From the list of significant genes after performing differential expression analysis on the SON region using 10x Genomics' Loup Browser, 74/157 genes were unique to the males, 228/311 genes were unique to the females, and 83 genes (e.g., Avp and Oxt) were common to both sexes. Preliminary Gene Ontology (GO) Enrichment and pathway analyses revealed GO terms and pathways related to: 1) homeostatic processes, regulation of peptide hormone secretion, and ion transport for the common genes; 2) ribosomes and translation for the significant genes unique to males; and 3) neurotransmitter release cycle and synaptic transmission for the significant genes unique to females, as some examples. These spatially-resolved transcriptomic data suggest potential sex differences in SON gene expression that may be associated with processes and pathways important for osmoregulation and fluid balance. Future spatial transcriptomic studies will investigate changes in SON gene expression that contribute to sex differences in cellular mechanisms involved in body fluid homeostasis and possibly pathophysiology.
    DOI:  https://doi.org/10.1096/fasebj.2022.36.S1.R3166
  10. Nature. 2022 May 11.
    Tumour driver mutations compromise between cancer growth and immune responses.
      
    Keywords:  Cancer; Cell biology; Immunology
    DOI:  https://doi.org/10.1038/d41586-022-01138-8
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