bims-ectoca Biomed News
on Epigenetic control of tolerance in cancer
Issue of 2021‒07‒04
37 papers selected by
Ankita Daiya, Birla Institute of Technology and Science
  1. Cancer models in preclinical research: A chronicle review of advancement in effective cancer research.
  2. Mitochondrial creatine kinase 1 in non-small cell lung cancer progression and hypoxia adaptation.
  3. Integrative Multi-Omics Analysis of Identified NUF2 as a Candidate Oncogene Correlates With Poor Prognosis and Immune Infiltration in Non-Small Cell Lung Cancer.
  4. Silibinin Regulates Tumor Progression and Tumorsphere Formation by Suppressing PD-L1 Expression in Non-Small Cell Lung Cancer (NSCLC) Cells.
  5. Ring finger protein 19A is overexpressed in non-small cell lung cancer and mediates p53 ubiquitin-degradation to promote cancer growth.
  6. Single-Cell RNA-Seq Reveals Transcriptomic Heterogeneity and Post-Traumatic Osteoarthritis-Associated Early Molecular Changes in Mouse Articular Chondrocytes.
  7. Role of Long Non-Coding RNA Polymorphisms in Cancer Chemotherapeutic Response.
  8. Exploiting epigenetic dependencies in ovarian cancer therapy.
  9. Applications of Single-Cell Omics in Tumor Immunology.
  10. Functional Implications of the Dynamic Regulation of EpCAM during Epithelial-to-Mesenchymal Transition.
  11. Regulation of Chromatin Organization in Cell Stemness: The Emerging Role of Long Non-coding RNAs.
  12. Epigenetics of Most Aggressive Solid Tumors: Pathways, Targets and Treatments.
  13. Metabolic Reprogramming of Colorectal Cancer Cells and the Microenvironment: Implication for Therapy.
  14. The Sex-Related Interplay between TME and Cancer: On the Critical Role of Estrogen, MicroRNAs and Autophagy.
  15. Towards a Better Understanding of the Relationships between Galectin-7, p53 and MMP-9 during Cancer Progression.
  16. The genome-wide binding profile for human RE1 Silencing Transcription factor unveils a unique genetic circuitry in hippocampus.
  17. A Key Pathway to Cancer Resilience: The Role of Autophagy in Glioblastomas.
  18. Tumor immunology in the age of single-cell genomics.
  19. Integrins Within the Tumor Microenvironment: Biological Functions, Importance for Molecular Targeting, and Cancer Therapeutics Innovation.
  20. Mitochondrial nanomedicine: Subcellular organelle-specific delivery of molecular medicines.
  21. Transcriptional Profiling of Cardiac Cells Links Age-Dependent Changes in Acetyl-CoA Signaling to Chromatin Modifications.
  22. Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing.
  23. Computational analysis of alternative polyadenylation from standard RNA-seq and single-cell RNA-seq data.
  24. Dying to Survive-The p53 Paradox.
  25. Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies.
  26. Causal interactions from proteomic profiles: Molecular data meet pathway knowledge.
  27. Tumor suppressor p53 cross-talks with TRIM family proteins.
  28. Towards a "druggable" epitranscriptome: Compounds that target RNA modifications in cancer.
  29. Transcription Factors: The Fulcrum Between Cell Development and Carcinogenesis.
  30. Breast tumor stiffness instructs bone metastasis via maintenance of mechanical conditioning.
  31. Mitochondrial tumor suppressors - the energetic enemies of tumor progression.
  32. The MicroRNA Family Gets Wider: The IsomiRs Classification and Role.
  33. Extracellular matrix gene expression signatures as cell type and cell state identifiers.
  34. Integrated Analysis of the Transcriptome Profile Reveals the Potential Roles Played by Long Noncoding RNAs in Immunotherapy for Sarcoma.
  35. Identifying distinct heterochromatin regions using combinatorial epigenetic probes in live cells.
  36. Epigenetic roles of PIWI proteins and piRNAs in colorectal cancer.
  37. New Insights into the Clinical Implications of Yes-Associated Protein in Lung Cancer: Roles in Drug Resistance, Tumor Immunity, Autophagy, and Organoid Development.
  1. Animal Model Exp Med. 2021 Jun;4(2): 87-103
    Cancer models in preclinical research: A chronicle review of advancement in effective cancer research.
    Humna Sajjad, Saiqa Imtiaz, Tayyaba Noor, Yusra Hasan Siddiqui, Anila Sajjad, Muhammad Zia.
      Cancer is a major stress for public well-being and is the most dreadful disease. The models used in the discovery of cancer treatment are continuously changing and extending toward advanced preclinical studies. Cancer models are either naturally existing or artificially prepared experimental systems that show similar features with human tumors though the heterogeneous nature of the tumor is very familiar. The choice of the most fitting model to best reflect the given tumor system is one of the real difficulties for cancer examination. Therefore, vast studies have been conducted on the cancer models for developing a better understanding of cancer invasion, progression, and early detection. These models give an insight into cancer etiology, molecular basis, host tumor interaction, the role of microenvironment, and tumor heterogeneity in tumor metastasis. These models are also used to predict novel cancer markers, targeted therapies, and are extremely helpful in drug development. In this review, the potential of cancer models to be used as a platform for drug screening and therapeutic discoveries are highlighted. Although none of the cancer models is regarded as ideal because each is associated with essential caveats that restraint its application yet by bridging the gap between preliminary cancer research and translational medicine. However, they promise a brighter future for cancer treatment.
    Keywords:  cancer cell lines; computational cancer models; genetically engineered mouse models; organoids; patient‐derived xenografts; personalized medicine
    DOI:  https://doi.org/10.1002/ame2.12165
  2. Respir Res. 2021 Jul 01. 22(1): 190
    Mitochondrial creatine kinase 1 in non-small cell lung cancer progression and hypoxia adaptation.
    Ming Li, Huan Liu, Juan Li, Shuai Guo, Yan Lv.
      BACKGROUND: Hypoxia is a prominent feature of solid cancer. This research aims to expose the role of mitochondrial creatine kinase 1 (CKMT1) in non-small cell lung cancer (NSCLC) progression and hypoxia adaptation.METHODS: The mRNA and protein expression of CKMT1 in NSCLC tissues were detected by using GEPIA web, immunohistochemistry and qRT-PCR. For hypoxia, cells were exposed to the 1% O2 atmosphere. The protein levels of HIF-1α and CKMT1 in H1650 and H1299 cells exposed to hypoxia were determined by western blot. The roles of CKMT1 on the proliferation, invasion and hypoxia adaptation of NSCLC cells were measured by CCK8, colony formation and transwell assays. Luciferase activity assay and HIF1 specific inhibitor (LW6) assay indicated the related function of hypoxia and CKMT1.
    RESULTS: CKMT1 was highly expressed in NSCLC tissues, and the high level of CKMT1 was significantly correlated with the high pathological grade of NSCLC. Knockdown of CKMT1 inhibited the cell proliferation and invasion of H1650 and H1299 cells, which could be rescued by hypoxia. Hypoxia induced the accumulation of HIF-1α and the expression of CKMT1 in H1650 and H1299 cells. Furthermore, HIF-1 as a transcription factor of CKMT1, could up-regulated the expression of CKMT1 under hypoxia.
    CONCLUSIONS: In summary, CKMT1 has the potential as a target for NSCLC hypoxic targeted therapy.
    Keywords:  HIF-1; Hypoxia; Mitochondrial creatine kinase 1; NSCLC; Proliferation
    DOI:  https://doi.org/10.1186/s12931-021-01765-1
  3. Front Oncol. 2021 ;11 656509
    Integrative Multi-Omics Analysis of Identified NUF2 as a Candidate Oncogene Correlates With Poor Prognosis and Immune Infiltration in Non-Small Cell Lung Cancer.
    Mengqing Chen, Shangkun Li, Yuling Liang, Yue Zhang, Dan Luo, Wenjun Wang.
      Background: Lung cancer is one of the most common malignant tumors and the leading causes of cancer-related deaths worldwide. As a component of the nuclear division cycle 80 complex, NUF2 is a part of the conserved protein complex related to the centromere. Although the high expression of NUF2 has been reported in many different types of human cancers, the multi-omics analysis in non-small cell lung cancer (NSCLC) of NUF2 remains to be elucidated.Methods: In this analysis, NUF2 expression difference analysis in non-small cell lung cancer was evaluated by Oncomine, TIMER, GEO, and TCGA database. And the prognosis analysis of NUF2 based on Kaplan-Meier was performed. R language was used to analyze the differential expression genes, functional annotation and protein-protein interaction (PPI). GSEA analysis of differential expression genes was also carried out. Mechanism analysis about exploring the characteristic of NUF2, multi-omics, and correlation analysis was carried out using UALCAN, cBioportal, GEPIA, TIMER, and TISIDB, respectively.
    Results: The expression of NUF2 in NSCLC, both lung adenocarcinoma (LUAD) and squamous lung cancer (LUSC), was significantly higher than that in normal tissues. The analysis of UALCAN database samples proved that NUF2 expression was connected with stage and smoking habits. Meanwhile, the overall survival curve also validated that high expression of NUF2 has a poorer prognosis in NSCLC. GO, KEGG, GSEA, subcellular location from COMPARTMENTS indicated that NUF2 may regulate the cell cycle. Correlation analysis also showed that NUF2 was mainly positively associated with cell cycle and tumor-related genes. NUF2 altered group had a poorer prognosis than unaltered group in NSCLC. Immune infiltration analysis showed that the NUF2 expression mainly have negatively correlation with immune cells and immune subtypes in LUAD and LUSC. Furthermore, quantitative PCR was used to validate the expression difference of NUF2 in LUAD and LUSC.
    Conclusion: Our findings elucidated that NUF2 may play an important role in cell cycle, and significantly associated with tumor-related gene in NSCLC; we consider that NUF2 may be a prognostic biomarkers in NSCLC.
    Keywords:  NUF2; immune infiltration; multi-omics; non-small cell lung cancer; prognosis
    DOI:  https://doi.org/10.3389/fonc.2021.656509
  4. Cells. 2021 Jun 29. pii: 1632. [Epub ahead of print]10(7):
    Silibinin Regulates Tumor Progression and Tumorsphere Formation by Suppressing PD-L1 Expression in Non-Small Cell Lung Cancer (NSCLC) Cells.
    Alexis Rugamba, Dong Young Kang, Nipin Sp, Eun Seong Jo, Jin-Moo Lee, Se Won Bae, Kyoung-Jin Jang.
      Recently, natural compounds have been used globally for cancer treatment studies. Silibinin is a natural compound extracted from Silybum marianum (milk thistle), which has been suggested as an anticancer drug through various studies. Studies on its activity in various cancers are undergoing. This study demonstrated the molecular signaling behind the anticancer activity of silibinin in non-small cell lung cancer (NSCLC). Quantitative real-time polymerase chain reaction and Western blotting analysis were performed for molecular signaling analysis. Wound healing assay, invasion assay, and in vitro angiogenesis were performed for the anticancer activity of silibinin. The results indicated that silibinin inhibited A549, H292, and H460 cell proliferation in a concentration-dependent manner, as confirmed by the induction of G0/G1 cell cycle arrest and apoptosis and the inhibition of tumor angiogenesis, migration, and invasion. This study also assessed the role of silibinin in suppressing tumorsphere formation using the tumorsphere formation assay. By binding to the epidermal growth factor receptor (EGFR), silibinin downregulated phosphorylated EGFR expression, which then inhibited its downstream targets, the JAK2/STAT5 and PI3K/AKT pathways, and thereby reduced matrix metalloproteinase, PD-L1, and vascular endothelial growth factor expression. Binding analysis demonstrated that STAT5 binds to the PD-L1 promoter region in the nucleus and silibinin inhibited the STAT5/PD-L1 complex. Altogether, silibinin could be considered as a candidate for tumor immunotherapy and cancer stem cell-targeted therapy.
    Keywords:  EGFR; JAK2/STAT5b; MMP2; NSCLC; PD-L1; PI3K/AKT; silibinin; tumorsphere
    DOI:  https://doi.org/10.3390/cells10071632
  5. J Cell Mol Med. 2021 Jun 29.
    Ring finger protein 19A is overexpressed in non-small cell lung cancer and mediates p53 ubiquitin-degradation to promote cancer growth.
    Yu Cheng, Yujiao Hu, Huanxi Wang, Zhi Zhao, Xizi Jiang, Yao Zhang, Jiameng Zhang, Yue Tong, Xueshan Qiu.
      The expression pattern, biological functions and the related mechanisms of the ring finger protein 19A (RNF19A) in non-small cell lung cancer (NSCLC) remain poorly understood. This study aimed to explore the role of RNF19A, as well as the underlying potential mechanism, in the development of NSCLC. Here, we found that RNF19A was overexpressed in NSCLC tissues, and RNF19A expression in NSCLC tissue samples was associated with NSCLC carcinogenesis and poor outcome. RNF19A promoted the proliferation of NSCLC cells and inhibited apoptosis. RNF19A reduced p53, p21 and BAX expression and induced Cyclin D1, CDK4, CDK6 and BCL2 expression. The inhibitory effect of RNF19A knockdown on proliferation was partially rescued by p53 silencing. RNF19A interacted with p53, shortened p53 half-life and mediated p53 ubiquitin-degradation. Collectively, we suggest that RNF19A plays a critical oncogenic role in lung carcinogenesis by disrupting the function of p53. RNF19A may serve as a new biomarker and/or target for NSCLC management.
    Keywords:  RNF19A; carcinogenesis; non-small cell lung cancer; p53; ubiquitin
    DOI:  https://doi.org/10.1111/jcmm.16674
  6. Cells. 2021 Jun 10. pii: 1462. [Epub ahead of print]10(6):
    Single-Cell RNA-Seq Reveals Transcriptomic Heterogeneity and Post-Traumatic Osteoarthritis-Associated Early Molecular Changes in Mouse Articular Chondrocytes.
    Aimy Sebastian, Jillian L McCool, Nicholas R Hum, Deepa K Murugesh, Stephen P Wilson, Blaine A Christiansen, Gabriela G Loots.
      Articular cartilage is a connective tissue lining the surfaces of synovial joints. When the cartilage severely wears down, it leads to osteoarthritis (OA), a debilitating disease that affects millions of people globally. The articular cartilage is composed of a dense extracellular matrix (ECM) with a sparse distribution of chondrocytes with varying morphology and potentially different functions. Elucidating the molecular and functional profiles of various chondrocyte subtypes and understanding the interplay between these chondrocyte subtypes and other cell types in the joint will greatly expand our understanding of joint biology and OA pathology. Although recent advances in high-throughput OMICS technologies have enabled molecular-level characterization of tissues and organs at an unprecedented resolution, thorough molecular profiling of articular chondrocytes has not yet been undertaken, which may be in part due to the technical difficulties in isolating chondrocytes from dense cartilage ECM. In this study, we profiled articular cartilage from healthy and injured mouse knee joints at a single-cell resolution and identified nine chondrocyte subtypes with distinct molecular profiles and injury-induced early molecular changes in these chondrocytes. We also compared mouse chondrocyte subpopulations to human chondrocytes and evaluated the extent of molecular similarity between mice and humans. This work expands our view of chondrocyte heterogeneity and rapid molecular changes in chondrocyte populations in response to joint trauma and highlights potential mechanisms that trigger cartilage degeneration.
    Keywords:  PTOA; cartilage; chondrocyte heterogeneity; gene expression; knee injury; osteoarthritis; scRNA-seq
    DOI:  https://doi.org/10.3390/cells10061462
  7. J Pers Med. 2021 Jun 04. pii: 513. [Epub ahead of print]11(6):
    Role of Long Non-Coding RNA Polymorphisms in Cancer Chemotherapeutic Response.
    Zheng Zhang, Meng Gu, Zhongze Gu, Yan-Ru Lou.
      Genetic polymorphisms are defined as the presence of two or more different alleles in the same locus, with a frequency higher than 1% in the population. Since the discovery of long non-coding RNAs (lncRNAs), which refer to a non-coding RNA with a length of more than 200 nucleotides, their biological roles have been increasingly revealed in recent years. They regulate many cellular processes, from pluripotency to cancer. Interestingly, abnormal expression or dysfunction of lncRNAs is closely related to the occurrence of human diseases, including cancer and degenerative neurological diseases. Particularly, their polymorphisms have been found to be associated with altered drug response and/or drug toxicity in cancer treatment. However, molecular mechanisms are not yet fully elucidated, which are expected to be discovered by detailed studies of RNA-protein, RNA-DNA, and RNA-lipid interactions. In conclusion, lncRNAs polymorphisms may become biomarkers for predicting the response to chemotherapy in cancer patients. Here we review and discuss how gene polymorphisms of lncRNAs affect cancer chemotherapeutic response. This knowledge may pave the way to personalized oncology treatments.
    Keywords:  cancer chemotherapy; drug response; drug toxicity; gene polymorphisms; personalized oncology
    DOI:  https://doi.org/10.3390/jpm11060513
  8. Int J Cancer. 2021 Jul 02.
    Exploiting epigenetic dependencies in ovarian cancer therapy.
    Aisling Y Coughlan, Giuseppe Testa.
      Ovarian cancer therapy has remained fundamentally unchanged for 50 years, with surgery and chemotherapy still the frontline treatments. Typically asymptomatic until advanced stages, ovarian cancer is known as 'the silent killer'. Consequently, it has one of the worst 5-year survival rates, as low as 30%. The most frequent driver mutations are found in well-defined tumor suppressors, such as p53 and BRCA1/2. In recent years it has become clear that, like the majority of other cancers, many epigenetic regulators are altered in ovarian cancer, including EZH2, SMARCA2/4 and ARID1A. Disruption of epigenetic regulators often leads to loss of transcriptional control, aberrant cell fate trajectories and disruption of senescence, apoptotic and proliferation pathways. These mitotically-inherited epigenetic alterations are particularly promising targets for therapy as they are largely reversible. Consequently, many drugs targeting chromatin modifiers and other epigenetic regulators are at various stages of clinical trials for other cancers. Understanding the mechanisms by which ovarian cancer-specific epigenetic processes are disrupted in patients can allow for informed targeting of epigenetic pathways tailored for each patient. In recent years, there have been groundbreaking new advances in disease modelling through ovarian cancer organoids; these models, alongside single-cell transcriptomic and epigenomic technologies, allow the elucidation of the epigenetic pathways deregulated in ovarian cancer. As a result, ovarian cancer therapy may finally be ready to advance to next-generation treatments. Here, we review the major developments in ovarian cancer, including genetics, model systems and technologies available for their study and the implications of applying epigenetic therapies to ovarian cancer. This article is protected by copyright. All rights reserved.
    Keywords:  Ovarian cancer; chromatin remodeling; disease modelling; epigenetic drugs; precision oncology
    DOI:  https://doi.org/10.1002/ijc.33727
  9. Front Immunol. 2021 ;12 697412
    Applications of Single-Cell Omics in Tumor Immunology.
    Junwei Liu, Saisi Qu, Tongtong Zhang, Yufei Gao, Hongyu Shi, Kaichen Song, Wei Chen, Weiwei Yin.
      The tumor microenvironment (TME) is an ecosystem that contains various cell types, including cancer cells, immune cells, stromal cells, and many others. In the TME, cancer cells aggressively proliferate, evolve, transmigrate to the circulation system and other organs, and frequently communicate with adjacent immune cells to suppress local tumor immunity. It is essential to delineate this ecosystem's complex cellular compositions and their dynamic intercellular interactions to understand cancer biology and tumor immunology and to benefit tumor immunotherapy. But technically, this is extremely challenging due to the high complexities of the TME. The rapid developments of single-cell techniques provide us powerful means to systemically profile the multiple omics status of the TME at a single-cell resolution, shedding light on the pathogenic mechanisms of cancers and dysfunctions of tumor immunity in an unprecedently resolution. Furthermore, more advanced techniques have been developed to simultaneously characterize multi-omics and even spatial information at the single-cell level, helping us reveal the phenotypes and functionalities of disease-specific cell populations more comprehensively. Meanwhile, the connections between single-cell data and clinical characteristics are also intensively interrogated to achieve better clinical diagnosis and prognosis. In this review, we summarize recent progress in single-cell techniques, discuss their technical advantages, limitations, and applications, particularly in tumor biology and immunology, aiming to promote the research of cancer pathogenesis, clinically relevant cancer diagnosis, prognosis, and immunotherapy design with the help of single-cell techniques.
    Keywords:  TCR (T cell receptor); biomarkers; cancer; immunotherapy; single-cell omics
    DOI:  https://doi.org/10.3389/fimmu.2021.697412
  10. Biomolecules. 2021 Jun 29. pii: 956. [Epub ahead of print]11(7):
    Functional Implications of the Dynamic Regulation of EpCAM during Epithelial-to-Mesenchymal Transition.
    Taylor C Brown, Narendra V Sankpal, William E Gillanders.
      Epithelial cell adhesion molecule (EpCAM) is a transmembrane glycoprotein expressed in epithelial tissues. EpCAM forms intercellular, homophilic adhesions, modulates epithelial junctional protein complex formation, and promotes epithelial tissue homeostasis. EpCAM is a target of molecular therapies and plays a prominent role in tumor biology. In this review, we focus on the dynamic regulation of EpCAM expression during epithelial-to-mesenchymal transition (EMT) and the functional implications of EpCAM expression on the regulation of EMT. EpCAM is frequently and highly expressed in epithelial cancers, while silenced in mesenchymal cancers. During EMT, EpCAM expression is downregulated by extracellular signal-regulated kinases (ERK) and EMT transcription factors, as well as by regulated intramembrane proteolysis (RIP). The functional impact of EpCAM expression on tumor biology is frequently dependent on the cancer type and predominant oncogenic signaling pathways, suggesting that the role of EpCAM in tumor biology and EMT is multifunctional. Membrane EpCAM is cleaved in cancers and its intracellular domain (EpICD) is transported into the nucleus and binds β-catenin, FHL2, and LEF1. This stimulates gene transcription that promotes growth, cancer stem cell properties, and EMT. EpCAM is also regulated by epidermal growth factor receptor (EGFR) signaling and the EpCAM ectoderm (EpEX) is an EGFR ligand that affects EMT. EpCAM is expressed on circulating tumor and cancer stem cells undergoing EMT and modulates metastases and cancer treatment responses. Future research exploring EpCAM's role in EMT may reveal additional therapeutic opportunities.
    Keywords:  cancer stem cells (CSCs); circulating tumor cells (CTCs); epithelial cancers; epithelial cell adhesion molecule (EpCAM); epithelial-to-mesenchymal transition (EMT); metastasis
    DOI:  https://doi.org/10.3390/biom11070956
  11. Stem Cell Rev Rep. 2021 Jun 28.
    Regulation of Chromatin Organization in Cell Stemness: The Emerging Role of Long Non-coding RNAs.
    Hesam Dehghani.
      Chromatin is organized as chromosome territories in the nucleus of an interphase cell. The cell-type- and cell-state-specific organization of chromatin including the location, volume, compaction level, and spatial arrangement of chromosome territories are the major determinants of genome function. In addition, in response to different signaling stimuli and regulatory cues, it is the dynamic adaptation of chromatin structure that establishes and organizes transcriptional programs. It is known that varying levels of stemness are defined by gene regulatory networks. Accordingly, chromatin is the main milieu to host the transcriptional programs and gene regulatory networks responsible for the stemness status of a cell. In this review, our current understanding of the spatial organization of chromatin and the ways by which it defines stemness are discussed. In particular, the role of lncRNAs that regulate and affect chromatin organization and stemness properties are delineated. These roles can be categorized into the topics of specific binding to and epigenetic regulation of the promoter of pluripotency genes, their interaction with transcription factors, coordinating the intra- and inter-chromosomal looping of pluripotency-related genes, and their RNA-independent functions. This review brings together the results of studies that have begun to clarify the emerging roles of lncRNAs in the regulation of chromatin organization adapted for stemness and cancer plasticity.
    Keywords:  Cancer plasticity; Chromatin organization; Genome architecture; Stemness; Transcription; lncRNAs
    DOI:  https://doi.org/10.1007/s12015-021-10209-8
  12. Cancers (Basel). 2021 Jun 27. pii: 3209. [Epub ahead of print]13(13):
    Epigenetics of Most Aggressive Solid Tumors: Pathways, Targets and Treatments.
    Javier Martinez-Useros, Mario Martin-Galan, Maria Florez-Cespedes, Jesus Garcia-Foncillas.
      Highly aggressive tumors are characterized by a highly invasive phenotype, and they display chemoresistance. Furthermore, some of the tumors lack expression of biomarkers for target therapies. This is the case of small-cell lung cancer, triple-negative breast cancer, pancreatic ductal adenocarcinoma, glioblastoma, metastatic melanoma, and advanced ovarian cancer. Unfortunately, these patients show a low survival rate and most of the available drugs are ineffective. In this context, epigenetic modifications have emerged to provide the causes and potential treatments for such types of tumors. Methylation and hydroxymethylation of DNA, and histone modifications, are the most common targets of epigenetic therapy, to influence gene expression without altering the DNA sequence. These modifications could impact both oncogenes and tumor suppressor factors, which influence several molecular pathways such as epithelial-to-mesenchymal transition, WNT/β-catenin, PI3K-mTOR, MAPK, or mismatch repair machinery. However, epigenetic changes are inducible and reversible events that could be influenced by some environmental conditions, such as UV exposure, smoking habit, or diet. Changes in DNA methylation status and/or histone modification, such as acetylation, methylation or phosphorylation, among others, are the most important targets for epigenetic cancer therapy. Therefore, the present review aims to compile the basic information of epigenetic modifications, pathways and factors, and provide a rationale for the research and treatment of highly aggressive tumors with epigenetic drugs.
    Keywords:  acetylation; advanced ovarian cancer; epigenetic; glioblastoma; metastatic melanoma; methylation; non-coding RNA; pancreatic ductal adenocarcinoma; small-cell lung cancer; triple-negative breast cancer
    DOI:  https://doi.org/10.3390/cancers13133209
  13. Int J Mol Sci. 2021 Jun 10. pii: 6262. [Epub ahead of print]22(12):
    Metabolic Reprogramming of Colorectal Cancer Cells and the Microenvironment: Implication for Therapy.
    Miljana Nenkov, Yunxia Ma, Nikolaus Gaßler, Yuan Chen.
      Colorectal carcinoma (CRC) is one of the most frequently diagnosed carcinomas and one of the leading causes of cancer-related death worldwide. Metabolic reprogramming, a hallmark of cancer, is closely related to the initiation and progression of carcinomas, including CRC. Accumulating evidence shows that activation of oncogenic pathways and loss of tumor suppressor genes regulate the metabolic reprogramming that is mainly involved in glycolysis, glutaminolysis, one-carbon metabolism and lipid metabolism. The abnormal metabolic program provides tumor cells with abundant energy, nutrients and redox requirements to support their malignant growth and metastasis, which is accompanied by impaired metabolic flexibility in the tumor microenvironment (TME) and dysbiosis of the gut microbiota. The metabolic crosstalk between the tumor cells, the components of the TME and the intestinal microbiota further facilitates CRC cell proliferation, invasion and metastasis and leads to therapy resistance. Hence, to target the dysregulated tumor metabolism, the TME and the gut microbiota, novel preventive and therapeutic applications are required. In this review, the dysregulation of metabolic programs, molecular pathways, the TME and the intestinal microbiota in CRC is addressed. Possible therapeutic strategies, including metabolic inhibition and immune therapy in CRC, as well as modulation of the aberrant intestinal microbiota, are discussed.
    Keywords:  CRC therapy; colorectal cancer; intestinal microbiota; metabolism; the tumor microenvironment
    DOI:  https://doi.org/10.3390/ijms22126262
  14. Cancers (Basel). 2021 Jun 30. pii: 3287. [Epub ahead of print]13(13):
    The Sex-Related Interplay between TME and Cancer: On the Critical Role of Estrogen, MicroRNAs and Autophagy.
    Paola Matarrese, Gianfranco Mattia, Maria Teresa Pagano, Giada Pontecorvi, Elena Ortona, Walter Malorni, Alessandra Carè.
      The interplay between cancer cells and the tumor microenvironment (TME) has a fundamental role in tumor progression and response to therapy. The plethora of components constituting the TME, such as stroma, fibroblasts, endothelial and immune cells, as well as macromolecules, e.g., hormones and cytokines, and epigenetic factors, such as microRNAs, can modulate the survival or death of cancer cells. Actually, the TME can stimulate the genetically regulated programs that the cell puts in place under stress: apoptosis or, of interest here, autophagy. However, the implication of autophagy in tumor growth appears still undefined. Autophagy mainly represents a cyto-protective mechanism that allows cell survival but, in certain circumstances, also leads to the blocking of cell cycle progression, possibly leading to cell death. Since significant sex/gender differences in the incidence, progression and response to cancer therapy have been widely described in the literature, in this review, we analyzed the roles played by key components of the TME, e.g., estrogen and microRNAs, on autophagy regulation from a sex/gender-based perspective. We focused our attention on four paradigmatic and different forms of cancers-colon cancer, melanoma, lymphoma, and lung cancer-concluding that sex-specific differences may exert a significant impact on TME/cancer interaction and, thus, tumor growth.
    Keywords:  autophagy; cancer; gender; microRNA; sex; sex hormones; tumor microenvironment
    DOI:  https://doi.org/10.3390/cancers13133287
  15. Biomolecules. 2021 Jun 14. pii: 879. [Epub ahead of print]11(6):
    Towards a Better Understanding of the Relationships between Galectin-7, p53 and MMP-9 during Cancer Progression.
    Yves St-Pierre.
      It has been almost 25 years since the discovery of galectin-7. This member of the galectin family has attracted interest from many working in the cancer field given its highly restricted expression profile in epithelial cells and the fact that cancers of epithelial origin (carcinoma) are among the most frequent and deadly cancer subtypes. Initially described as a p53-induced gene and associated with apoptosis, galectin-7 is now recognized as having a protumorigenic role in many cancer types. Several studies have indeed shown that galectin-7 is associated with aggressive behavior of cancer cells and induces expression of MMP-9, a member of the matrix metalloproteinases (MMP) family known to confer invasive behavior to cancer cells. It is therefore not surprising that many studies have examined its relationships with p53 and MMP-9. However, the relationships between galectin-7 and p53 and MMP-9 are not always clear. This is largely because p53 is often mutated in cancer cells and such mutations drastically change its functions and, consequently, its association with galectin-7. In this review, we discuss the functional relationships between galectin-7, p53 and MMP-9 and reconcile some apparently contradictory observations. A better understanding of these relationships will help to develop a working hypothesis and model that will provide the basis for further research in the hope of establishing a new paradigm for tackling the role of galectin-7 in cancer.
    Keywords:  MMP-9; cancer; gain-of-function; galectin-7; p53
    DOI:  https://doi.org/10.3390/biom11060879
  16. J Neurosci. 2021 Jun 29. pii: JN-RM-2059-20. [Epub ahead of print]
    The genome-wide binding profile for human RE1 Silencing Transcription factor unveils a unique genetic circuitry in hippocampus.
    James C McGann, Michael A Spinner, Saurabh K Garg, Karin A Mullendorff, Randall L Woltjer, Gail Mandel.
      Early studies in mouse neurodevelopment led to the discovery of the RE1 Silencing Transcription Factor (REST) and its role as a master repressor of neuronal gene expression. Recently, REST was reported to also repress neuronal genes in the human adult brain. These genes were found to be involved in pro-apoptotic pathways and their repression, associated with increased REST levels during aging, were found to be neuroprotective and conserved across species. However, direct genome-wide REST binding profiles for REST in adult brain have not been identified for any species. Here, we apply this approach to mouse and human hippocampus. We find an expansion of REST binding sites in the human hippocampus that are lacking in both mouse hippocampus and other human non-neuronal cell types. The unique human REST binding sites are associated with genes involved in innate immunity processes and inflammation signaling which, on the basis of histology and recent public transcriptomic analyses, suggest that these new target genes are repressed in glia. We propose that the increases in REST expression in mid-adulthood presage the beginning of brain aging, and that human REST function has evolved to protect the longevity and function of both neurons and glia in human brain.SIGNIFICANCE STATEMENTThe REST repressor has served historically as a model for gene regulation during mouse neurogenesis. Recent studies of REST have also suggested a conserved role for REST repressor function across lower species during aging. However, direct genome-wide studies for REST have been lacking for human brain. Here, we perform the first genome-wide analysis of REST binding in both human and mouse hippocampus. The majority of REST-occupied genes in human hippocampus are distinct from those in mouse. Further, the REST-associated genes unique to human hippocampus represent a new set related to innate immunity and inflammation, where their gene dysregulation has been implicated in aging-related neuropathology such as Alzheimer's disease.
    DOI:  https://doi.org/10.1523/JNEUROSCI.2059-20.2021
  17. Front Oncol. 2021 ;11 652133
    A Key Pathway to Cancer Resilience: The Role of Autophagy in Glioblastomas.
    Elisa Helena Farias Jandrey, Marcelle Bezerra, Lilian Tiemi Inoue, Frank B Furnari, Anamaria Aranha Camargo, Érico Tosoni Costa.
      There are no effective strategies for the successful treatment of glioblastomas (GBM). Current therapeutic modalities effectively target bulk tumor cells but leave behind marginal GBM cells that escape from the surgical margins and radiotherapy field, exhibiting high migratory phenotype and resistance to all available anti-glioma therapies. Drug resistance is mostly driven by tumor cell plasticity: a concept associated with reactivating transcriptional programs in response to adverse and dynamic conditions from the tumor microenvironment. Autophagy, or "self-eating", pathway is an emerging target for cancer therapy and has been regarded as one of the key drivers of cell plasticity in response to energy demanding stress conditions. Many studies shed light on the importance of autophagy as an adaptive mechanism, protecting GBM cells from unfavorable conditions, while others recognize that autophagy can kill those cells by triggering a non-apoptotic cell death program, called 'autophagy cell death' (ACD). In this review, we carefully analyzed literature data and conclude that there is no clear evidence indicating the presence of ACD under pathophysiological settings in GBM disease. It seems to be exclusively induced by excessive (supra-physiological) stress signals, mostly from in vitro cell culture studies. Instead, pre-clinical and clinical data indicate that autophagy is an emblematic example of the 'dark-side' of a rescue pathway that contributes profoundly to a pro-tumoral adaptive response. From a standpoint of treating the real human disease, only combinatorial therapy targeting autophagy with cytotoxic drugs in the adjuvant setting for GBM patients, associated with the development of less toxic and more specific autophagy inhibitors, may inhibit adaptive response and enhance the sensibility of glioma cells to conventional therapies.
    Keywords:  autophagy; cell invasion; drug resistance; glioblastoma; intratumoral heterogeneity (ITH); pro-tumoral
    DOI:  https://doi.org/10.3389/fonc.2021.652133
  18. J Leukoc Biol. 2021 Jun 28.
    Tumor immunology in the age of single-cell genomics.
    Lingyu Zhao, Lili Ren, Shuangshu Gao, Jun Wang, Xiaobo Li, Lei Zhang, Yuanyuan Zhu, Hanjie Li.
      Immunotherapies that were developed based on our understandings of tumor immunology have revolutionized cancer treatment. However, the success of immunotherapy is eclipsed by several grand challenges, including low response rate, intrinsic/acquired resistance and adverse effects. While a deeper understanding of the interaction between tumor and our immune system, especially the tumor immune niche, is essential to overcome those challenges, we are limited by the fact that most of our knowledge about tumor immunology is based on studies analyzing bulk populations of cells, which are often unable to fully characterize the various cell types and states engaged in immune cell functions. The advent of cutting single-cell genomic technologies empowers us to dissect the tumor immune niche in a genome-wide and spatially resolved manner in single cells, trace their clonal histories, and unveil their regulatory circuits. Future studies on tumor immunology in the age of single-cell genomics, therefore, hold the promise to develop more effective and precise immunotherapies for human cancers. In this perspective, we will discuss how advanced single-cell genomics approaches will revolutionize tumor immunology research and immunotherapies by catering the demand in the field of tumor immunology.
    Keywords:  cancer; immunotherapy; oncology; single-cell sequencing
    DOI:  https://doi.org/10.1002/JLB.5MR0321-170R
  19. OMICS. 2021 Jun 30.
    Integrins Within the Tumor Microenvironment: Biological Functions, Importance for Molecular Targeting, and Cancer Therapeutics Innovation.
    Kevin Dzobo.
      Many cellular functions important for solid tumor initiation and progression are mediated by members of the integrin family, a diverse family of cell attachment receptors. With recent studies emphasizing the role of the tumor microenvironment (TME) in tumor initiation and progression, it is not surprising that considerable attention is being paid to integrins. Several integrin antagonists are under clinical trials, with many demonstrating promising activity in patients with different cancers. A deeper knowledge of the functions of integrins within the TME is still required and might lead to better inhibitors being discovered. Integrin expression is commonly dysregulated in many tumors with integrins playing key roles in signaling as well as promotion of tumor cell invasion and migration. Integrins also play a major role in adhesion of circulating tumor cells to new sites and the resulting formation of secondary tumors. Furthermore, integrins have demonstrated the ability to promoting stem cell-like properties in tumor cells as well as drug resistance. Anti-integrin therapies rely heavily on the doses or concentrations used as these determine whether the drugs act as antagonists or as integrin agonists. This expert review offers the latest synthesis in terms of the current knowledge of integrins functions within the TME and as potential molecular targets for cancer therapeutics innovation.
    Keywords:  drug resistance; integrins; metastasis; migration; solid tumors; therapeutic targeting; tumor microenvironment
    DOI:  https://doi.org/10.1089/omi.2021.0069
  20. Nanomedicine. 2021 Jun 24. pii: S1549-9634(21)00065-4. [Epub ahead of print] 102422
    Mitochondrial nanomedicine: Subcellular organelle-specific delivery of molecular medicines.
    Lara Milane, Saket Dolare, Tanjheela Jahan, Mansoor Amiji.
      As mitochondria network together to act as the master sensors and effectors of apoptosis, ATP production, reactive oxygen species management, mitophagy/autophagy, and homeostasis; this organelle is an ideal target for pharmaceutical manipulation. Mitochondrial dysfunction contributes to many diseases, for example, β-amyloid has been shown to interfere with mitochondrial protein import and induce apoptosis in Alzheimer's Disease while some forms of Parkinson's Disease are associated with dysfunctional mitochondrial PINK1 and Parkin proteins. Mitochondrial medicine has applications in the treatment of an array of pathologies from cancer to cardiovascular disease. A challenge of mitochondrial medicine is directing therapies to a sub-cellular target. Nanotechnology based approaches combined with mitochondrial targeting strategies can greatly improve the clinical translation and effectiveness of mitochondrial medicine. This review discusses mitochondrial drug delivery approaches and applications of mitochondrial nanomedicines. Nanomedicine approaches have the potential to drive the success of mitochondrial therapies into the clinic.
    Keywords:  Drug delivery; Mitochondria; Mitochondriotropic; Nanomedicine
    DOI:  https://doi.org/10.1016/j.nano.2021.102422
  21. Int J Mol Sci. 2021 Jun 29. pii: 6987. [Epub ahead of print]22(13):
    Transcriptional Profiling of Cardiac Cells Links Age-Dependent Changes in Acetyl-CoA Signaling to Chromatin Modifications.
    Justin Kurian, Veronica Bohl, Michael Behanan, Sadia Mohsin, Mohsin Khan.
      Metabolism has emerged as a regulator of core stem cell properties such as proliferation, survival, self-renewal, and multilineage potential. Metabolites serve as secondary messengers, fine-tuning signaling pathways in response to microenvironment alterations. Studies show a role for central metabolite acetyl-CoA in the regulation of chromatin state through changes in histone acetylation. Nevertheless, metabolic regulators of chromatin remodeling in cardiac cells in response to increasing biological age remains unknown. Previously, we identified novel cardiac-derived stem-like cells (CTSCs) that exhibit increased functional properties in the neonatal heart (nCTSC). These cells are linked to a unique metabolism which is altered with CTSC aging (aCTSC). Here, we present an in-depth, RNA-sequencing-based (RNA-Seq) bioinformatic with cluster analysis that details a distinct epigenome present in nCTSCs but not in aCTSCs. Gene Ontology (GO) and pathway enrichment reveal biological processes, including metabolism, gene regulation enriched in nCTSCs, and STRING analysis that identifies a network of genes related to acetyl-CoA that can potentially influence chromatin remodeling. Additional validation by Western blot and qRT-PCR shows increased acetyl-CoA signaling and histone acetylation in nCTSCs compared to aCTSCs. In conclusion, our data reveal that the link between metabolism and histone acetylation in cardiac cells is altered with the aging of the cardiac tissue.
    Keywords:  RNA sequencing; acetyl-CoA; bioinformatics; cardiac stem cells; chromatin remodeling; epigenetics; metabolism
    DOI:  https://doi.org/10.3390/ijms22136987
  22. Biology (Basel). 2021 Jun 05. pii: 503. [Epub ahead of print]10(6):
    Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing.
    Aidan S Marshall, Nick S Jones.
      Next-generation sequencing technologies have revolutionised the study of biological systems by enabling the examination of a broad range of tissues. Its application to single-cell genomics has generated a dynamic and evolving field with a vast amount of research highlighting heterogeneity in transcriptional, genetic and epigenomic state between cells. However, compared to these aspects of cellular heterogeneity, relatively little has been gleaned from single-cell datasets regarding cellular mitochondrial heterogeneity. Single-cell sequencing techniques can provide coverage of the mitochondrial genome which allows researchers to probe heteroplasmies at the level of the single cell, and observe interactions with cellular function. In this review, we give an overview of two popular single-cell modalities-single-cell RNA sequencing and single-cell ATAC sequencing-whose throughput and widespread usage offers researchers the chance to probe heteroplasmy combined with cell state in detailed resolution across thousands of cells. After summarising these technologies in the context of mitochondrial research, we give an overview of recent methods which have used these approaches for discovering mitochondrial heterogeneity. We conclude by highlighting current limitations of these approaches and open problems for future consideration.
    Keywords:  heterogeneity; heteroplasmy; mitochondria; scATAC-seq; scRNA-seq
    DOI:  https://doi.org/10.3390/biology10060503
  23. Methods Enzymol. 2021 ;pii: S0076-6879(21)00128-2. [Epub ahead of print]655 225-243
    Computational analysis of alternative polyadenylation from standard RNA-seq and single-cell RNA-seq data.
    Yipeng Gao, Wei Li.
      Alternative polyadenylation (APA) is a major mechanism of post-transcriptional regulation in various cellular processes including cell proliferation and differentiation. Since conventional APA profiling methods have not been widely adopted, global APA studies are very limited. In this chapter, we summarize current computational methods for analyzing APA in standard RNA-seq and scRNA-seq data and describe two state-of-the-art bioinformatic algorithms DaPars and scDaPars in detail. The bioinformatic pipelines for both DaPars and scDaPars are presented and the application of both algorithms are highlighted.
    Keywords:  Alternative polyadenylation; RNA-sequencing; Single-cell RNA-sequencing
    DOI:  https://doi.org/10.1016/bs.mie.2021.03.015
  24. Cancers (Basel). 2021 Jun 29. pii: 3257. [Epub ahead of print]13(13):
    Dying to Survive-The p53 Paradox.
    Andrea Lees, Tamas Sessler, Simon McDade.
      The p53 tumour suppressor is best known for its canonical role as "guardian of the genome", activating cell cycle arrest and DNA repair in response to DNA damage which, if irreparable or sustained, triggers activation of cell death. However, despite an enormous amount of work identifying the breadth of the gene regulatory networks activated directly and indirectly in response to p53 activation, how p53 activation results in different cell fates in response to different stress signals in homeostasis and in response to p53 activating anti-cancer treatments remains relatively poorly understood. This is likely due to the complex interaction between cell death mechanisms in which p53 has been activated, their neighbouring stressed or unstressed cells and the local stromal and immune microenvironment in which they reside. In this review, we evaluate our understanding of the burgeoning number of cell death pathways affected by p53 activation and how these may paradoxically suppress cell death to ensure tissue integrity and organismal survival. We also discuss how these functions may be advantageous to tumours that maintain wild-type p53, the understanding of which may provide novel opportunity to enhance treatment efficacy.
    Keywords:  apoptosis; cell death; p53; targeted therapy
    DOI:  https://doi.org/10.3390/cancers13133257
  25. Cancers (Basel). 2021 Jun 16. pii: 3016. [Epub ahead of print]13(12):
    Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies.
    Cora Palanca-Ballester, Aitor Rodriguez-Casanova, Susana Torres, Silvia Calabuig-Fariñas, Francisco Exposito, Diego Serrano, Esther Redin, Karmele Valencia, Eloisa Jantus-Lewintre, Angel Diaz-Lagares, Luis Montuenga, Juan Sandoval, Alfonso Calvo.
      Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term "liquid biopsy" (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from "bench to bedside".
    Keywords:  DNA methylation; cancer; epigenetic biomarkers; micro-RNAs
    DOI:  https://doi.org/10.3390/cancers13123016
  26. Patterns (N Y). 2021 Jun 11. 2(6): 100257
    Causal interactions from proteomic profiles: Molecular data meet pathway knowledge.
    Özgün Babur, Augustin Luna, Anil Korkut, Funda Durupinar, Metin Can Siper, Ugur Dogrusoz, Alvaro Sebastian Vaca Jacome, Ryan Peckner, Karen E Christianson, Jacob D Jaffe, Paul T Spellman, Joseph E Aslan, Chris Sander, Emek Demir.
      We present a computational method to infer causal mechanisms in cell biology by analyzing changes in high-throughput proteomic profiles on the background of prior knowledge captured in biochemical reaction knowledge bases. The method mimics a biologist's traditional approach of explaining changes in data using prior knowledge but does this at the scale of hundreds of thousands of reactions. This is a specific example of how to automate scientific reasoning processes and illustrates the power of mapping from experimental data to prior knowledge via logic programming. The identified mechanisms can explain how experimental and physiological perturbations, propagating in a network of reactions, affect cellular responses and their phenotypic consequences. Causal pathway analysis is a powerful and flexible discovery tool for a wide range of cellular profiling data types and biological questions. The automated causation inference tool, as well as the source code, are freely available at http://causalpath.org.
    Keywords:  cancer; causal pathway analysis; proteomics
    DOI:  https://doi.org/10.1016/j.patter.2021.100257
  27. Genes Dis. 2021 Jul;8(4): 463-474
    Tumor suppressor p53 cross-talks with TRIM family proteins.
    Juan Liu, Cen Zhang, Xue Wang, Wenwei Hu, Zhaohui Feng.
      p53 is a key tumor suppressor. As a transcription factor, p53 accumulates in cells in response to various stress signals and selectively transcribes its target genes to regulate a wide variety of cellular stress responses to exert its function in tumor suppression. In addition to tumor suppression, p53 is also involved in many other physiological and pathological processes, e.g. anti-infection, immune response, development, reproduction, neurodegeneration and aging. To maintain its proper function, p53 is under tight and delicate regulation through different mechanisms, particularly the posttranslational modifications. The tripartite motif (TRIM) family proteins are a large group of proteins characterized by the RING, B-Box and coiled-coil (RBCC) domains at the N-terminus. TRIM proteins play important roles in regulation of many fundamental biological processes, including cell proliferation and death, DNA repair, transcription, and immune response. Alterations of TRIM proteins have been linked to many diseases including cancer, infectious diseases, developmental disorders, and neurodegeneration. Interestingly, recent studies have revealed that many TRIM proteins are involved in the regulation of p53, and at the same time, many TRIM proteins are also regulated by p53. Here, we review the cross-talk between p53 and TRIM proteins, and its impact upon cellular biological processes as well as cancer and other diseases.
    Keywords:  Cancer; Posttranslational modification; TRIM proteins; Tumor suppressor; Ubiquitination; p53
    DOI:  https://doi.org/10.1016/j.gendis.2020.07.003
  28. Br J Pharmacol. 2021 Jun 29.
    Towards a "druggable" epitranscriptome: Compounds that target RNA modifications in cancer.
    María Berdasco, Manel Esteller.
      Epitranscriptomics is an exciting emerging area that studies biochemical modifications of RNA. The field is boosted by the technical efforts of the last decade to characterize and quantify RNA modifications which have led to a map of post-transcripcional RNA marks in normal cell fate and develoment. However, the scientific interest has been fueled by the discovery of aberrant epitranscriptomes associated with human diseases, mainly cancer. The challenge is now to see whether epitrancriptomics offers a tunable mechanims to be targeted by small- molecule intervention. In this review, we will describe the principal RNA modifications (with a focus on mRNA), summarize the latest scientific evidences of their dysregulation in cancer and provide an overview of the state-of-the-art drug discovery to target the epitranscriptome. Finally, we will discuss the principal challenges in the field of chemical biology and drug development to increase the potential of targeted-RNA for clinical benefit.
    Keywords:  A-to-I-editing; Epitranscriptomics; RNA methylation; pseudouridine; cancer; small-molecule inhibitors; therapy
    DOI:  https://doi.org/10.1111/bph.15604
  29. Front Oncol. 2021 ;11 681377
    Transcription Factors: The Fulcrum Between Cell Development and Carcinogenesis.
    Zeyaul Islam, Ameena Mohamed Ali, Adviti Naik, Mohamed Eldaw, Julie Decock, Prasanna R Kolatkar.
      Higher eukaryotic development is a complex and tightly regulated process, whereby transcription factors (TFs) play a key role in controlling the gene regulatory networks. Dysregulation of these regulatory networks has also been associated with carcinogenesis. Transcription factors are key enablers of cancer stemness, which support the maintenance and function of cancer stem cells that are believed to act as seeds for cancer initiation, progression and metastasis, and treatment resistance. One key area of research is to understand how these factors interact and collaborate to define cellular fate during embryogenesis as well as during tumor development. This review focuses on understanding the role of TFs in cell development and cancer. The molecular mechanisms of cell fate decision are of key importance in efforts towards developing better protocols for directed differentiation of cells in research and medicine. We also discuss the dysregulation of TFs and their role in cancer progression and metastasis, exploring TF networks as direct or indirect targets for therapeutic intervention, as well as specific TFs' potential as biomarkers for predicting and monitoring treatment responses.
    Keywords:  cancer mechanisms; cell fate; clinical relevance; pluripotency; transcription factors; tumorigenesis
    DOI:  https://doi.org/10.3389/fonc.2021.681377
  30. Cell Rep. 2021 Jun 29. pii: S2211-1247(21)00664-1. [Epub ahead of print]35(13): 109293
    Breast tumor stiffness instructs bone metastasis via maintenance of mechanical conditioning.
    Adam W Watson, Adam D Grant, Sara S Parker, Samantha Hill, Michael B Whalen, Jayati Chakrabarti, Michael W Harman, Mackenzie R Roman, Brittany L Forte, Cody C Gowan, Raúl Castro-Portuguez, Lindsey K Stolze, Christian Franck, Darren A Cusanovich, Yana Zavros, Megha Padi, Casey E Romanoski, Ghassan Mouneimne.
      While the immediate and transitory response of breast cancer cells to pathological stiffness in their native microenvironment has been well explored, it remains unclear how stiffness-induced phenotypes are maintained over time after cancer cell dissemination in vivo. Here, we show that fibrotic-like matrix stiffness promotes distinct metastatic phenotypes in cancer cells, which are preserved after transition to softer microenvironments, such as bone marrow. Using differential gene expression analysis of stiffness-responsive breast cancer cells, we establish a multigenic score of mechanical conditioning (MeCo) and find that it is associated with bone metastasis in patients with breast cancer. The maintenance of mechanical conditioning is regulated by RUNX2, an osteogenic transcription factor, established driver of bone metastasis, and mitotic bookmarker that preserves chromatin accessibility at target gene loci. Using genetic and functional approaches, we demonstrate that mechanical conditioning maintenance can be simulated, repressed, or extended, with corresponding changes in bone metastatic potential.
    Keywords:  ATACseq; RUNX2; biomechanics; bone metastasis; breast cancer; matrix stiffness; mechanical memory; osteolysis; phenotypic plasticity; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.celrep.2021.109293
  31. Cancer Res. 2021 Jun 28. pii: canres.0518.2021. [Epub ahead of print]
    Mitochondrial tumor suppressors - the energetic enemies of tumor progression.
    Pavel Jakoube, Valentina Cutano, Juan M Gonzà Lez-Morena, Zuzana Keckesova.
      Tumor suppressors represent a critical line of defense against tumorigenesis. Their mechanisms of action and the pathways they are involved in provide important insights into cancer progression, vulnerabilities, and treatment options. While nuclear and cytosolic tumor suppressors have been extensively investigated, relatively little is known about tumor suppressors localized within the mitochondria. However, recent research has begun to uncover the roles of these important proteins in suppressing tumorigenesis. Here we review this newly developing field and summarize available information on mitochondrial tumor suppressors.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-0518
  32. Front Cell Dev Biol. 2021 ;9 668648
    The MicroRNA Family Gets Wider: The IsomiRs Classification and Role.
    Luisa Tomasello, Rosario Distefano, Giovanni Nigita, Carlo M Croce.
      MicroRNAs (miRNAs or miRs) are the most characterized class of non-coding RNAs and are engaged in many cellular processes, including cell differentiation, development, and homeostasis. MicroRNA dysregulation was observed in several diseases, cancer included. Epitranscriptomics is a branch of epigenomics that embraces all RNA modifications occurring after DNA transcription and RNA synthesis and involving coding and non-coding RNAs. The development of new high-throughput technologies, especially deep RNA sequencing, has facilitated the discovery of miRNA isoforms (named isomiRs) resulting from RNA modifications mediated by enzymes, such as deaminases and exonucleases, and differing from the canonical ones in length, sequence, or both. In this review, we summarize the distinct classes of isomiRs, their regulation and biogenesis, and the active role of these newly discovered molecules in cancer and other diseases.
    Keywords:  isomiRs; microRNA; microRNA biogenesis; novel microRNA in cancer; variants
    DOI:  https://doi.org/10.3389/fcell.2021.668648
  33. Matrix Biol Plus. 2021 Jun;10 100069
    Extracellular matrix gene expression signatures as cell type and cell state identifiers.
    Fabio Sacher, Christian Feregrino, Patrick Tschopp, Collin Y Ewald.
      Transcriptomic signatures based on cellular mRNA expression profiles can be used to categorize cell types and states. Yet whether different functional groups of genes perform better or worse in this process remains largely unexplored. Here we test the core matrisome - that is, all genes coding for structural proteins of the extracellular matrix - for its ability to delineate distinct cell types in embryonic single-cell RNA-sequencing (scRNA-seq) data. We show that even though expressed core matrisome genes correspond to less than 2% of an entire cellular transcriptome, their RNA expression levels suffice to recapitulate essential aspects of cell type-specific clustering. Notably, using scRNA-seq data from the embryonic limb, we demonstrate that core matrisome gene expression outperforms random gene subsets of similar sizes and can match and exceed the predictive power of transcription factors. While transcription factor signatures generally perform better in predicting cell types at early stages of chicken and mouse limb development, i.e., when cells are less differentiated, the information content of the core matrisome signature increases in more differentiated cells. Moreover, using cross-species analyses, we show that these cell type-specific signatures are evolutionarily conserved. Our findings suggest that each cell type produces its own unique extracellular matrix, or matreotype, which becomes progressively more refined and cell type-specific as embryonic tissues mature.
    Keywords:  Cell type; Limb development; Matreotype; Matrisome; scRNA-seq
    DOI:  https://doi.org/10.1016/j.mbplus.2021.100069
  34. Front Oncol. 2021 ;11 690486
    Integrated Analysis of the Transcriptome Profile Reveals the Potential Roles Played by Long Noncoding RNAs in Immunotherapy for Sarcoma.
    Boran Pang, Yongqiang Hao.
      Background: Long-term survival is still low for high-risk patients with soft tissue sarcoma treated with standard management options, including surgery, radiation, and chemotherapy. Immunotherapy is a promising new potential treatment paradigm. However, the application of immune checkpoint inhibitors for the treatment of patients with sarcoma did not yield promising results in a clinical trial. Therefore, there is a considerable need to identify factors that may lead to immune checkpoint inhibitor resistance.Methods: In this study, we performed a bioinformatic analysis of The Cancer Genome Atlas (TCGA) to detect key long noncoding RNAs (lncRNAs) that were correlated with immune checkpoint inhibitory molecules in sarcoma. The expression levels of these lncRNAs and their correlation with patient prognosis were explored. The upstream long noncoding RNAs were also examined via 450K array data from the TCGA. The potential roles of these lncRNAs were further examined via KEGG and GO analysis using DAVID online software. Finally, the relationship between these lncRNAs and immune cell infiltration in tumors and their effect on immune checkpoint inhibitors were further explored.
    Results: We identified lncRNAs correlated with tumor cell immune evasion in sarcoma. The expression of these lncRNAs was upregulated and correlated with worse prognosis in sarcoma and other human cancer types. Moreover, low DNA methylation occupation of these lncRNA loci was detected. Negative correlations between DNA methylation and lncRNA expression were also found in sarcoma and other human cancer types. KEGG and GO analyses indicated that these lncRNAs correlated with immune evasion and negative regulation of the immune response in sarcoma. Finally, high expression of these lncRNAs correlated with more suppressive immune cell infiltration and reduced sensitivity to immune checkpoint inhibitors in sarcoma and other human cancer types.
    Conclusion: Our results suggest that long noncoding RNAs confer immune checkpoint inhibitor resistance in human cancer. Further characterization of these lncRNAs may help to elucidate the mechanisms underlying immune checkpoint inhibitor resistance and uncover a novel therapeutic intervention point for immunotherapy.
    Keywords:  immune checkpoint inhibitor; immunotherapy; long noncoding RNA (lncRNA); resistance; sarcoma
    DOI:  https://doi.org/10.3389/fonc.2021.690486
  35. Biochim Biophys Acta Gene Regul Mech. 2021 Jun 24. pii: S1874-9399(21)00043-2. [Epub ahead of print]1864(8): 194725
    Identifying distinct heterochromatin regions using combinatorial epigenetic probes in live cells.
    Agnes Mendonca, Oscar F Sánchez, Junkai Xie, Ana Carneiro, Li Lin, Chongli Yuan.
      The 3D spatial organization of the genome controls gene expression and cell functionality. Heterochromatin (HC), which is the densely compacted and largely silenced part of the chromatin, is the driver for the formation and maintenance of nuclear organization in the mammalian nucleus. It is functionally divided into highly compact constitutive heterochromatin (cHC) and transcriptionally poised facultative heterochromatin (fHC). Long regarded as a static structure, the highly dynamic nature of the heterochromatin is being slowly understood and studied. These changes in HC occur on various temporal scales during the cell cycle and differentiation processes. Most methods that capture information about the heterochromatin are static techniques that cannot provide a readout of how the HC organization evolves with time. The delineation of specific areas such as fHC are also rendered difficult due to its diffusive nature and lack of specific features. Another degree of complexity in characterizing changes in heterochromatin occurs due to the heterogeneity in the HC organization of individual cells, necessitating single cell studies. Overall, there is a need for live cell compatible tools that can stably track the heterochromatin as it undergoes re-organization. In this work, we present an approach to track cHC and fHC based on the epigenetic hallmarks associated with them. Unlike conventional immunostaining approaches, we use small recombinant protein probes that allow us to dynamically monitor the HC by binding to modifications specific to the cHC and fHC, such as H3K9me3, DNA methylation and H3K27me3. We demonstrate the use of the probes to follow the changes in HC induced by drug perturbations at the single cell level. We also use the probe sets combinatorically to simultaneously track chromatin regions enriched in two selected epigenetic modifications using a FRET based approach that enabled us tracking distinctive chromatin features in situ.
    Keywords:  DNA methylation; Heterochromatin; Histone methylation
    DOI:  https://doi.org/10.1016/j.bbagrm.2021.194725
  36. Cancer Cell Int. 2021 Jun 30. 21(1): 328
    Epigenetic roles of PIWI proteins and piRNAs in colorectal cancer.
    Fatemeh Sadoughi, Seyyed Mehdi Mirhashemi, Zatollah Asemi.
      Small non-coding RNAs (sncRNAs) are a subgroup of non-coding RNAs, with less than 200 nucleotides length and no potential for coding proteins. PiRNAs, a member of sncRNAs, were first discovered more than a decade ago and have attracted researcher's attention because of their gene regulatory function both in the nucleus and in the cytoplasm. Recent investigations have found that the abnormal expression of these sncRNAs is involved in many human diseases, including cancers. Colorectal cancer (CRC), as a common gastrointestinal malignancy, is one of the important causes of cancer-related deaths through the entire world and appears to be a consequence of mutation in the genome and epigenetic alterations. The aim of this review is to realize whether there is a relationship between CRC and piRNAs or not.
    Keywords:  Colorectal cancer; Epigenetic; PIWI protein; PiRNA
    DOI:  https://doi.org/10.1186/s12935-021-02034-3
  37. Cancers (Basel). 2021 Jun 20. pii: 3069. [Epub ahead of print]13(12):
    New Insights into the Clinical Implications of Yes-Associated Protein in Lung Cancer: Roles in Drug Resistance, Tumor Immunity, Autophagy, and Organoid Development.
    Geon Yoo, Dongil Park, Yoonjoo Kim, Chaeuk Chung.
      Despite significant innovations in lung cancer treatment, such as targeted therapy and immunotherapy, lung cancer is still the principal cause of cancer-associated death. Novel strategies to overcome drug resistance and inhibit metastasis in cancer are urgently needed. The Hippo pathway and its effector, Yes-associated protein (YAP), play crucial roles in lung development and alveolar differentiation. YAP is known to mediate mechanotransduction, an important process in lung homeostasis and fibrosis. In lung cancer, YAP promotes metastasis and confers resistance against chemotherapeutic drugs and targeted agents. Recent studies revealed that YAP directly controls the expression of programmed death-ligand 1 (PD-L1) and modulates the tumor microenvironment (TME). YAP not only has a profound relationship with autophagy in lung cancer but also controls alveolar differentiation, and is responsible for tubular structure formation in lung organoids. In this review, we discuss the various roles and clinical implications of YAP in lung cancer and propose that targeting YAP can be a promising strategy for treating lung cancer.
    Keywords:  EGFR-TKI; Hippo pathway; PD-L1; TAZ; YAP; autophagy; drug-resistance; lung cancer; organoid
    DOI:  https://doi.org/10.3390/cancers13123069
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