bims-ectoca 2023-08-06 papers

bims-ectoca

Biomed News

on Epigenetic control of tolerance in cancer

Issue of 2023–08–06
eight papers selected by
Ankita Daiya, Birla Institute of Technology and Science

May the force be with you: Nuclear condensates function beyond transcription control: Potential nongenetic functions of nuclear condensates in physiological and pathological conditions.
Cancer cell plasticity during tumor progression, metastasis and response to therapy.
Transcription Factor Dynamics: One Molecule at a Time.
Integration of single-cell sequencing and bulk expression data reveals chemokine signaling pathway in proliferating cells is associated with the survival outcome of osteosarcoma.
ANXA2 and Rac1 negatively regulates autophagy and osteogenic differentiation in osteosarcoma cells to confer CDDP resistance.
Expression of EZH2 and H3K27me3 predicts tumor biology of urothelial carcinoma.
Feature selection translates drug response predictors from cell lines to patients.
Role of exosomes in transferring chemoresistance through modulation of cancer glycolytic cell metabolism.

Bioessays. 2023 Aug 02. e2300075

May the force be with you: Nuclear condensates function beyond transcription control: Potential nongenetic functions of nuclear condensates in physiological and pathological conditions.

Maria Luce Negri, Sarah D'Annunzio, Giulia Vitali, Alessio Zippo.

  Over the past decade, research has revealed biomolecular condensates' relevance in diverse cellular functions. Through a phase separation process, they concentrate macromolecules in subcompartments shaping the cellular organization and physiology. In the nucleus, biomolecular condensates assemble relevant biomolecules that orchestrate gene expression. We here hypothesize that chromatin condensates can also modulate the nongenetic functions of the genome, including the nuclear mechanical properties. The importance of chromatin condensates is supported by the genetic evidence indicating that mutations in their members are causative of a group of rare Mendelian diseases named chromatinopathies (CPs). Despite a broad spectrum of clinical features and the perturbations of the epigenetic machinery characterizing the CPs, recent findings highlighted negligible changes in gene expression. These data argue in favor of possible noncanonical functions of chromatin condensates in regulating the genome's spatial organization and, consequently, the nuclear mechanics. In this review, we discuss how condensates may impact nuclear mechanical properties, thus affecting the cellular response to mechanical cues and, eventually, cell fate and identity. Chromatin condensates organize macromolecules in the nucleus orchestrating the transcription regulation and mutations in their members are responsible for rare diseases named chromatinopathies. We argue that chromatin condensates, in concert with the nuclear lamina, may also govern the nuclear mechanical properties affecting the cellular response to external cues.

Keywords:  Kabuki syndrome; MLL4; chromatin condensates; epigenetics; mechanobiology; mechanotransduction; transcription control

DOI:  https://doi.org/10.1002/bies.202300075
Nat Cancer. 2023 Aug 03.

Cancer cell plasticity during tumor progression, metastasis and response to therapy.

Andrea Pérez-González, Kevin Bévant, Cédric Blanpain.

Cell plasticity represents the ability of cells to be reprogrammed and to change their fate and identity, enabling homeostasis restoration and tissue regeneration following damage. Cell plasticity also contributes to pathological conditions, such as cancer, enabling cells to acquire new phenotypic and functional features by transiting across distinct cell states that contribute to tumor initiation, progression, metastasis and resistance to therapy. Here, we review the intrinsic and extrinsic mechanisms driving cell plasticity that promote tumor growth and proliferation as well as metastasis and drug tolerance. Finally, we discuss how cell plasticity could be exploited for anti-cancer therapy.

DOI: https://doi.org/10.1038/s43018-023-00595-y
Annu Rev Cell Dev Biol. 2023 Aug 04.

Transcription Factor Dynamics: One Molecule at a Time.

Kaustubh Wagh, Diana A Stavreva, Arpita Upadhyaya, Gordon L Hager.

Cells must tightly regulate their gene expression programs and yet rapidly respond to acute biochemical and biophysical cues within their environment. This information is transmitted to the nucleus through various signaling cascades, culminating in the activation or repression of target genes. Transcription factors (TFs) are key mediators of these signals, binding to specific regulatory elements within chromatin. While live-cell imaging has conclusively proven that TF-chromatin interactions are highly dynamic, how such transient interactions can have long-term impacts on developmental trajectories and disease progression is still largely unclear. In this review, we summarize our current understanding of the dynamic nature of TF functions, starting with a historical overview of early live-cell experiments. We highlight key factors that govern TF dynamics and how TF dynamics, in turn, affect downstream transcriptional bursting. Finally, we conclude with open challenges and emerging technologies that will further our understanding of transcriptional regulation. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 39 is October 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-cellbio-022823-013847
BMC Med Genomics. 2023 Aug 03. 16(1): 180

Integration of single-cell sequencing and bulk expression data reveals chemokine signaling pathway in proliferating cells is associated with the survival outcome of osteosarcoma.

Lin Yu, Sun Hongyu, Chen Yuxi.

   BACKGROUND: Osteosarcoma, as the most common primary bone malignancy, is urgent to be well-studied on the biomarkers and therapeutic targets to improve the five-year survival rate. Transcriptomic analysis using single-cell RNA or bulk RNA sequencing has been developed to detect biomarkers in various cancer types.
METHODS AND RESULTS: We applied Scissor to combine single-cell RNA-seq data and bulk transcriptome data of osteosarcoma, providing cell-level information and sample phenotypes to identify the survival-associated cell subpopulations. By investigating the differences between the survival-associated cell subpopulations, we identified CCL21, CCL22, CCL24, CXCL11, CXCL12, CXCL13, GNAI2, and RAC2 in the proliferating cells that are significantly associated with osteosarcoma patient outcome. Then we assigned the risk score for each sample based on the cell proportion-normalized gene expression and validated it in the public dataset.
CONCLUSIONS: This study provides the clinical insight that chemokine signaling pathway genes (CCL21, CCL22, CCL24, CXCL11, CXCL12, CXCL13, GNAI2, and RAC2) in proliferating cells might be the potential biomarkers for treatment of osteosarcoma.

Keywords:  Biomarker; Chemokine signaling pathway; Osteosarcoma; Proliferating cells

DOI:  https://doi.org/10.1186/s12920-023-01617-5
Biochem Biophys Res Commun. 2023 Jul 03. pii: S0006-291X(23)00854-9. [Epub ahead of print]676 198-206

ANXA2 and Rac1 negatively regulates autophagy and osteogenic differentiation in osteosarcoma cells to confer CDDP resistance.

Baolong Pan, Yanyu Pan, Shuangneng Wang, Yingying Bai, Xuemei Hu, Yang Yang, Ling Wu, Jianping Liu.

   BACKGROUND: Cisplatin (CDDP) is a mainstay chemotherapeutic agent for OS treatment, but drug resistance has become a hurdle to limit its clinical effect. Autophagy plays an important role in CDDP resistance in OS, and in the present study we explored the role of ANXA2 and Rac1 in dictating CDDP sensitivity in OS cells.
METHODS: ANXA2 and Rac1 expression levels were examined by Western blot and autophagy induction was detected by transmission electron miscroscope (TEM) in the clinical samples and OS cell lines. CDDP resistant cells were established by exposing OS cells to increasing doses of CDDP. The effects of ANXA2 and Rac1 knockdown on CDDP sensitivity were evaluated in the cell and animal models.
RESULTS: Reduced autophagy was associated with the increased expression of ANXA2 and Rac1 in CDDP resistant OS tumor samples and cells. Autophagy suppression promoted CDDP resistance and inducing autophagy re-sensitized the resistant cells to CDDP treatment in vitro and in vivo. Further, knocking down ANXA2 or Rac1 re-activated autophagy and attenuated CDDP resistance in OS cells. We further demonstrated that CDDP resistant OS cells displayed a poorer osteogenic differentiation state when compared to the parental cell lines, which was significantly reversed by autophagy re-activation and ANXA2 or Rac1 silencing.
CONCLUSION: Our findings revealed a complicated interplay of ANXA2/Rac1, autophagy induction, and osteogenic differentiation in dictating CDDP resistance in OS cells, suggesting ANXA2 and Rac1 as promising targets to modulate autophagy and overcome CDDP resistance in OS cells.

Keywords:  ANXA2 and Rac1; Autophgy; Cisplatin (CDDP); Drug resistance; Osteogenic differentiation; Osteosarcoma (OS)

DOI:  https://doi.org/10.1016/j.bbrc.2023.07.006
Indian J Pathol Microbiol. 2023 Jul-Sep;66(3):66(3): 488-494

Expression of EZH2 and H3K27me3 predicts tumor biology of urothelial carcinoma.

Rasheeda Mohamedali, Suvradeep Mitra, Swarnendu Mandal, Prasant Nayak, Amit K Adhya, Suvendu Purkait.

   Background: Enhancer of zeste homolog 2 (EZH2) is one of the major epigenetic modifiers involved in the transcriptional repression of target genes through trimethylation of H3K27 (lysine 27 residue of histone H3). Deregulated expression of both EZH2 and H3K27me3 has been implicated in the biological behavior and prognostic outcome of various malignancies.
Aim: To assess the role of EZH2 and H3K27me3 in the carcinogenesis of urothelial carcinoma of urinary bladder.
Materials and Methods: One hundred fifty consecutive urothelial carcinoma cases of urinary bladder (54.7% high-grade) were included in this study. Immunohistochemical analysis for EZH2 and H3K27me3 was performed on whole tissue sections. A multiplication score obtained by multiplying staining intensity and proportion of positively stained neoplastic cells was used for assessment.
Results: EZH2 showed a significant correlation with the tumor grade and lamina propria invasion (p < 0.001). The cases with high EZH2 expression showed a significantly high proliferative index (Mean- 32.7%; p < 0.001). In contrast, negative and low expression of H3K27me3 was significantly more common in high-grade cases (p = 0.006). The expression of H3K27me3 was significantly associated with lamina propria (p = 0.01) and deep muscle invasion (p = 0.007). EZH2 showed a significantly higher expression in the high-grade invasive areas as compared to the high-grade non-invasive areas of the same tumor (p = 0.03).
Conclusions: This study establishes an important role of the key epigenetic regulators EZH2 and H3K27me3 in the pathobiology of urothelial carcinomas. Strong expression of EZH2 and weak expression of H3K27me3 are associated with higher grade, proliferative index and invasive behavior.

Keywords:  EZH2; Epigenetics; H3K27me3; urothelial carcinoma

DOI:  https://doi.org/10.4103/ijpm.ijpm_1267_21
Front Genet. 2023 ;14 1217414

Feature selection translates drug response predictors from cell lines to patients.

Shinsheng Yuan, Yen-Chou Chen, Chi-Hsuan Tsai, Huei-Wen Chen, Grace S Shieh.

  Targeted therapies and chemotherapies are prevalent in cancer treatment. Identification of predictive markers to stratify cancer patients who will respond to these therapies remains challenging because patient drug response data are limited. As large amounts of drug response data have been generated by cell lines, methods to efficiently translate cell-line-trained predictors to human tumors will be useful in clinical practice. Here, we propose versatile feature selection procedures that can be combined with any classifier. For demonstration, we combined the feature selection procedures with a (linear) logit model and a (non-linear) K-nearest neighbor and trained these on cell lines to result in LogitDA and KNNDA, respectively. We show that LogitDA/KNNDA significantly outperforms existing methods, e.g., a logistic model and a deep learning method trained by thousands of genes, in prediction AUC (0.70-1.00 for seven of the ten drugs tested) and is interpretable. This may be due to the fact that sample sizes are often limited in the area of drug response prediction. We further derive a novel adjustment on the prediction cutoff for LogitDA to yield a prediction accuracy of 0.70-0.93 for seven drugs, including erlotinib and cetuximab, whose pathways relevant to anti-cancer therapies are also uncovered. These results indicate that our methods can efficiently translate cell-line-trained predictors into tumors.

Keywords:  cancer; domain adaptation; drug response; feature selection; machine learning; prediction

DOI:  https://doi.org/10.3389/fgene.2023.1217414
Cytokine Growth Factor Rev. 2023 Jul 29. pii: S1359-6101(23)00035-7. [Epub ahead of print]

Role of exosomes in transferring chemoresistance through modulation of cancer glycolytic cell metabolism.

Mahrou Vahabi, Annalisa Comandatore, Marika A Franczak, Ryszard T Smolenski, Godefridus J Peters, Luca Morelli, Elisa Giovannetti.

  Chemoresistance constitute a major obstacle in cancer treatment, leading to limited options and decreased patient survival. Recent studies have revealed a novel mechanism of chemoresistance acquisition: the transfer of information via exosomes, small vesicles secreted by various cells. Exosomes play a crucial role in intercellular communication by carrying proteins, nucleic acids, and metabolites, influencing cancer cell behavior and response to treatment. One crucial mechanism of resistance is cancer metabolic reprogramming, which involves alterations in the cellular metabolic pathways to support the survival and proliferation of drug-resistant cancer cells. This metabolic reprogramming often includes increased glycolysis, providing cancer cells with the necessary energy and building blocks to evade the effects of chemotherapy. Notably, exosomes have been found to transport glycolytic enzymes, as identified in proteomic profiling, leading to the reprogramming of metabolic pathways, facilitating altered glucose metabolism and increased lactate production. As a result, they profoundly impact the tumor microenvironment, promoting tumor progression, survival, immune evasion, and drug resistance.Understanding the complexities of such exosome-mediated cell-to-cell communication might open new therapeutic avenues and facilitate biomarker development in managing cancers characterized by aggressive glycolytic features. Moreover, given the intricate nature of metabolic abnormalities combining future exosome-based-targeted therapies with existing treatments like chemotherapy, immunotherapy, and targeted therapies holds promise for achieving synergistic effects to overcome resistance and improve cancer treatment outcomes.

Keywords:  Cancer metabolism; Cell-to-cell communication; Chemoresistance; Exosomes; Glycolysis

DOI:  https://doi.org/10.1016/j.cytogfr.2023.07.004