bims-ectoca 2023-01-15 papers

bims-ectoca

Biomed News

on Epigenetic control of tolerance in cancer

Issue of 2023‒01‒15
nineteen papers selected by
Ankita Daiya
BITS Pilani

Epimutations and Their Effect on Chromatin Organization: Exciting Avenues for Cancer Treatment.
Tyrosine kinase SRC-induced YAP1-KLF5 module regulates cancer stemness and metastasis in triple-negative breast cancer.
Transcriptional activity mediated by β-CATENIN and TCF/LEF family members is completely dispensable for survival and propagation of multiple human colorectal cancer cell lines.
High Throughput Confined Migration Microfluidic Device for Drug Screening.
Ebastine exerts antitumor activity and induces autophagy by activating AMPK/ULK1 signaling in an IPMK-dependent manner in osteosarcoma.
Comprehensive analysis of a glycolysis and cholesterol synthesis-related genes signature for predicting prognosis and immune landscape in osteosarcoma.
Toosendanin reduces cisplatin resistance in ovarian cancer through modulating the miR-195/ERK/β-catenin pathway.
Evolution of Epigenetic Mechanisms and Signatures.
Epigenetic remodeling of the immune landscape in cancer: therapeutic hurdles and opportunities.
WNT5a Signaling through ROR2 Activates the Hippo Pathway to Suppress YAP1 Activity and Tumor Growth.
Early-life exercise primes the murine neural epigenome to facilitate gene expression and hippocampal memory consolidation.
Nucleophagy contributes to genome stability through degradation of type II topoisomerases A and B and nucleolar components.
Combination of automated sample preparation and micro-flow LC-MS for high-throughput plasma proteomics.
ROS-Generating Hyaluronic Acid-Modified Zirconium Dioxide-Acetylacetonate Nanoparticles as a Theranostic Platform for the Treatment of Osteosarcoma.
Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences.
Oxidative Stress and Nuclear Reprogramming: A Pilot Study of the Effects of Reactive Oxygen Species on Architectural and Epigenetic Landscapes.
Sestrin2 mediates FOXM1 expression to block the EMT process in non-small cell lung cancer through the AMPK/YAP pathway.
Nonhistone Lysine Methylation as a Protein Degradation Signal.
Mutational fitness landscape and drug resistance.

Cancers (Basel). 2022 Dec 29. pii: 215. [Epub ahead of print]15(1):

Epimutations and Their Effect on Chromatin Organization: Exciting Avenues for Cancer Treatment.

Asad Mohammad, Sudhakar Jha.

  The three-dimensional architecture of genomes is complex. It is organized as fibers, loops, and domains that form high-order structures. By using different chromosome conformation techniques, the complex relationship between transcription and genome organization in the three-dimensional organization of genomes has been deciphered. Epigenetic changes, such as DNA methylation and histone modification, are the hallmark of cancers. Tumor initiation, progression, and metastasis are linked to these epigenetic modifications. Epigenetic inhibitors can reverse these altered modifications. A number of epigenetic inhibitors have been approved by FDA that target DNA methylation and histone modification. This review discusses the techniques involved in studying the three-dimensional organization of genomes, DNA methylation and histone modification, epigenetic deregulation in cancer, and epigenetic therapies targeting the tumor.

Keywords:  DNA methylation; cancer; epigenetic inhibitors; epigenetics; histone modification

DOI:  https://doi.org/10.3390/cancers15010215
Cell Mol Life Sci. 2023 Jan 12. 80(2): 41

Tyrosine kinase SRC-induced YAP1-KLF5 module regulates cancer stemness and metastasis in triple-negative breast cancer.

Hailin Zou, Juan Luo, Yibo Guo, Tongyu Tong, Yuchen Liu, Yun Chen, Yunjun Xiao, Liping Ye, Chengming Zhu, Liang Deng, Bo Wang, Yihang Pan, Peng Li.

  SRC is the first identified oncogene, and its aberrant activation has been implicated as a driving event in tumor initiation and progression. However, its role in cancer stemness regulation and the underlying regulatory mechanism are still elusive. Here, we identified a YAP1 tyrosine phosphorylation-dependent YAP1-KLF5 oncogenic module, as the key downstream mediator of SRC kinase regulating cancer stemness and metastasis in triple-negative breast cancer (TNBC). SRC was overexpressed in TNBC patient tissues and its expression level was highly correlated with the tumor malignancy. SRC activation induced, while inhibition of SRC kinase reduced the cancer stemness, tumor cell growth and metastasis in vitro and in vivo. Transcriptomic and proteomic analysis revealed that SRC-mediated YAP1 tyrosine phosphorylation induced its interaction with Kruppel-like factor 5 (KLF5) to form a YAP1/TEAD-KLF5 complex in TNBC cells. YAP1-KLF5 association further promoted TEAD-mediated transcriptional program independently of canonical Hippo kinases, which eventually gave rise to the enhanced cancer stemness and metastasis. Disruption of YAP1-KLF5 module in TNBC cells dramatically attenuated the SRC-induced cancer stemness and metastasis in vitro and in vivo. Accordingly, co-upregulations of SRC and YAP1-KLF5 module in TNBC tissues were significantly positively correlated with the tumor malignance. Altogether, our work presents a novel tyrosine phosphorylation-dependent YAP1-KLF5 oncogenic module governing SRC-induced cancer stemness and metastasis in TNBC. Therefore, targeting YAP1/KLF5-mediated transcription may provide a promising strategy for TNBC treatment with SRC aberrantly activation.

Keywords:  Cancer stem cell; SRC kinase; Triple-negative breast cancer; YAP1-KLF5 module

DOI:  https://doi.org/10.1007/s00018-023-04688-w
Sci Rep. 2023 Jan 06. 13(1): 287

Transcriptional activity mediated by β-CATENIN and TCF/LEF family members is completely dispensable for survival and propagation of multiple human colorectal cancer cell lines.

Janna Fröhlich, Katja Rose, Andreas Hecht.

Unrestrained transcriptional activity of β-CATENIN and its binding partner TCF7L2 frequently underlies colorectal tumor initiation and is considered an obligatory oncogenic driver throughout intestinal carcinogenesis. Yet, the TCF7L2 gene carries inactivating mutations in about 10% of colorectal tumors and is non-essential in colorectal cancer (CRC) cell lines. To determine whether CRC cells acquire TCF7L2-independence through cancer-specific compensation by other T-cell factor (TCF)/lymphoid enhancer-binding factor (LEF) family members, or rather lose addiction to β-CATENIN/TCF7L2-driven gene expression altogether, we generated multiple CRC cell lines entirely negative for TCF/LEF or β-CATENIN expression. Survival of these cells and the ability to propagate them demonstrate their complete β-CATENIN- and TCF/LEF-independence. Nonetheless, one β-CATENIN-deficient cell line eventually became senescent, and absence of TCF/LEF proteins and β-CATENIN consistently impaired CRC cell proliferation, reminiscent of mitogenic effects of WNT/β-CATENIN signaling in the healthy intestine. Despite this common phenotype, β-CATENIN-deficient cells exhibited highly cell-line-specific gene expression changes with little overlap between β-CATENIN- and TCF7L2-dependent transcriptomes. Apparently, β-CATENIN and TCF7L2 independently control sizeable fractions of their target genes. The observed divergence of β-CATENIN and TCF7L2 transcriptional programs, and the finding that neither β-CATENIN nor TCF/LEF activity is strictly required for CRC cell survival has important implications when evaluating these factors as potential drug targets.

DOI: https://doi.org/10.1038/s41598-022-27261-0
Small. 2023 Jan 12. e2207194

High Throughput Confined Migration Microfluidic Device for Drug Screening.

Zihan Yang, Zhihang Zhou, Tongxu Si, Zhengdong Zhou, Li Zhou, Y Rebecca Chin, Liang Zhang, Xinyuan Guan, Mengsu Yang.

  Cancer metastasis is the major cause of cancer-related death. Excessive extracellular matrix deposition and increased stiffness are typical features of solid tumors, creating confined spaces for tumor cell migration and metastasis. Confined migration is involved in all metastasis steps. However, confined and unconfined migration inhibitors are different and drugs available to inhibit confined migration are rare. The main challenges are the modeling of confined migration, the suffering of low throughput, and others. Microfluidic device has the advantage to reduce reagent consumption and enhance throughput. Here, a microfluidic chip that can achieve multi-function drug screening against the collective migration of cancer cells under confined environment is designed. This device is applied to screen out effective drugs on confined migration among a novel mechanoreceptors compound library (166 compounds) in hepatocellular carcinoma, non-small lung cancer, breast cancer, and pancreatic ductal adenocarcinoma cells. Three compounds that can significantly inhibit confined migration in pan-cancer: mitochonic acid 5 (MA-5), SB-705498, and diphenyleneiodonium chloride are found. Finally, it is elucidated that these drugs targeted mitochondria, actin polymerization, and cell viability, respectively. In sum, a high-throughput microfluidic platform for screening drugs targeting confined migration is established and three novel inhibitors of confined migration in multiple cancer types are identified.

Keywords:  cancer metastasis; confined migration; drug screening; microfluidics

DOI:  https://doi.org/10.1002/smll.202207194
Int J Biol Sci. 2023 ;19(2): 537-551

Ebastine exerts antitumor activity and induces autophagy by activating AMPK/ULK1 signaling in an IPMK-dependent manner in osteosarcoma.

Zhen Pan, Shi-Jie Li, Hua Guo, Zhao-Hui Li, Xiang Fei, Shi-Min Chang, Qing-Cheng Yang, Dong-Dong Cheng.

  Numerous studies have confirmed that in addition to interfering with the tumor inflammatory environment, anti-inflammatory agents can directly increase apoptosis and sensitivity to conventional therapies and decrease invasion and metastasis, making them useful candidates for cancer therapy. Here, we first used high-throughput screening and had screened one compound candidate, ebastine (a H1-histamine receptor antagonist), for osteosarcoma therapy. Cell viability assays, colony formation assays, wound healing assays, and Transwell assays demonstrated that ebastine elicited antitumor effects in osteosarcoma cells. In addition, ebastine treatment exerted obvious effects on cell cycle arrest, metastasis inhibition, apoptosis and autophagy induction both in vitro and in vivo. Mechanistically, we observed that ebastine treatment triggered proapoptotic autophagy by activating AMPK/ULK1 signaling in osteosarcoma cells. Treatment with the AMPK inhibitor dorsomorphin reversed ebastine-induced apoptosis and autophagy. More importantly, we found that IPMK interacted with AMPK and functioned as a positive regulator of AMPK protein in osteosarcoma cells. A rescue study showed that the induction of autophagy and activation of the AMPK/ULK1 signaling pathway by ebastine treatment were reversed by IPMK knockdown, indicating that the activity of ebastine was IPMK dependent. We provide experimental evidence demonstrating that ebastine has antitumor activity in osteosarcoma and promotes autophagy by activating the AMPK/ULK1 signaling pathway, which is IPMK dependent. Our results provide insight into the clinical application potential of ebastine, which may represent a new potential therapeutic candidate for the treatment of osteosarcoma.

Keywords:  AMPK/ULK1 pathway; Ebastine; IPMK; autophagy; osteosarcoma

DOI:  https://doi.org/10.7150/ijbs.69541
Front Immunol. 2022 ;13 1096009

Comprehensive analysis of a glycolysis and cholesterol synthesis-related genes signature for predicting prognosis and immune landscape in osteosarcoma.

Fangxing Xu, Jinglong Yan, Zhibin Peng, Jingsong Liu, Zecheng Li.

  Background: Glycolysis and cholesterol synthesis are crucial in cancer metabolic reprogramming. The aim of this study was to identify a glycolysis and cholesterol synthesis-related genes (GCSRGs) signature for effective prognostic assessments of osteosarcoma patients.Methods: Gene expression data and clinical information were obtained from GSE21257 and TARGET-OS datasets. Consistent clustering method was used to identify the GCSRGs-related subtypes. Univariate Cox regression and LASSO Cox regression analyses were used to construct the GCSRGs signature. The ssGSEA method was used to analyze the differences in immune cells infiltration. The pRRophetic R package was utilized to assess the drug sensitivity of different groups. Western blotting, cell viability assay, scratch assay and Transwell assay were used to perform cytological validation.
Results: Through bioinformatics analysis, patients diagnosed with osteosarcoma were classified into one of 4 subtypes (quiescent, glycolysis, cholesterol, and mixed subtypes), which differed significantly in terms of prognosis and tumor microenvironment. Weighted gene co-expression network analysis revealed that the modules strongly correlated with glycolysis and cholesterol synthesis were the midnight blue and the yellow modules, respectively. Both univariate and LASSO Cox regression analyses were conducted on screened module genes to identify 5 GCSRGs (RPS28, MCAM, EN1, TRAM2, and VEGFA) constituting a prognostic signature for osteosarcoma patients. The signature was an effective prognostic predictor, independent of clinical characteristics, as verified further via Kaplan-Meier analysis, ROC curve analysis, univariate and multivariate Cox regression analysis. Additionally, GCSRGs signature had strong correlation with drug sensitivity, immune checkpoints and immune cells infiltration. In cytological experiments, we selected TRAM2 as a representative gene to validate the validity of GCSRGs signature, which found that TRAM2 promoted the progression of osteosarcoma cells. Finally, at the pan-cancer level, TRAM2 had been correlated with overall survival, progression free survival, disease specific survival, tumor mutational burden, microsatellite instability, immune checkpoints and immune cells infiltration.
Conclusion: Therefore, we constructed a GCSRGs signature that efficiently predicted osteosarcoma patient prognosis and guided therapy.

Keywords:  TRAM2; cholesterol; glycolysis; immune; osteosarcoma; prognosis; signature

DOI:  https://doi.org/10.3389/fimmu.2022.1096009
Phytomedicine. 2023 Jan;pii: S0944-7113(22)00659-6. [Epub ahead of print]109 154571

Toosendanin reduces cisplatin resistance in ovarian cancer through modulating the miR-195/ERK/β-catenin pathway.

Ge Wang, Lu Li, Yan Li, Li-Hong Zhang.

  BACKGROUND: Cisplatin (DDP) resistance is prevalent in ovarian cancer (OC) patients and contributes to the poor prognosis. Therefore, it is of great significance to develop new agent to intervene and even reverse DDP resistance in OC. Toosendanin (TSN), a triterpenoid extracted from the bark or fruits of Melia toosendan Sieb et Zucc, has been proved to possess significant antitumor activities. However, the efficacy of TSN on DDP resistance in OC has not been reported yet.PURPOSE: The aim of this study is to investigate the effects of TSN on DDP resistance in OC and explore the molecular mechanism in vitro and in vivo.
METHODS: Human OC cell line (SKOV3) and DDP-resistant cell line (SKOV3/DDP) were used. Cell proliferation was measured by CCK-8 and colony formation assay. Annexin V/PI double staining and hoechst 33342 nuclear staining were employed to detect cell apoptosis. Transwell and wound-healing assay were used to determine the invasion and migration potential of cells respectively. Quantitative real-time PCR (qPCR) and western blotting were performed to detect the expression of molecules related to miR-195/ERK/β-catenin pathway. The effects and mechanism of TSN on DDP resistance of OC in vivo was investigated using xenograft model, TUNEL staining assay and immunohistochemistry.
RESULTS: TSN improved the DDP sensitivity of SKOV3/DDP cells in vitro and in vivo, reflected in promoting inhibition of proliferation, invasion, migration and epithelial mesenchymal transformation (EMT) as well as induction of apoptosis by DDP. TSN could modulate the miR-195/ERK/β-catenin axis by upregulating the miR-195-5p expression and then suppressing ERK/GSK3β/β-catenin pathway which were activated in SKOV3/DDP cells. Moreover, co-treatment of β-catenin pathway activator LiCl or miR-195-5p silencing partially recovered the DDP resistance which was previously repressed by TSN.
CONCLUSION: Both in vitro and in vivo data demonstrated that TSN could reduce DDP resistance in OC through regulating the miR-195/ERK/β-catenin pathway, highlighting the potential of TSN as an effective agent for favoring overcoming clinical DDP resistance in OC.

Keywords:  Cisplatin; ERK/GSK3β/β-catenin pathway; Ovarian cancer; Toosendanin; miR-195-5p

DOI:  https://doi.org/10.1016/j.phymed.2022.154571
Cells. 2022 Dec 27. pii: 109. [Epub ahead of print]12(1):

Evolution of Epigenetic Mechanisms and Signatures.

Alla Kalmykova, Anton Buzdin.

DNA methylation, histone posttranslational modifications, higher-order chromatin organization and regulation by noncoding RNAs are considered as the basic mechanisms underlying the epigenetic memory [...].

DOI: https://doi.org/10.3390/cells12010109
J Biomed Sci. 2023 Jan 10. 30(1): 3

Epigenetic remodeling of the immune landscape in cancer: therapeutic hurdles and opportunities.

Feng-Ming Tien, Hsuan-Hsuan Lu, Shu-Yung Lin, Hsing-Chen Tsai.

  The tumor immune microenvironment represents a sophisticated ecosystem where various immune cell subtypes communicate with cancer cells and stromal cells. The dynamic cellular composition and functional characteristics of the immune landscape along the trajectory of cancer development greatly impact the therapeutic efficacy and clinical outcome in patients receiving systemic antitumor therapy. Mounting evidence has suggested that epigenetic mechanisms are the underpinning of many aspects of antitumor immunity and facilitate immune state transitions during differentiation, activation, inhibition, or dysfunction. Thus, targeting epigenetic modifiers to remodel the immune microenvironment holds great potential as an integral part of anticancer regimens. In this review, we summarize the epigenetic profiles and key epigenetic modifiers in individual immune cell types that define the functional coordinates of tumor permissive and non-permissive immune landscapes. We discuss the immunomodulatory roles of current and prospective epigenetic therapeutic agents, which may open new opportunities in enhancing cancer immunotherapy or overcoming existing therapeutic challenges in the management of cancer.

Keywords:  Adaptive immunity; Chromatin accessibility; DNA methylation; Epigenetic therapy; Histone modifications; Immunotherapy; Innate immunity; Tumor immune microenvironment

DOI:  https://doi.org/10.1186/s12929-022-00893-0
Cancer Res. 2023 Jan 09. pii: CAN-22-3003. [Epub ahead of print]

WNT5a Signaling through ROR2 Activates the Hippo Pathway to Suppress YAP1 Activity and Tumor Growth.

Keshan Wang, Fen Ma, Seiji Arai, Yun Wang, Andreas Varkaris, Larysa Poluben, Olga Voznesensky, Fang Xie, Xiaoping Zhang, Xin Yuan, Steven P Balk.

Noncanonical Wnt signaling by WNT5a has oncogenic and tumor suppressive activities, but downstream pathways mediating these specific effects remain to be fully established. In a subset of prostate cancer organoid culture and xenograft models, inhibition of Wnt synthesis stimulated growth, while WNT5a or a WNT5a mimetic peptide (Foxy5) markedly suppressed tumor growth. WNT5a caused a ROR2-dependent decrease in YAP1 activity that was associated with increased phosphorylation of MST1/2, LATS1, MOB1, and YAP1, indicating Hippo pathway activation. Deletion of MST1/2 abrogated the WNT5a response. WNT5a similarly activated Hippo in ROR2-expressing melanoma cells, while WNT5a in ROR2-negative cells suppressed Hippo. This suppression was associated with increased inhibitory phosphorylation of NF2/Merlin that was not observed in ROR2-expressing cells. WNT5a also increased mRNA encoding Hippo pathway components including MST1 and MST2 and was positively correlated with these components in prostate cancer clinical datasets. Conversely, ROR2 and WNT5a expression were stimulated by YAP1, and correlated with increased YAP1 activity in clinical datasets, revealing a WNT5a/ROR2 negative feedback loop to modulate YAP1 activity. Together these findings identify Hippo pathway activation as a mechanism that mediates the tumor suppressive effects of WNT5a and indicate that expression of ROR2 may be a predictive biomarker for responsiveness to WNT5a-mimetic drugs.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-3003
Commun Biol. 2023 Jan 07. 6(1): 18

Early-life exercise primes the murine neural epigenome to facilitate gene expression and hippocampal memory consolidation.

Anthony M Raus, Tyson D Fuller, Nellie E Nelson, David A Valientes, Anita Bayat, Autumn S Ivy.

Aerobic exercise is well known to promote neuroplasticity and hippocampal memory. In the developing brain, early-life exercise (ELE) can lead to persistent improvements in hippocampal function, yet molecular mechanisms underlying this phenomenon have not been fully explored. In this study, transgenic mice harboring the "NuTRAP" (Nuclear tagging and Translating Ribosome Affinity Purification) cassette in Emx1 expressing neurons ("Emx1-NuTRAP" mice) undergo ELE during adolescence. We then simultaneously isolate and sequence translating mRNA and nuclear chromatin from single hippocampal homogenates containing Emx1-expressing neurons. This approach allowed us to couple translatomic with epigenomic sequencing data to evaluate the influence of histone modifications H4K8ac and H3K27me3 on translating mRNA after ELE. A subset of ELE mice underwent a hippocampal learning task to determine the gene expression and epigenetic underpinnings of ELE's contribution to improved hippocampal memory performance. From this experiment, we discover gene expression - histone modification relationships that may play a critical role in facilitated memory after ELE. Our data reveal candidate gene-histone modification interactions and implicate gene regulatory pathways involved in ELE's impact on hippocampal memory.

DOI: https://doi.org/10.1038/s42003-022-04393-7
J Cell Sci. 2023 Jan 01. pii: jcs260563. [Epub ahead of print]136(1):

Nucleophagy contributes to genome stability through degradation of type II topoisomerases A and B and nucleolar components.

Gabriel Muciño-Hernández, Pilar Sarah Acevo-Rodríguez, Sandra Cabrera-Benitez, Adán Oswaldo Guerrero, Horacio Merchant-Larios, Susana Castro-Obregón.

  The nuclear architecture of mammalian cells can be altered as a consequence of anomalous accumulation of nuclear proteins or genomic alterations. Most of the knowledge about nuclear dynamics comes from studies on cancerous cells. How normal healthy cells maintain genome stability, avoiding accumulation of nuclear damaged material, is less understood. Here, we describe that primary mouse embryonic fibroblasts develop a basal level of nuclear buds and micronuclei, which increase after etoposide-induced DNA double-stranded breaks. Both basal and induced nuclear buds and micronuclei colocalize with the autophagic proteins BECN1 and LC3B (also known as MAP1LC3B) and with acidic vesicles, suggesting their clearance by nucleophagy. Some of the nuclear alterations also contain autophagic proteins and type II DNA topoisomerases (TOP2A and TOP2B), or the nucleolar protein fibrillarin, implying they are also targets of nucleophagy. We propose that basal nucleophagy contributes to genome and nuclear stability, as well as in response to DNA damage.

Keywords:  Autophagy; DNA damage; Mammalian nucleophagy; Micronuclei; Nucleolus

DOI:  https://doi.org/10.1242/jcs.260563
Clin Proteomics. 2023 Jan 07. 20(1): 3

Combination of automated sample preparation and micro-flow LC-MS for high-throughput plasma proteomics.

Xueting Ye, Xiaozhen Cui, Luobin Zhang, Qiong Wu, Xintong Sui, An He, Xinyou Zhang, Ruilian Xu, Ruijun Tian.

  BACKGROUND: Non-invasive detection of blood-based markers is a critical clinical need. Plasma has become the main sample type for clinical proteomics research because it is easy to obtain and contains measurable protein biomarkers that can reveal disease-related physiological and pathological changes. Many efforts have been made to improve the depth of its identification, while there is an increasing need to improve the throughput and reproducibility of plasma proteomics analysis in order to adapt to the clinical large-scale sample analysis.METHODS: We have developed and optimized a robust plasma analysis workflow that combines an automated sample preparation platform with a micro-flow LC-MS-based detection method. The stability and reproducibility of the workflow were systematically evaluated and the workflow was applied to a proof-of-concept plasma proteome study of 30 colon cancer patients from three age groups.
RESULTS: This workflow can analyze dozens of samples simultaneously with high reproducibility. Without protein depletion and prefractionation, more than 300 protein groups can be identified in a single analysis with micro-flow LC-MS system on a Orbitrap Exploris 240 mass spectrometer, including quantification of 35 FDA approved disease markers. The quantitative precision of the entire workflow was acceptable with median CV of 9%. The preliminary proteomic analysis of colon cancer plasma from different age groups could be well separated with identification of potential colon cancer-related biomarkers.
CONCLUSIONS: This workflow is suitable for the analysis of large-scale clinical plasma samples with its simple and time-saving operation, and the results demonstrate the feasibility of discovering significantly changed plasma proteins and distinguishing different patient groups.

Keywords:  Automated samples preparation; High throughput; Micro-flow LC–MS; Plasma proteome profiling

DOI:  https://doi.org/10.1186/s12014-022-09390-w
Nanomaterials (Basel). 2022 Dec 22. pii: 54. [Epub ahead of print]13(1):

ROS-Generating Hyaluronic Acid-Modified Zirconium Dioxide-Acetylacetonate Nanoparticles as a Theranostic Platform for the Treatment of Osteosarcoma.

Giovanna Chianese, Ines Fasolino, Chiara Tramontano, Luca De Stefano, Claudio Imparato, Antonio Aronne, Luigi Ambrosio, Maria Grazia Raucci, Ilaria Rea.

  Materials that are able to produce free radicals have gained increasing attention for environmental and biomedical purposes. Free radicals, such as the superoxide anion (O2•-), act as secondary messengers in many physiological pathways, such as cell survival. Therefore, the production of free radicals over physiological levels has been exploited in the treatment of different types of cancer, including osteosarcoma (OS). In most cases, the production of reactive oxygen species (ROS) by materials is light-induced and requires the use of chemical photosensitisers, making it difficult and expensive. Here, for the first time, we propose photoluminescent hybrid ZrO2-acetylacetonate nanoparticles (ZrO2-acac NPs) that are capable of generating O2•- without light activation as an adjuvant for the treatment of OS. To increase the uptake and ROS generation in cancer cells, we modify the surface of ZrO2-acac NPs with hyaluronic acid (HA), which recognizes and binds to the surface antigen CD44 overexpressed on OS cells. Since these nanoparticles emit in the visible range, their uptake into cancer cells can be followed by a label-free approach. Overall, we show that the generation of O2•- is toxic to OS cells and can be used as an adjuvant treatment to increase the efficacy of conventional drugs.

Keywords:  cancer therapy; functionalization; hybrid zirconia; nanoparticles; osteosarcoma; photoluminescence; reactive oxygen species

DOI:  https://doi.org/10.3390/nano13010054
BMC Genomics. 2023 Jan 13. 24(1): 17

Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences.

Daniel Lindhorst, Marc S Halfon.

  BACKGROUND: Transcriptional enhancers are essential for gene regulation, but how these regulatory elements are best defined remains a significant unresolved question. Traditional definitions rely on activity-based criteria such as reporter gene assays, while more recently, biochemical assays based on chromatin-level phenomena such as chromatin accessibility, histone modifications, and localized RNA transcription have gained prominence.RESULTS: We examine here whether these two types of definitions, activity-based and chromatin-based, effectively identify the same sets of sequences. We find that, concerningly, the overlap between the two groups is strikingly limited. Few of the data sets we compared displayed statistically significant overlap, and even for those, the degree of overlap was typically small (below 40% of sequences). Moreover, a substantial batch effect was observed in which experiment set rather than experimental method was a primary driver of whether or not chromatin-defined enhancers showed a strong overlap with reporter gene-defined enhancers.
CONCLUSIONS: Our results raise important questions as to the appropriateness of both old and new enhancer definitions, and suggest that new approaches are required to reconcile the poor agreement among existing methods for defining enhancers.

Keywords:  ATAC-seq; CRM; Cis-regulation; Enhancer; Gene regulation; Histone modification; Reporter gene

DOI:  https://doi.org/10.1186/s12864-023-09123-9
Int J Mol Sci. 2022 Dec 21. pii: 153. [Epub ahead of print]24(1):

Oxidative Stress and Nuclear Reprogramming: A Pilot Study of the Effects of Reactive Oxygen Species on Architectural and Epigenetic Landscapes.

Claudio Casali, Stella Siciliani, Luca Galgano, Marco Biggiogera.

  Cell genome integrity is continuously threatened by various sources, both endogenous and exogenous. Oxidative stress causes a multitude of damages, severely affecting cell viability, fidelity of genetic information inheritance, and determining profound alterations in gene expression. Epigenetics represents a major form of gene expression modulation, influencing DNA accessibility to transcription factors and the overall nuclear architecture. When assessing the stress-induced epigenome reprogramming, widely diffused biochemical and molecular approaches commonly fail to incorporate analyses such as architectural chromatin alterations and target molecules precise spatial localization. Unveiling the significance of the nuclear response to the oxidative stress, as well as the functional effects over the chromatin organization, may reveal targets and strategies for approaches aiming at limiting the impact on cellular stability. For these reasons, we utilized potassium bromate treatment, a stressor able to induce DNA damages without altering the cellular microenvironment, hence purely modeling nuclear oxidative stress. By means of high-resolution techniques, we described profound alterations in DNA and histone epigenetic modifications and in chromatin organization in response to the reactive oxygen species.

Keywords:  EZH2; antioxidants; chromatin remodeling; epigenetics; gene expression regulation; histone post-translational modification; oxidative stress; potassium bromate

DOI:  https://doi.org/10.3390/ijms24010153
Neoplasma. 2023 Jan 09. pii: 220711N705. [Epub ahead of print]

Sestrin2 mediates FOXM1 expression to block the EMT process in non-small cell lung cancer through the AMPK/YAP pathway.

Yuan-Li Wang, Qi Wang, Hua Li, Cai-Chun Wang, Yan-Lin Ma, Zhong Han.

Non-small cell lung cancer (NSCLC) is characterized by high incidence and mortality, severely threatening human health. The infinite growth and metastasis of NSCLC cells result in a poor prognosis. Therefore, our study was to investigate the mechanism of Sestrin2 on the epithelial-mesenchymal transition (EMT) process of NSCLC cells. Human embryonic lung fibroblasts, NSCLC cell lines, and nude mice were experimental subjects in this study. qRT-PCR and western blot were performed to evaluate the mRNA and protein expression of genes. CCK-8 and EdU assay were conducted to detect cell proliferation. The scratch test and Transwell assay were applied to examine cell migration and invasion. The bioinformatics analysis and Co-IP assay were employed to predict and consolidate the interaction between YAP and TEAD. We found the expression of Sestrin2 was declined but the expression of YAP was elevated in NSCLC cells. Sestrin2 sufficiency or YAP silencing could effectively impair cell growth and metastasis. Mechanistically, YAP interacted with TEAD to enhance FOXM1 expression. Additionally, the elevation of FOXM1 abolished the inhibitory influences of Sestrin2 sufficiency on NSCLC cell growth, invasion, and EMT process. Eventually, Sestrin2 elevation attenuated tumor growth in mice via modulation of the AMPK/YAP/FOXM1 axis, which was reversed by FOXM1 overexpression. Our consequences suggested Sestrin2 could inhibit the activation of YAP via prompting AMPK phosphorylation and then suppress FOXM1 expression through the interplay between YAP and TEAD to impair the capacities of NSCLC cell proliferation, migration, invasion, and EMT. This study provided a novel mechanism of Sestrin2 in NSCLC.

DOI: https://doi.org/10.4149/neo_2022_220711N705
J Chem. 2022 ;pii: 1969299. [Epub ahead of print]2022

Nonhistone Lysine Methylation as a Protein Degradation Signal.

Nicholas A Lehning, Brad E Morrison.

Protein degradation is a fundamental feature of cellular life, and malfunction of this process is implicated in human disease. Ubiquitin tagging is the best characterized mechanism of targeting a protein for degradation; however, there are a growing number of distinct mechanisms which have also been identified that carry out this essential function. For example, covalent tagging of proteins with sequestosome-1 targets them for selective autophagy. Degradation signals are not exclusively polypeptides such as ubiquitin, NEDD8, and sequestosome-1. Phosphorylation, acetylation, and methylation are small covalent additions that can also direct protein degradation. The diversity of substrate sequences and overlap with other pleotrophic functions for these smaller signaling moieties has made their characterization more challenging. However, these small signals might be responsible for orchestrating a large portion of the protein degradation activity in the cell. As such, there has been increasing interest in lysine methylation and associated lysine methyltransferases (KMTs), beyond canonical histone protein modification, in mediating protein degradation in a variety of contexts. This review focuses on the current evidence for lysine methylation as a protein degradation signal with a detailed discussion of the class of enzymes responsible for this phenomenon.

DOI: https://doi.org/10.1155/2022/1969299
Curr Opin Struct Biol. 2023 Jan 06. pii: S0959-440X(22)00204-4. [Epub ahead of print]78 102525

Mutational fitness landscape and drug resistance.

Julia Flynn, Neha Samant, Gily Schneider-Nachum, Tsepal Tenzin, Daniel N A Bolon.

Robust technology has been developed to systematically quantify fitness landscapes that provide valuable opportunities to improve our understanding of drug resistance and define new avenues to develop drugs with reduced resistance susceptibility. We outline the critical importance of drug resistance studies and the potential for fitness landscape approaches to contribute to this effort. We describe the major technical advancements in mutational scanning, which is the primary approach used to quantify protein fitness landscapes. There are many complex steps to consider in planning and executing mutational scanning projects including developing a selection scheme, generating mutant libraries, tracking the frequency of variants using next-generation sequencing, and processing and interpreting the data. Key experimental parameters impacting each of these steps are discussed to aid in planning fitness landscape studies. There is a strong need for improved understanding of drug resistance, and fitness landscapes provide a promising new approach.

DOI: https://doi.org/10.1016/j.sbi.2022.102525