bims-ectoca Biomed News
on Epigenetic control of tolerance in cancer
Issue of 2024–12–22
thirteen papers selected by
Ankita Daiya, OneCell Diagnostics Inc.



  1. Biochim Biophys Acta Rev Cancer. 2024 Dec 13. pii: S0304-419X(24)00176-8. [Epub ahead of print]1880(1): 189245
      Cells are compartmentalized into different organelles to ensure precise spatial temporal control and efficient operation of cellular processes. Membraneless organelles, also known as biomolecular condensates, are emerging as previously underappreciated ways of organizing cellular functions. Condensates allow local concentration of protein, RNA, or DNA molecules with shared functions, thus facilitating spatiotemporal control of biochemical reactions spanning a range of cellular processes. Studies discussed herein have shown that aberrant formation of condensates is associated with various diseases such as cancers. Here, we summarize how condensates mechanistically contribute to malignancy-related cellular processes, including genomic instability, epigenetic rewiring, oncogenic transcriptional activation, and signaling. An improved understanding of condensate formation and dissolution will enable development of new cancer therapies. Finally, we address the remaining challenges in the field and suggest future efforts to better integrate condensates into cancer research.
    Keywords:  Biomolecular condensates; Cancer; Cell biology; Phase separation; Signaling
    DOI:  https://doi.org/10.1016/j.bbcan.2024.189245
  2. Sci Adv. 2024 Dec 20. 10(51): eadr5947
      The nucleus is at the nexus of mechanotransduction and the final barrier for most first line chemotherapeutics. Here, we study the intersection between nuclear-cytoskeletal coupling and chemotherapy nuclear internalization. We find that chronic and acute modulation of intracellular filaments changes nuclear influx of doxorubicin (DOX). Rapid changes in cell strain by disruption of cytoskeletal and nuclear filaments sensitize nuclei to DOX, whereas chronic reduction of cell strain desensitize nuclei to DOX. Extracted nuclei from invasive cancer cells lines from different tissues have distinct nuclear permeability to DOX. Last, we show that mechano-priming of cells by paclitaxel markedly improves DOX nuclear internalization, rationalizing the observed drug synergies. Our findings reveal that nuclear uptake is a critical, previously unquantified aspect of drug resistance. With nuclear permeability to chemotherapy being tunable via modulation of nuclear mechanotransduction, mechano-priming may be useful to help overcome drug resistance in the future.
    DOI:  https://doi.org/10.1126/sciadv.adr5947
  3. Cancers (Basel). 2024 Dec 02. pii: 4041. [Epub ahead of print]16(23):
      Background/Objectives: Advances in treatment options have barely improved the prognosis of ovarian carcinoma (OC) in recent decades. The inherent heterogeneity of OC underlies challenges in treatment (development) and patient stratification. One hurdle for effective drug development is the lack of patient-representative disease models available for preclinical drug research. Based on quantitative measurement of signal transduction pathway (STP) activity in cell lines, we aimed to identify cell line models that better mirror the different clinical subtypes of OC. Methods: The activity of seven oncogenic STPs (signal transduction pathways) was determined by previously described STP technology using transcriptome data from untreated OC cell lines available in the GEO database. Hierarchal clustering of cell lines was performed based on STP profiles. Associations between cell line histology (original tumor), cluster, and STP profiles were analyzed. Subsequently, STP profiles of clinical OC tissue samples were matched with OC cell lines. Results: Cell line search resulted in 80 cell line transcriptome data from 23 GEO datasets, with 51 unique cell lines. These cell lines were derived from eight different histological OC subtypes (as determined for the primary tumor). Clustering revealed seven clusters with unique STP profiles. When borderline tumors (n = 6), high-grade serous (n = 51) and low-grade (n = 31) OC were matched with cell lines, twelve different cell lines were identified as potentially patient-representative OC cell line models. Conclusions: Based on STP activity, we identified twelve different cell lines that were the most representative of the common subtypes of OC. These findings are important to improve drug development for OC.
    Keywords:  cell line; cluster analysis; drug development; ovarian cancer; ovarian carcinoma; signal transduction pathway
    DOI:  https://doi.org/10.3390/cancers16234041
  4. Transl Cancer Res. 2024 Nov 30. 13(11): 6540-6549
      Non-small cell lung cancer (NSCLC) represents over 80% of lung cancer cases and has a high mortality worldwide, however, targeting common epidermal growth-factor receptor (EGFR) alterations (i.e., del19, L858R) has provided a paradigm shift in the treatment of NSCLC. Uncommon EGFR mutations, however, show variable efficacy to EGFR-targeted drugs depending on the molecular alterations within exons 18-21 which underlying biological mechanism are far from being clear. The substitution mutations of G719X in exon 18, L861Q in exon 21, S768I in exon 20, and exon 20 insertions are the most frequent mutations among the uncommon mutations. The development of fourth-generation EGFR-tyrosine kinase inhibitor (TKIs) has gained increased interest as these drugs are able to inhibit resistance mutations (e.g., C797S) often detected in NSCLC patients' resistance to third-generation EGFR TKIs. BDTX-1535 is an orally bioavailable, brain-penetrating, mutation-selective, irreversible EGFR inhibitor with significant antitumour activity in NSCLCs and glioblastomas (phase I/II trials ongoing). It is a fourth-generation EGFR inhibitor that was found to overcome resistance to osimertinib in preclinical models and has shown promising activity in NSCLC patients harbouring C797S mutations. In experimental models BDTX-1535 was found to inhibit all common EGFR mutations and more than 50 of uncommon mutations including T790M, C797S, L718X, E709X, S784F, V834L and A289V, however, exon 20 insertions are inhibited to a much lesser extent. In addition, mutations in the extracellular domain of the EGF receptor (e.g., EGFRvII, III, IV) can be blocked as well. It should be noted that in up to 50% of all NSCLC patients who progress following osimertinib or other EGFR TKI therapy no underlying resistance mechanism can be identified suggesting that non-mutational signal transduction pathways may also be operative, and intratumoural heterogeneity has been found to be a major contributor to resistance and it consists of three main mechanisms: (I) drug-tolerant persister (DTP) cells, (II) chromosomal instability, and (III) extrachromosomal extracellular DNA (ecDNA) (seen in over 50% of NSCLCs) suggesting that novel EGFR TKIs will include many challenges in sufficiently targeting on-target resistance mechanisms. The development of novel drugs that can overcome TKI resistance in NSCLC patients harbouring the C797S mutation and beyond is, therefore, eagerly warranted.
    Keywords:  C797S; Non-small cell lung cancer (NSCLC); driver mutations; novel drugs; resistance mechanisms
    DOI:  https://doi.org/10.21037/tcr-24-690
  5. bioRxiv. 2024 Dec 04. pii: 2024.12.04.626780. [Epub ahead of print]
      KDM5 family proteins are best known for their demethylation of the promoter proximal chromatin mark H3K4me3. KDM5-regulated transcription is critical in the brain, with variants in the X-linked paralog KDM5C causing the intellectual disability (ID) disorder Claes-Jensen syndrome. Although the demethylase activity of KDM5C is known to be important for neuronal function, the contribution of non-enzymatic activities remain less characterized. We therefore used Drosophila to model the ID variant Kdm5 L854F , which disrupts a C5HC2 zinc finger adjacent to the enzymatic JmjC domain. Kdm5 L854F causes similar transcriptional changes in the brain to a demethylase dead strain, Kdm5 J1310C * , despite having little effect on enzymatic activity. KDM5 L854F is also distinct from KDM5 J1310C * in its reduced interactions with insulator proteins and enhancement of position effect variegation. Instead, the common transcriptional deficits likely result from both the JmjC and C5HC2 domains driving proper genomic organization through their activity in promoting proper loop architecture.
    DOI:  https://doi.org/10.1101/2024.12.04.626780
  6. Biochimie. 2024 Dec 13. pii: S0300-9084(24)00299-2. [Epub ahead of print]
      Pancreatic ductal adenocarcinoma (PDAC) remains as one of the most lethal malignancies. c-MET is an important oncogenic kinase involved in PDAC progression. We determined the anticancer effect of c-MET inhibitors, crizotinib and cabozantinib, combined with chemotherapeutic agents, doxorubicin, oxaliplatin and gemcitabine, against different PDAC and a lung adenocarcinoma cell line expressing different levels of c-MET. MTT assay was performed to assess cell growth inhibition. Synergistic combinations were evaluated in spheroid cultures, while apoptosis was determined through Hoechst33258 staining. The effect of drug combinations on cell cycle and apoptosis induction was examined by RNase/PI flow cytometric assay. We also evaluated reactive oxygen species (ROS) levels using 2',7'-dichlorofluorescein-diacetate (DCFH-DA) assay to explore the possible mechanisms contributing to synergism. Combination of crizotinib or cabozantinib with doxorubicin exhibited synergistic effects in c-MET overexpressing cells. Conversely, combinations of c-MET inhibitors with other agents were additive or even antagonistic. Combination index (CI) values calculated with Calcusyn software were 0.631-0.730 for crizotinib and 0.542-0.746 for cabozantinib co-administrations. Synergistic combinations showed significant spheroid growth inhibition and apoptosis induction in Suit-2, c-MET dependent PDAC cells. These combinations also significantly increased the number of cells in both apoptotic sub-G1 phase and the G2/M phase compared to single-drug treatment. Increased ROS production seemed to be a possible mechanism underlying synergism. In conclusion, c-MET inhibitors synergize with DNA damaging agent, doxorubicin, in cancer cells with c-MET overexpression, indicating that these combination therapies may be a promising cancer therapeutic strategy.
    Keywords:  Combination therapy; DNA damaging agents; free radicals; kinase inhibitors; targeted therapy
    DOI:  https://doi.org/10.1016/j.biochi.2024.12.006
  7. Genome Med. 2024 Dec 18. 16(1): 145
       BACKGROUND: The introduction of poly(ADP-ribose) polymerase (PARP) inhibitors represented a paradigm shift in the treatment of ovarian cancer. Genomic data from patients with high-grade ovarian cancer in six phase II/III trials involving the PARP inhibitor olaparib were analyzed to better understand patterns and potential causes of genomic instability.
    PATIENTS AND METHODS: Homologous recombination deficiency (HRD) was assessed in 2147 tumor samples from SOLO1, PAOLA-1, Study 19, SOLO2, OPINION, and LIGHT using next-generation sequencing technology. Genomic instability scores (GIS) were assessed in BRCA1 and/or BRCA2 (BRCA)-mutated (BRCAm), non-BRCA homologous recombination repair-mutated (non-BRCA HRRm), and non-HRRm tumors.
    RESULTS: BRCAm was identified in 1021/2147 (47.6%) tumors. BRCAm tumors had significantly higher GIS than non-BRCAm tumors (P < 0.001) and high biallelic loss (815/838; 97.3%) regardless of germline (658/672; 97.9%) or somatic (101/108; 93.5%) BRCAm status. In non-BRCA HRRm tumors (n = 121) a similar proportion were HRD-positive (GIS ≥ 42: 55/121; 45.5%) relative to HRD-negative (GIS < 42: 52/121; 43.0%). GIS was highly variable in non-BRCA HRRm (median 42 [interquartile range (IQR) 29-58]) and non-HRRm (n = 1005; median 32 [IQR 20-55]) tumors. Gene mutations with high GIS included HRR genes BRIP1 (median 46 [IQR 41-58]), RAD51C (median 58 [IQR 48-66]), RAD51D (median 62 [IQR 54-69]), and PALB2 (median 64 [IQR 58-74]), and non-HRR genes NF1 (median 49 [IQR 25-60]) and RB1 (median 55 [IQR 30-71]). CCNE1-amplified and PIK3CA-mutated tumors had low GIS (CCNE1-amplified: median 24 [IQR 18-29]; PIK3CA-mutated: median 32 [IQR 14-52]) and were predominantly non-BRCAm.
    CONCLUSIONS: These analyses provide valuable insight into patterns of genomic instability and potential drivers of HRD, besides BRCAm, in ovarian cancer and will help guide future research into the potential clinical effectiveness of anti-cancer treatments in ovarian cancer, including PARP inhibitors as well as other precision oncology agents.
    TRIAL REGISTRATION: The SOLO1 trial was registered at ClinicalTrials.gov (NCT01844986) on April 30, 2013; the PAOLA-1 trial was registered at ClinicalTrials.gov (NCT02477644) on June 18, 2015 (retrospectively registered); Study 19 was registered at ClinicalTrials.gov (NCT00753545) on September 12, 2008 (retrospectively registered); the SOLO2 trial was registered at ClinicalTrials.gov (NCT01874353) on June 7, 2013; the OPINION trial was registered at ClinicalTrials.gov (NCT03402841) on January 3, 2018; the LIGHT trial was registered at ClinicalTrials.gov (NCT02983799) on November 4, 2016.
    Keywords:  Genomic instability; Olaparib; Ovarian cancer; Translational research
    DOI:  https://doi.org/10.1186/s13073-024-01413-5
  8. Cell Death Dis. 2024 Dec 18. 15(12): 912
      The fusion event between EML4 and ALK drives a significant oncogenic activity in 5% of non-small cell lung cancer (NSCLC). Even though potent ALK-tyrosine kinase inhibitors (ALK-TKIs) are successfully used for the treatment of EML4-ALK-positive NSCLC patients, a subset of those patients eventually acquire resistance during their therapy. Here, we investigate the kinase responses in EML4-ALK V1 and V3-harbouring NSCLC cancer cells after acute inhibition with ALK TKI, lorlatinib (LOR). Using phosphopeptide chip array and upstream kinase prediction analysis, we identified a group of phosphorylated tyrosine peptides including ERBB and AKT proteins that are upregulated upon ALK-TKI treatment in EML4-ALK-positive NSCLC cell lines. Dual inhibition of ALK and ERBB receptors or AKT disrupts RAS/MAPK and AKT/PI3K signalling pathways, and enhances apoptosis in EML4-ALK + NSCLC cancer cells. Heregulin, an ERBB3 ligand, differentially modulates the sensitivity of EML4-ALK cell lines to ALK inhibitors. We found that EML4-ALK cells made resistant to LOR are sensitive to inhibition of ERBB and AKT. These findings emphasize the important roles of AKT and ERBB3 to regulate signalling after acute LOR treatment, identifying them as potential targets that may be beneficial to prevent adaptive resistance to EML4-ALK-targeted therapies in NSCLC.
    DOI:  https://doi.org/10.1038/s41419-024-07272-7
  9. J Nanobiotechnology. 2024 Dec 16. 22(1): 753
       BACKGROUND: Immunotherapy for colorectal cancer (CRC) with microsatellite stability (MSS) and mismatch repair proficiency (pMMR) has shown limited success in clinical trials. The combination of immunomodulators and immune checkpoint inhibitors (ICIs) is a potential strategy for treating CRC.
    METHODS: Histone deacetylase (HDAC) and indoleamine 2,3-dioxygenase 1 (IDO1) expression in CRC tissues and adjacent normal tissues was analyzed via database analysis, immunohistochemistry, and western blotting. A nanodrug designated as NP-I/P was subsequently formulated, encapsulating an IDO1 inhibitor (IDO1i; namely, epacadostat) and an immunomodulatory HDAC inhibitor (HDACi; namely, panobinostat). The antitumor efficacy of the nanoparticles and their effects on tumor microenvironment features were evaluated via in vitro and in vivo experiments.
    RESULTS: In the present study, we found that HDAC overexpression and IDO1 expression were attenuated in MSS/pMMR CRC. Thus, a nanodrug designated as NP-I/P was formulated to encapsulate epacadostat and panobinostat. In vitro, NP-I/P treatment promoted the apoptosis of tumor cells and induced the release of damage-associated molecular patterns, thereby leading to cell death-associated immune activation. The in vivo results revealed that NP-I/P treatment reversed the immunosuppressive phenotype of the microenvironment by inducing tumor immunogenic cell death (ICD), promoting CD8+ T cell infiltration, and reducing the numbers of Tregs, tumor-associated macrophages, and myeloid-derived suppressor cells. Finally, the results of the patient-derived xenograft and patient-derived organoid models demonstrated that NP-I/P treatment triggered tumor cell death and modulated the immune microenvironment in human CRC.
    CONCLUSION: The combination of IDO1 and HDAC inhibitors represents a promising strategy for CRC treatment, and NP-I/P is a candidate for clinical trials.
    Keywords:  Colorectal cancer; HDAC; IDO1; Microsatellite stability; Tumor microenvironment
    DOI:  https://doi.org/10.1186/s12951-024-02936-0
  10. Hum Immunol. 2024 Dec 18. pii: S0198-8859(24)00484-1. [Epub ahead of print]86(1): 111221
      RNA interference (RNAi) is a primordial biological process that protects against external intrusion. SiRNA has the potential to selectively silence disease-related genes in a sequence-specific way, thus offering a promising therapeutic approach. The efficacy of siRNA-based therapies in cancer treatment has gained significant recognition due to multiple studies demonstrating its ability to effectively suppress cancer cells' growth and multiplication. Moreover, siRNA-based medicines have shown considerable promise in enhancing the sensitivity of cancer cells to chemotherapy and other treatment methods by suppressing genes that play a role in the development of drug resistance. Exploring and identifying functional genes linked to cancer cell characteristics and drug resistance is crucial for developing effective siRNAs for cancer treatment and advancing targeted and personalized therapeutics. Targeting and silencing genes in charge of resistance mechanisms, such as those involved in drug efflux, cell survival, or DNA repair, is possible with siRNA therapy in the context of drug resistance, especially cancer. Through inhibiting these genes, siRNA therapy can prevent resistance and restore the efficacy of traditional medications. This review addresses the potential of siRNAs in addressing drug resistance in human tumours, opening up new possibilities in cancer therapy. This review article offers a non-systematic summary of how different siRNA types contribute to cancer cells' treatment resistance. Using pertinent keywords, sources were chosen from reliable databases, including PubMed, Scopus, and Google Scholar. The review covered essential papers in this area and those that mainly addressed the function of siRNA in drug resistance. The articles examined in connection with the title of this review were primarily published from 2020 onward and are based on in vitro studies. Furthermore, this article examines the potential barriers and prospective perspectives of siRNA therapies.
    Keywords:  Cancer; Drug resistance; Molecular immunology; siRNA
    DOI:  https://doi.org/10.1016/j.humimm.2024.111221
  11. Can J Urol. 2024 Dec;31(6): 12060-12071
       INTRODUCTION: It is unclear whether laterality has prognostic implications for patients with renal cell carcinoma (RCC). Some suggest that left sided tumors may have worse survival outcomes. The purpose of this study is to associate tumor characteristics and clinical outcomes with laterality in patients with RCC.
    MATERIALS AND METHODS: Patients with RCC were identified in the National Cancer Database between 2004-2020. Patients were categorized as having either localized, regional or metastatic disease. Time-series charts were generated to demonstrate laterality differences and variance over time. Multivariable Cox proportional hazards regression was utilized to associate laterality with overall survival, stratified by clinical stage. Kaplan-Meier estimates were utilized to visualize survival functions.
    RESULTS: A total of 306,196 patients were included, 156,450 (51.1%) had right sided tumors and 283,282 (92.5%) had localized RCC. Localized tumors were more likely to be right sided (0.51 [95% CI 0.50-0.52], p < 0.001). Metastatic and regional tumors (cN+M0) were more likely to be left sided (0.48 [0.47-0.49], p < 0.001; and 0.43 [0.41-0.45], p < 0.001; respectively). For localized disease, smaller tumors were more likely to be right sided (< 2 cm: 0.52 [0.51-0.52], p < 0.001), while tumors > 7cm showed no significant site association (0.49 [0.49-0.50], p = 0.07). When stratified by staging, there were no significant associations between laterality and OS (localized RCC: HR 1.01 [0.99-1.02], p = 0.50; metastatic RCC: 1.03 [1.00-1.07], p = 0.7; cN+M0 RCC: 0.96 [0.86-1.07], p = 0.50).
    CONCLUSIONS: Left-sided RCC tumors are associated with larger tumor size and a higher propensity for regional nodal involvement and distant metastases. However, they do not demonstrate more aggressive behavior leading to meaningful survival differences.
    Keywords:  renal cell carcinoma; tumor laterality
  12. Med. 2024 Dec 13. pii: S2666-6340(24)00415-X. [Epub ahead of print]5(12): 1463-1465
      Precision oncology aims to match the right drug(s) to the right patient. Equally important is ensuring that precision therapies are offered at the right time. Transformative, rather than incremental, outcome improvement may require treatment at diagnosis rather than in the advanced/metastatic setting after genomic evolution.
    DOI:  https://doi.org/10.1016/j.medj.2024.10.017
  13. Hematol Oncol Clin North Am. 2024 Dec 17. pii: S0889-8588(24)00148-5. [Epub ahead of print]
      Gene expression signatures (GES) are a powerful tool in oncology used for classification, prognostication, and therapeutic response prediction of malignancies. In this article, we review the disease site guidelines by the National Comprehensive Cancer Network that use GES for treatment planning and clinical use. We identified 4 cancer types for which treatment decisions are frequently influenced by GES. Future developments in the field of GES are likely to include expanded data sources to personalize radiation therapy dosing and predict response to immunotherapy. Ongoing challenges in GES may be addressed to ensure that all patients with cancer benefit from precision oncology.
    Keywords:  Biomarker; Gene expression signature; Genomics; Multiomics; Predictive modeling; Therapeutic response prediction
    DOI:  https://doi.org/10.1016/j.hoc.2024.11.003