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Circadian rhythm is ubiquitous in nature. Circadian clock genes such as Bmal1 and Clock form a multi-level transcription-translation feedback network, and regulate a variety of physiological and pathological processes, including bone and cartilage metabolism. Deletion of the core clock gene Bmal1 leads to pathological bone alterations, while the phenotypes are not consistent. Studies have shown that multiple signaling pathways are involved in the process of Bmal1 regulating bone and cartilage metabolism, but the exact regulatory mechanisms remain unclear. This paper reviews the signaling pathways by which Bmal1 regulates bone/cartilage metabolism, the upstream regulatory factors that control Bmal1, and the current Bmal1 knockout mouse models for research. We hope to provide new insights for the prevention and treatment of bone/cartilage diseases related to circadian rhythms. [ABSTRACT FROM AUTHOR]

Many human diseases are the result of early developmental defects. As most paediatric diseases and disorders are rare, children are critically underrepresented in research. Functional genomics studies primarily rely on adult tissues and lack critical cell states in specific developmental windows. In parallel, little is known about the conservation of developmental programmes across non-human primate (NHP) species, with implications for human evolution. Here we introduce the developmental Genotype-Tissue Expression (dGTEx) projects, which span humans and NHPs and aim to integrate gene expression, regulation and genetics data across development and species. The dGTEx cohort will consist of 74 tissue sites across 120 human donors from birth to adulthood, and developmentally matched NHP age groups, with additional prenatal and adult animals, with 126 rhesus macaques (Macaca mulatta) and 72 common marmosets (Callithrix jacchus). The data will comprise whole-genome sequencing, extensive bulk, single-cell and spatial gene expression profiles, and chromatin accessibility data across tissues and development. Through community engagement and donor diversity, the human dGTEx study seeks to address disparities in genomic research. Thus, dGTEx will provide a reference human and NHP dataset and tissue bank, enabling research into developmental changes in expression and gene regulation, childhood disorders and the effect of genetic variation on development.The developmental Genotype-Tissue Expression (dGTEx) projects will catalogue and integrate gene expression, regulation and genetics data across 120 human donors from birth to adulthood with developmentally matched non-human primates, including 126 rhesus macaques and 72 common marmosets. [ABSTRACT FROM AUTHOR]

Cancer remains a leading cause of mortality globally and a major health burden, with chemotherapy often serving as the primary therapeutic option for patients with advanced-stage disease, partially compensating for the limitations of non-curative treatments. However, the emergence of chemotherapy resistance significantly limits its efficacy, posing a major clinical challenge. Moreover, heterogeneity of resistance mechanisms across cancer types complicates the development of universally effective diagnostic and therapeutic approaches. Understanding the molecular mechanisms of chemoresistance and identifying strategies to overcome it are current research focal points. This review provides a comprehensive analysis of the key molecular mechanisms underlying chemotherapy resistance, including drug efflux, enhanced DNA damage repair (DDR), apoptosis evasion, epigenetic modifications, altered intracellular drug metabolism, and the role of cancer stem cells (CSCs). We also examine specific causes of resistance in major cancer types and highlight various molecular targets involved in resistance. Finally, we discuss current strategies aiming at overcoming chemotherapy resistance, such as combination therapies, targeted treatments, and novel drug delivery systems, while proposing future directions for research in this evolving field. By addressing these molecular barriers, this review lays a foundation for the development of more effective cancer therapies aimed at mitigating chemotherapy resistance. [ABSTRACT FROM AUTHOR]

Breast cancer is one of cancer's most deadly varieties. Its variability makes the development of personalized therapies very difficult. Therefore, improvement of classic chemotherapy is still one of the important challenges of cancer research. We addressed this issue applying nanotechnology to verify the influence of silver nanoparticles (AgNPs) on doxorubicin (DOX) anticancer activity and assess if the size of AgNPs affects their interactions with DOX. We employed a broad spectrum of biophysical methods, characterizing 5 and 50 nm AgNPs interactions with DOX using UV–Vis spectroscopy, dynamic light scattering, fluorescence spectroscopy, and atomic force microscopy imaging. Biological effects of observed AgNPs-DOX interactions were assessed utilizing MTT and 3D Matrigel assays on SKBR3 and MDA-MB-231 breast cancer cell lines. Obtained results indicate direct interactions between AgNPs and DOX. Furthermore, AgNPs size influences their interactions with DOX, as evidenced by differences in the heteroaggregates formation observed in biophysical experiments and further supported by in vitro biological assays. We detected reduction of tumor cell viability and/or colony sizes of the analyzed cancer cell lines, registering differences linked to the observed phenomenon. However, the effects may be limited to the outer borders of the tumor microenvironment as evidenced by the 3D model. Summing up, we observed diverse patterns of interactions and biological effects for different sizes of AgNPs with DOX providing insight how the nanoparticles' size affects their interactions with other biologically active compounds. Moreover, obtained data can be further used in experiments on the reduction of tumor size i.e. before the surgical intervention. [ABSTRACT FROM AUTHOR]

Despite ongoing advances in cancer therapy, the results for the treatment of breast cancer are not satisfactory. The advent of nanotechnology promises to be an essential tool to improve drug delivery effectiveness in cancer therapy. Nanotechnology provides an opportunity to enhance the treatment modality by preventing degradation, improving tumour targeting, and controlling drug release. Recent advances have revealed several strategies to prevent cancer metastasis using nano-drug delivery systems (NDDS). These strategies include the design of appropriate nanocarriers loaded with anti-cancer drugs that target the optimization of physicochemical properties, modulate the tumour microenvironment, and target biomimetic techniques. Nanocarriers have emerged as a preferential approach in the chemotropic treatment for breast cancer due to their pivotal role in safeguarding the therapeutic agents against degradation. They facilitate efficient drug concentration in targeted cells, surmount the resistance of drugs, and possess a small size. Nevertheless, these nanocarrier(s) have some limitations, such as less permeability across the barrier and low bioavailability of loaded drugs. To overcome these challenges, integrating external stimuli has been employed, encompassing infrared light, thermal stimulation, microwaves, and X-rays. Among these stimuli, ultrasound-triggered nanocarriers have gained significant attention due to their cost-effectiveness, non-invasive nature, specificity, ability to penetrate tissues, and capacity to deliver elevated drug concentrations to intended targets. This article comprehensively reviews recent advancements in different nanocarriers for breast cancer chemotherapy. It also delves into the associated hurdles and offers valuable insights into the prospective directions for this innovative field. [ABSTRACT FROM AUTHOR]

Indole scaffolds are well-documented for their biological accessibility and broader therapeutic applications. The cellular interaction of the indole moiety and its intrinsic effects on cell transduction and proliferation mechanisms in cancer biology have been widely acknowledged. Despite available reports on anticancer indoles, the structural insights of indole compounds in targeting drug-resistant breast cancer have yet to be elaborated upon. Breast cancer is emerging as the most common cancer in women worldwide, affecting more than two million women annually. Considering the optimistic evidence found in recent studies on the druggability of indole derivatives for breast cancer, this review presents indole compounds of interest with anti-breast cancer activity, along with their structural insights and mechanisms. This review updates several interesting facts related to the indole interacting pathway suitable for drug-resistant breast cancer. Furthermore, the clinical pharmacokinetic and toxicity reports of these compounds are very impressive. This integrative view of indole compounds will undoubtedly pave the way for further exploratory research in the discovery of newer indole-based chemotherapeutics as efficacious leads for breast cancer. [ABSTRACT FROM AUTHOR]

In consideration of the chromones' therapeutic potential and anticancer activity, a new series of chromanone derivatives have been synthesized through a straightforward reaction between 6-formyl-7-hydroxy-5-methoxy-2-methylchromone (2) and various organic active compounds. The cytotoxic activity of the newly synthesized congeners was investigated against MCF-7 (human breast cancer), HCT-116 (colon cancer), HepG2 (liver cancer), and normal skin fibroblast cells (BJ1). The obtained data indicated that compounds 14b, 17, and 19 induce cytotoxic activity in the breast MCF7, while compounds 6a, 6b, 11 and 14c showed highly potent activity in the colon cancer cell lines. Overall, the results demonstrate that the potential cytotoxic effects of the studied compounds may be based on their ability to induce DNA fragmentation in cancer cell lines, down-regulate the expression level of CDK4 as well as the anti-apoptotic gene Bcl-2 and up-regulate the expression of the pro-apoptotic genes P53 and Bax. Furthermore, compounds 14b and 14c showed a dual mechanism of action by inducing apoptosis and cell cycle arrest. The docking studies showed that the binding affinity of the most active cytotoxic compounds within the active pocket of the CDK4 enzyme is stronger due to hydrophobic and H-bonding interactions. These results were found to be consistent with the experimental results. [ABSTRACT FROM AUTHOR]

Cyclin-dependent kinase 8 (CDK8) has emerged as a promising target for inhibiting cancer cell function, intensifying efforts towards the development of CDK8 inhibitors as potential cancer therapeutics. Mutations in CDK8, a protein kinase, are also implicated as a primary factor associated with tumor formation. In this study, we identified potential inhibitors through virtual screening for CDK8 and single amino acid mutations in CDK8, namely D173A (Aspartate 173 mutate to Alanine), D189N (Aspartate 189 mutate to Asparagine), T196A (Threonine 196 mutate to Alanine) and T196D (Threonine 196 mutate to Aspartate). Four databases (CHEMBEL, ZINC, MCULE, and MolPort) containing 65,209,131 molecules have been searched to identify new inhibitors for CDK8 and its single mutations. In the first step, structure-based pharmacophore modeling in the Pharmit server was used to select the compounds to know the inhibitors. Then molecules with better predicted drug-like molecule properties were selected. The final filter used to select more effective inhibitors among the previously selected molecules was molecular docking. Finally, 13 hits for CDK8, 11 hits for D173A, 11 hits for D189N, 15 hits for T196A, and 12 hits for T196D were considered potential inhibitors. A majority of the virtual screening hits exhibited satisfactorily predict pharmacokinetic characteristics and toxicity properties. [ABSTRACT FROM AUTHOR]

Isatin (indol-2,3-dione), a secondary metabolite of tryptophan, has been used as the core structure to design several compounds that have been tested and identified as potent inhibitors of apoptosis, potential antitumor agents, anticonvulsants, and antiviral agents. In this work, several analogs of isatin hybrids have been synthesized and characterized, and their activities were established as inhibitors of both Aurora A kinase and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike/host angiotensin-converting enzyme II (ACE2) interactions. Amongst the synthesized isatin hybrids, compounds 6a, 6f, 6g, and 6m exhibited Aurora A kinase inhibitory activities (with IC50 values < 5 μ M), with GScore values of −7.9, −7.6, −8.2 and −7.7 kcal/mol, respectively. Compounds 6g and 6i showed activities in blocking SARS-CoV-2 spike/ACE2 binding (with IC50 values in the range < 30 μ M), with GScore values of −6.4 and −6.6 kcal/mol, respectively. Compounds 6f, 6g, and 6i were both capable of inhibiting spike/ACE2 binding and blocking Aurora A kinase. Pharmacophore profiling indicated that compound 6g tightly fits Aurora A kinase and SARS-CoV-2 pharmacophores, while 6d fits SARS-CoV-2 and 6l fits Aurora A kinase pharmacophore. This work is a proof of concept that some existing cancer drugs may possess antiviral properties. Molecular modeling showed that the active compound for each protein adopted different binding modes, hence interacting with a different set of amino acid residues in the binding site. The weaker activities against spike/ACE2 could be explained by the small sizes of the ligands that fail to address the important interactions for binding to the ACE2 receptor site. [ABSTRACT FROM AUTHOR]

Cancer is a group of diseases in which cells grow uncontrollably and can spread into other tissues. Various studies consider the interactions between cancer cells and the immune system as well as different types of treatment. Mathematical models have been used to study the growth of cancerous cells. We study a fractional order model that describes some aspects of the interactions among host, effector immune, and cancer cells. A drug treatment is considered to analyse the cancerous cells proliferation. Due to the chemotherapy, we split the fractional equation of the cancerous cells into drug sensitivity and resistance. We show that not only the chemotherapy but also the drug resistance plays an important role in the growth rate of cancer cells. [ABSTRACT FROM AUTHOR]

Cancer is responsible for approximately 10 million deaths worldwide, with 70% of the deaths occurring in low- and middle-income countries; as such safer and more effective anti-cancer drugs are required. Therefore, the potential benefits of Ziziphus nummularia and Ziziphus spina-christi as sources of anti-cancer agents were investigated. Z. nummularia and Z. spina-christi extracts were prepared using chloroform, ethanol, ethyl acetate, and water. The extracts' anti-cancer properties were determined using the MTT Cell Viability Assay in four cancer cell lines: breast (KAIMRC2 and MDA-MB-231), colorectal (HCT8), and liver (HepG2). The ApoTox-Glo Triplex Assay and high-content imaging (HCI)-Apoptosis Assay were used to assess KAIMRC2 and HCT8 cells further. In addition, KAIMRC2 cells were tested for microtubule staining, and AKT/mTOR protein expression was determined by western blot analysis. Liquid chromatography-mass spectrometry (LC–MS) was performed to identify the secondary metabolites in the ethanol and ethyl acetate extracts, followed by in silico techniques to predict molecular targets and interactions, safety, and pharmacokinetic profile for identified metabolites. Out of the eight extracts, the ethanolic extract of Z. nummularia, exhibited the most potent activity against KAIMRC2 cells with an IC50 value of 29.2 μg/ml. Cancer cell treatment with the ethanolic extract of Z. nummularia resulted in a dose-dependent decrease in cell viability with increased apoptosis and cytotoxic effects. Microtubule staining showed a disrupted microtubular network. The ethanolic extract treatment of KAIMRC2 cells led to upregulated expression of pAKT and pmTOR. In silico studies predicted luteolin-7-O-glucoside to be a ligand for tubulin with the highest docking score (− 7.686) and similar binding interactions relative to the native ligand. Further computational analysis of the metabolites showed acceptable pharmacokinetic and safety profiles, although ethanolic extract metabolites were predicted to have cardiotoxic effects. Ethanolic extraction is optimal for solubilizing active anticancer metabolites from Z. nummularia, which may act by causing M-phase arrest via inhibition of tubulin polymerization. Luteolin-7-O-glucoside is the lead candidate for further research and development as an anti-cancer agent. In addition, this study suggests that herbal treatment could switch on mechanisms of adaptation and survival in cancer cells. [ABSTRACT FROM AUTHOR]

The progression of metastasis, a complex systemic disease, is facilitated by interactions between tumor cells and their isolated microenvironments. Over the past few decades, researchers have investigated the metastatic spread of cancer extensively, identifying multiple stages in the process, such as intravasation, extravasation, tumor latency, and the development of micrometastasis and macrometastasis. The premetastatic niche is established in target organs by the accumulation of aberrant immune cells and extracellular matrix proteins. The "seed and soil" idea, which has become widely known and accepted, is being used to this day to guide cancer studies. Changes in the local and systemic immune systems have a major impact on whether an infection spreads or not. The belief that the immune response may play a role in slowing tumor growth and may be beneficial against the metastatic disease underpins the responsiveness shown in the immunological landscape of metastasis. Various hypotheses on the phylogenesis of metastases have been proposed in the past. The primary tumor's secreting factors shape the intratumoral microenvironment and the immune landscape, allowing this progress to be made. Therefore, it is evident that among disseminated tumor cells, there are distinct phenotypes that either carry budding for metastasis or have the ability to obtain this potential or in systemic priming through contact with substantial metastatic niches that have implications for medicinal chemistry. Concurrent immunity signals that the main tumor induces an immune response that may not be strong enough to eradicate the tumor. Immunotherapy's success with some cancer patients shows that it is possible to effectively destroy even advanced-stage tumors by modifying the microenvironment and tumor-immune cell interactions. This review focuses on the metastasome in colorectal carcinoma and the therapeutic implications of site-specific metastasis, systemic priming, tumor spread, and the relationship between the immune system and metastasis. [ABSTRACT FROM AUTHOR]

A receptor-based pharmacophore model describing the binding features required for the multi-kinase inhibition of the target kinases (VEGFR-2, FGFR-1, and BRAF) were constructed and validated. It showed a good overall quality in discriminating between the active and the inactive in a compiled test set compounds with F1 score of 0.502 and Mathew's correlation coefficient of 0.513. It described the ligand binding to the hinge region Cys or Ala, the glutamate residue of the Glu-Lys αC helix conserved pair, the DFG motif Asp at the activation loop, and the allosteric back pocket next to the ATP binding site. Moreover, excluded volumes were used to define the steric extent of the binding sites. The application of the developed pharmacophore model in virtual screening of an in-house scaffold dataset resulted in the identification of a benzimidazole-based scaffold as a promising hit within the dataset. Compounds 8a-u were designed through structural optimization of the hit benzimidazole-based scaffold through (un)substituted aryl substitution on 2 and 5 positions of the benzimidazole ring. Molecular docking simulations and ADME properties predictions confirmed the promising characteristics of the designed compounds in terms of binding affinity and pharmacokinetic properties, respectively. The designed compounds 8a-u were synthesized, and they demonstrated moderate to potent VEGFR-2 inhibitory activity at 10 µM. Compound 8u exhibited a potent inhibitory activity against the target kinases (VEGFR-2, FGFR-1, and BRAF) with IC50 values of 0.93, 3.74, 0.25 µM, respectively. The benzimidazole derivatives 8a-u were all selected by the NCI (USA) to conduct their anti-proliferation screening. Compounds 8a and 8d resulted in a potent mean growth inhibition % (GI%) of 97.73% and 92.51%, respectively. Whereas compounds 8h, 8j, 8k, 8o, 8q, 8r, and 8u showed a mean GI% > 100% (lethal effect). The most potent compounds on the NCI panel of 60 different cancer cell lines were progressed further to NCI five-dose testing. The benzimidazole derivatives 8a, 8d, 8h, 8j, 8k, 8o, 8q, 8r and 8u exhibited potent anticancer activity on the tested cell lines reaching sub-micromolar range. Moreover, 8u was found to induce cell cycle arrest of MCF-7 cell line at the G2/M phase and accumulating cells at the sub-G1 phase as a result of cell apoptosis. [ABSTRACT FROM AUTHOR]

Mathematical models of cancer and bacterial evolution have generally stemmed from a gene-centric framework, assuming clonal evolution via acquisition of resistance-conferring mutations and selection of their corresponding subpopulations. More recently, the role of phenotypic plasticity has been recognized and models accounting for phenotypic switching between discrete cell states (e.g., epithelial and mesenchymal) have been developed. However, seldom do models incorporate both plasticity and mutationally driven resistance, particularly when the state space is continuous and resistance evolves in a continuous fashion. In this paper, we develop a framework to model plastic and mutational mechanisms of acquiring resistance in a continuous gradual fashion. We use this framework to examine ways in which cancer and bacterial populations can respond to stress and consider implications for therapeutic strategies. Although we primarily discuss our framework in the context of cancer and bacteria, it applies broadly to any system capable of evolving via plasticity and genetic evolution. [ABSTRACT FROM AUTHOR]

Background and Aim: Previous reports have suggested IFI16 as a tumor suppressor in hepatocellular carcinoma (HC). Nonetheless, the biological significance of IFI16 and its mechanism concerning resistance to cisplatin (DDP) in HC requires further exploration. Methods: Samples of tumor and corresponding para-carcinoma tissues were acquired from patients with HC. Furthermore, DDP-resistant cell lines of HC, specifically HCC, Huh7 and Hepatoblastoma, HepG3, were generated by gradually increasing the concentration of DDP. Cell apoptosis and DNA damage were evaluated by utilizing flow cytometry assay and TUNEL staining. The interaction between IFI16 and interferon regulatory factor 3 (IRF3) proteins were analyzed using Co-Immunoprecipitation (Co-IP) assay. In vivo assays were conducted by establishing HC subcutaneous xenograft tumor models. Results: The study found a reduction in IFI16 expression in both HC tissues and DDP-resistant HC cell lines. The binding of IFI16 to IRF3 regulated DNA damage-associated markers in vitro. Overexpression of IFI16 heightened the susceptibility of DDP-induced apoptosis and DNA damage, which was counteracted by IRF3 knockdown, while strengthened by IRF3 overexpression. Moreover, overexpression of IFI16 diminished in vivo DDP-resistant HC tumorigenicity. Conclusion: In summary, our findings suggest that IFI16 serves as a tumor suppressor in HC by promoting DNA damage via its interaction with IRF3, thereby reversing DDP resistance. Cisplatin-induced damage in tumor cells, with the involvement of DNA repair, leads to survival of tumor cells, manifesting as drug resistance of the tumor. However, the binding of IRF3 and IFI16 inhibits DNA repair, resulting in the ultimate fate of cell death. [ABSTRACT FROM AUTHOR]

Two new dichlorophenylfurylnicotinamidine regioisomers and were prepared from the corresponding dichlorophenylfurylnicotinonitriles when treated with lithium bis(trimethylsilyl)amide and subsequent deprotection, then hydrogen chloride salt formation. Nicotinonitriles were prepared employing a Suzuki coupling conditions for 6-(5-bromofuran-2-yl)nicotinonitrile with dichlorophenylboronic acids. Computational assessments provided insights into electronic structure and chemical reactivity. Their antiproliferative activities against 60 cancer cell lines spanning 9 tissue types were evaluated. 6-[5-(2,4-Dichlorophenyl)furan-2-yl]nicotinamidine dihydrochloride exhibited the highest overall potency with median GI50 of 1.65 μM. Molecular modeling showed the smallest HOMO-LUMO gap for analogue 6-[5-(3,4-dichlorophenyl)furan-2-yl]nicotinamidine dihydrochloride (1.91 eV), followed by 6-[5-(2,4-dichlorophenyl)furan-2-yl]nicotinamidine dihydrochloride (1.92 eV), relative to the lead 3,5-dichloro compound I (2.62 eV), suggesting 6-[5-(3,4-dichlorophenyl)furan-2-yl]nicotinamidine dihydrochloride has the highest chemical reactivity among the investigated amidines. Structure–activity analysis revealed the ability to modulate potency and toxicity through variations to the dichlorophenyl ring. The most responsive cell line was SR leukemia, with GI50 values of 0.31 μM and 0.55 μM for 6-[5-(2,4-dichlorophenyl)furan-2-yl]nicotinamidine dihydrochloride and 6-[5-(3,4-dichlorophenyl)furan-2-yl]nicotinamidine dihydrochloride, respectively. We demonstrate the potential to rationally shift the therapeutic profile from overtly cytotoxic towards more cytostatic behavior through substituent changes to the terminal phenyl ring. Importantly, the synergistic integration of synthetic chemistry, biological screening, and computational analyses enabled key structure-activity relationships to be established, paving the way for further lead optimization efforts. Our interdisciplinary approach blending organic synthesis with high-throughput antiproliferative evaluation and quantum chemical modeling provides a framework amenable to systematic improvement of this novel chemotype. These initial promising findings warrant ongoing medicinal chemistry endeavors to identify clinical candidates boasting enhanced selectivity and wider therapeutic windows. [ABSTRACT FROM AUTHOR]

Meningioma is the most common central nervous system (CNS) tumor. In recent decades, several efforts have been made to eradicate this disease. Surgery and radiotherapy remain the standard treatment options for these tumors. Drug therapy comes to play its role when both surgery and radiotherapy fail to treat the tumor. This mostly happens when the tumors are close to vital brain structures and are nonbenign. Although a wide variety of chemotherapeutic drugs and molecular targeted drugs such as tyrosine kinase inhibitors, alkylating agents, endocrine drugs, interferon, and targeted molecular pathway inhibitors have been studied, the roles of numerous drugs remain unexplored. Recent interest is growing toward studying and engineering exosomes for the treatment of different types of cancer including meningioma. The latest studies have shown the involvement of exosomes in the theragnostic of various cancers such as the lung and pancreas in the form of biomarkers, drug delivery vehicles, and vaccines. Proper attention to this new emerging technology can be a boon in finding the consistent treatment of meningioma. [ABSTRACT FROM AUTHOR]

Non-Hodgkin lymphoma (NHL) is one of the most common cancer types. Deregulated signaling pathways can trigger certain NHL subtypes, including Diffuse Large B-cell lymphoma. NF-ĸB signaling pathway, which is responsible for the proliferation, growth, and survival of cells, has an essential role in lymphoma development. Although different signals control NF-ĸB activation in various lymphoid malignancies, the characteristic one is the CARD11-BCL10-MALT1 (CBM) complex. The CBM complex is responsible for the initiation of adaptive immune response. Our study is focused on the molecular docking of ten polyphenols as potential CARD11-BCL10-MALT1 complex inhibitors, essentially through MALT1 inhibition. Molecular docking was performed by Auto Dock Tools and AutoDock Vina tool, while SwissADME was used for drug-likeness and absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis of the ligands. Out of 66 ligands that were used in this study, we selected and visualized five. Selection criteria were based on the binding energy score and position of the ligands on the used protein. 2D and 3D visualizations showed interactions of ligands with the protein. Five ligands are considered potential inhibitors of MALT1, thus affecting NF-ĸB signaling pathway. However, additional in vivo and in vitro studies are required to confirm their mechanism of inhibition. [ABSTRACT FROM AUTHOR]

Epidermal growth factor receptor (EGFR) promotes tumorigenic characteristics and activates cancer-associated signaling pathways such as Wnt/-catenin, transforming growth factor (TGF-β), and phosphoinositide-3-kinase (PI3K). Several inhibitors have been reported to suppress the activity of EGFR and are being used in cancer treatment. However, patients in the malignant stage of cancer show resistance to those inhibitors, opening a wide space for research to discover novel inhibitors. Therefore, we carried out machine learning and virtual screening to discover novel inhibitors with high affinity against EGFR-TK. Initially, a library of 2640 chalcones were screened out using a machine-learning model developed based on the random forest algorithm, exhibiting high sensitivity and a Receiver Operating Characteristic curve (ROC area) of 0.99. Furthermore, out of the initial 2640 screened compounds, 412 compounds exhibiting potential activity are subjected to evaluation for drug-likeness properties through different filters: Blood–brain barrier penetration, Lipinski's rule, CMC-50 like rule, Veber rule, and Ghose filter, alongside Cell Line Cytotoxicity Prediction. A total of 30 compounds that successfully pass through all these filters are selected for molecular docking. Of these, 6 compounds display substantial binding affinity and closer interaction with the conserved catalytic residues of the target EGFR-TK compared to the reference molecule (erlotinib). Furthermore, molecular dynamics simulation studies were conducted on four compounds (CID-375861, CID-375862, CID-23636403, and CID-259166) to confirm the stability of the docked complexes over a 100 ns simulation trajectory. Additionally, the binding free energy calculations by MMPBSA reveal that these four chalcone compounds exhibit strong affinity towards the EGFR-TK enzyme, with binding free energies of − 65.421 kJ/mol, − 94.266 kJ/mol, − 80.044 kJ/mol, and − 79.734 kJ/mol, respectively. The findings from this investigation highlight a set of promising chalcone compounds that have the potential to be developed into effective drugs for the treatment of various cancers. Further research and development on these compounds could pave the way for novel therapeutic interventions. [ABSTRACT FROM AUTHOR]

The lethality of epithelial ovarian cancer (OC) is largely due to a high rate of recurrence and development of chemoresistance, which requires synergy between cancer cells and the tumor microenvironment (TME) and is thought to involve cancer stem cells. Our analysis of gene expression microarray data from paired primary and recurrent OC tissues revealed significantly elevated expression of the gene encoding periostin (POSTN) in recurrent OC compared to matched primary tumors (p = 0.015). Secreted POSTN plays a role in the extracellular matrix, facilitating epithelial cell migration and tissue regeneration. We therefore examined how elevated extracellular POSTN, as we found is present in recurrent OC, impacts OC cell functions and phenotypes, including stemness. OC cells cultured with conditioned media with high levels of periostin (CMPOSTNhigh) exhibited faster migration (p = 0.0044), enhanced invasiveness (p = 0.006), increased chemoresistance (p < 0.05), and decreased apoptosis as compared to the same cells cultured with control medium (CMCTL). Further, CMPOSTNhigh-cultured OC cells exhibited an elevated stem cell side population (p = 0.027) along with increased expression of cancer stem cell marker CD133 relative to CMCTL-cultured cells. POSTN-transfected 3T3-L1 cells that were used to generate CMPOSTNhigh had visibly enhanced intracellular and extracellular lipids, which was also linked to increased OC cell expression of fatty acid synthetase (FASN) that functions as a central regulator of lipid metabolism and plays a critical role in the growth and survival of tumors. Additionally, POSTN functions in the TME were linked to AKT pathway activities. The mean tumor volume in mice injected with CMPOSTNhigh-cultured OC cells was larger than that in mice injected with CMCTL-cultured OC cells (p = 0.0023). Taken together, these results show that elevated POSTN in the extracellular environment leads to more aggressive OC cell behavior and an increase in cancer stemness, suggesting that increased levels of stromal POSTN during OC recurrence contribute to more rapid disease progression and may be a novel therapeutic target. Furthermore, they also demonstrate the utility of having matched primary-recurrent OC tissues for analysis and support the need for better understanding of the molecular changes that occur with OC recurrence to develop ways to undermine those processes. [ABSTRACT FROM AUTHOR]

Some relevant emerging properties of intelligent systems are "adaptation to a changing environment," "reaction to unexpected situations," "capacity of problem solving," and "ability to communicate." Single cells have remarkable abilities to adapt, make adequate context-dependent decision, take constructive actions, and communicate, thus theoretically meeting all the above-mentioned requirements. From a biological point of view, cancer can be viewed as an invasive species, composed of cells that move from primary to distant sites, being continuously exposed to changes in the environmental conditions. Blood represents the first hostile habitat that a cancer cell encounters once detached from the primary site, so that cancer cells must rapidly carry out multiple adaptation strategies to survive. The aim of this review was to deepen the adaptation mechanisms of cancer cells in the blood microenvironment, particularly referring to four adaptation strategies typical of animal species (phenotypic adaptation, metabolic adaptation, niche adaptation, and collective adaptation), which together define the broad concept of biological intelligence. We provided evidence that the required adaptations (either structural, metabolic, and related to metastatic niche formation) and "social" behavior are useful principles allowing putting into a coherent frame many features of circulating cancer cells. This interpretative frame is described by the comparison with analog behavioral traits typical of various animal models. [ABSTRACT FROM AUTHOR]

Current genome-wide studies have indicated that a great number of long non-coding RNAs (lncRNAs) are transcribed from the human genome and appeared as crucial regulators in a variety of cellular processes. Many studies have displayed a significant function of lncRNAs in the regulation of autophagy. Autophagy is a macromolecular procedure in cells in which intracellular substrates and damaged organelles are broken down and recycled to relieve cell stress resulting from nutritional deprivation, irradiation, hypoxia, and cytotoxic agents. Autophagy can be a double-edged sword and play either a protective or a damaging role in cells depending on its activation status and other cellular situations, and its dysregulation is related to tumorigenesis in various solid tumors. Autophagy induced by various therapies has been shown as a unique mechanism of resistance to anti-cancer drugs. Growing evidence is showing the important role of lncRNAs in modulating drug resistance via the regulation of autophagy in a variety of cancers. The role of lncRNAs in drug resistance of cancers is controversial; they may promote or suppress drug resistance via either activation or inhibition of autophagy. Mechanisms by which lncRNAs regulate autophagy to affect drug resistance are different, mainly mediated by the negative regulation of micro RNAs. In this review, we summarize recent studies that investigated the role of lncRNAs/autophagy axis in drug resistance of different types of solid tumors. [ABSTRACT FROM AUTHOR]

Objectives: Cancer drug resistance is a multifaceted phenomenon. The present review article aims to comprehensively analyze the cellular and molecular aspects of drug resistance in cancer and the strategies employed to overcome it. Evidence acquisition: A systematic search of relevant literature was conducted using electronic databases such as PubMed, Scopus, and Web of Science using appropriate key words. Original research articles and secondary literature were taken into consideration in reviewing the development in the field. Results and conclusions: Cancer drug resistance is a pervasive challenge that causes many treatments to fail therapeutically. Despite notable advances in cancer treatment, resistance to traditional chemotherapeutic agents and novel targeted medications remains a formidable hurdle in cancer therapy leading to cancer relapse and mortality. Indeed, a majority of patients with metastatic cancer experience are compromised on treatment efficacy because of drug resistance. The multifaceted nature of drug resistance encompasses various factors, such as tumor heterogeneity, growth kinetics, immune system, microenvironment, physical barriers, and the emergence of undruggable cancer drivers. Additionally, alterations in drug influx/efflux transporters, DNA repair mechanisms, and apoptotic pathways further contribute to resistance, which may manifest as either innate or acquired traits, occurring prior to or following therapeutic intervention. Several strategies such as combination therapy, targeted therapy, development of P-gp inhibitors, PROTACs and epigenetic modulators are developed to overcome cancer drug resistance. The management of drug resistance is compounded by the patient and tumor heterogeneity coupled with cancer’s ability to evade treatment. Gaining further insight into the mechanisms underlying medication resistance is imperative for the development of effective therapeutic interventions and improved patient outcomes. [ABSTRACT FROM AUTHOR]

The polyaneuploid cancer cell (PACC) state promotes cancer lethality by contributing to survival in extreme conditions and metastasis. Recent experimental evidence suggests that post-therapy PACC-derived recurrent populations display cross-resistance to classes of therapies with independent mechanisms of action. We hypothesize that this can occur through PACC memory, whereby cancer cells that have undergone a polyaneuploid transition (PAT) reenter the PACC state more quickly or have higher levels of innate resistance. In this paper, we build on our prior mathematical models of the eco-evolutionary dynamics of cells in the 2N+ and PACC states to investigate these two hypotheses. We show that although an increase in innate resistance is more effective at promoting cross-resistance, this trend can also be produced via PACC memory. We also find that resensitization of cells that acquire increased innate resistance through the PAT have a considerable impact on eco-evolutionary dynamics and extinction probabilities. This study, though theoretical in nature, can help inspire future experimentation to tease apart hypotheses surrounding how cross-resistance in structured cancer populations arises. [ABSTRACT FROM AUTHOR]

Purpose: A 3-biomarker homologous recombination deficiency (HRD) score is a key component of a currently FDA-approved companion diagnostic assay to identify HRD in patients with ovarian cancer using a threshold score of ≥ 42, though recent studies have explored the utility of a lower threshold (GIS ≥ 33). The present study evaluated whether the ovarian cancer thresholds may also be appropriate for major breast cancer subtypes by comparing the genomic instability score (GIS) distributions of BRCA1/2-deficient estrogen receptor–positive breast cancer (ER + BC) and triple-negative breast cancer (TNBC) to the GIS distribution of BRCA1/2-deficient ovarian cancer. Methods: Ovarian cancer and breast cancer (ER + BC and TNBC) tumors from ten study cohorts were sequenced to identify pathogenic BRCA1/2 mutations, and GIS was calculated using a previously described algorithm. Pathologic complete response (pCR) to platinum therapy was evaluated in a subset of TNBC samples. For TNBC, a threshold was set and threshold validity was assessed relative to clinical outcomes. Results: A total of 560 ovarian cancer, 805 ER + BC, and 443 TNBC tumors were included. Compared to ovarian cancer, the GIS distribution of BRCA1/2-deficient samples was shifted lower for ER + BC (p = 0.015), but not TNBC (p = 0.35). In the subset of TNBC samples, univariable logistic regression models revealed that GIS status using thresholds of ≥ 42 and ≥ 33 were significant predictors of response to platinum therapy. Conclusions: This study demonstrated that the GIS thresholds used for ovarian cancer may also be appropriate for TNBC, but not ER + BC. GIS thresholds in TNBC were validated using clinical response data to platinum therapy. [ABSTRACT FROM AUTHOR]

Despite improvements in extracranial therapy, survival rate for patients suffering from brain metastases remains very poor. This is coupled with the incidence of brain metastases continuing to rise. In this review, we focus on core contributions of the blood–brain barrier to the origin of brain metastases. We first provide an overview of the structure and function of the blood–brain barrier under physiological conditions. Next, we discuss the emerging idea of a pre-metastatic niche, namely that secreted factors and extracellular vesicles from a primary tumor site are able to travel through the circulation and prime the neurovasculature for metastatic invasion. We then consider the neurotropic mechanisms that circulating tumor cells possess or develop that facilitate disruption of the blood–brain barrier and survival in the brain's parenchyma. Finally, we compare and contrast brain metastases at the blood–brain barrier to the primary brain tumor, glioma, examining the process of vessel co-option that favors the survival and outgrowth of brain malignancies. [ABSTRACT FROM AUTHOR]

Tumor recurrence, driven by the evolution of drug resistance is a major barrier to therapeutic success in cancer. Tumor drug resistance is often caused by genetic alterations such as point mutation, which refers to the modification of a single genomic base pair, or gene amplification, which refers to the duplication of a region of DNA that contains a gene. These mechanisms typically confer varying degrees of resistance, and they tend to occur at vastly different frequencies. Here we investigate the dependence of tumor recurrence dynamics on these mechanisms of resistance, using stochastic multi-type branching process models. We derive tumor extinction probabilities and deterministic estimates for the tumor recurrence time, defined as the time when an initially drug sensitive tumor surpasses its original size after developing resistance. For models of amplification-driven and mutation-driven resistance, we prove law of large numbers results regarding the convergence of the stochastic recurrence times to their mean. Additionally, we prove sufficient and necessary conditions for a tumor to escape extinction under the gene amplification model, discuss behavior under biologically relevant parameters, and compare the recurrence time and tumor composition in the mutation and amplification models both analytically and using simulations. In comparing these mechanisms, we find that the ratio between recurrence times driven by amplification versus mutation depends linearly on the number of amplification events required to acquire the same degree of resistance as a mutation event, and we find that the relative frequency of amplification and mutation events plays a key role in determining the mechanism under which recurrence is more rapid for any specific system. In the amplification-driven resistance model, we also observe that increasing drug concentration leads to a stronger initial reduction in tumor burden, but that the eventual recurrent tumor population is less heterogeneous, more aggressive and harbors higher levels of drug-resistance. [ABSTRACT FROM AUTHOR]

This study was aimed to identify a novel metastasis-promoting molecule and elucidate its functional and prognostic roles in cervical cancer. DDIT4 (DNA-damage-inducible transcript 4), a hypoxia-inducible gene, was identified by analyzing multiple microarray databases. The correlation between DDIT4 expression in immunohistochemistry and clinicopathological characteristics in the public database and our cohort was evaluated by statistical analysis. Transwell® assay and wound-healing assay to determine cell migration and invasion were performed. DDIT4 was knocked down using siRNA or lentiviral vectors. The potential downstream pathways of DDIT4 were explored and verified by a gene set enrichment analysis and western blotting. The in vivo metastatic capability was determined with the use of an intraperitoneal injection mouse model. In the analysis of the public database and our cohort, DDIT4 high expression was significantly related to short overall survival and lymph node metastasis in patients with early-stage cervical cancer. The knockdown of DDIT4 attenuated the migration and invasion activity of tumor cells in vitro and reduced the expression of epithelial–mesenchymal transition (EMT)-related proteins and the NF-κB pathway in cervical cancer cells. DDIT4 also promoted tumor progression in the mouse model. Our results indicate that DDIT4 can be a prognostic indicator in cervical cancer and promote lymph node metastasis, augmenting malignancy via the EMT and NF-kB pathways. [ABSTRACT FROM AUTHOR]

Many research studies have recently been conducted to develop effective and low-toxicity cancer drugs. In this study, in vitro induction of cytotoxic and apoptotic effects in A-375 melanoma and MCF-7 breast cancer cells with alginate nanoparticles containing Syzygium aromaticum (clove) essential oil and eugenol were investigated. First, GC–MS identified compounds of clove EO–MS; three major compounds identified were eugenol (66%), trans-caryophyllene (12%), and eugenol acetate (10%). Afterward, alginate nanoparticles containing clove essential oil and eugenol (Alg-clove and Alg-eugenol) with particle sizes of 122±7 nm (PDI 0.33 and SPAN 0.72) and 87±8 nm (PDI 0.25 and SPAN 0.66) were prepared. Then, Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) confirmed successful loading in the alginate nanoparticles. Next, cell viability was determined using the MTT cell proliferation assay. After that, Bax and Bcl-2 gene expression ratio was evaluated to study the presence of apoptotic cell death using real-time polymerase chain reaction (RT-PCR). As a result, a dose-dependent cytotoxic effect against the proliferation of both cancer cell lines was observed. IC50 values of Alg-clove on A-375 and MCF-7 cells were close together: 358.3 (286–448) and 321.9 (196–529) μg/ml. These values for Alg-eugenol were obtained as 757.5 (407–950) and 328.8 (202–536) μg/ml. Moreover, after treatment with both particles, the expression ratio of Bax and Bcl-2 genes increased and showed these particles had impressive apoptotic effects on both cancer cell lines. The results proved that Alg-clove and Alg-eugenol have proper cytotoxicity against cancer cells and could apply to complementary medicine. [ABSTRACT FROM AUTHOR]

Callithrix jacchus and C. penicillata have successfully established anthropogenic introduced populations throughout Rio de Janeiro state, where the endangered buffy-tufted-ear marmoset, Callithrix aurita, naturally occurs. These three species can produce fertile hybrids, which represent a challenge to C. aurita conservation. Callithrix anthropogenic hybrids show an overall increase in phenotypic variation and in genetic diversity in relation to parental populations and can also form hybrid swarms. Here, we examined ear tuft variation, cranial morphometrics and mitochondrial DNA sequences in three marmoset species (C. jacchus, C. penicillata and C. aurita) and their hybrids from anthropogenic environments in several localities of Rio de Janeiro state. Our data suggest that the sample evaluated is mostly composed of hybrids of C. jacchus and C. penicillata, excepted by one individual which has C. aurita ancestry. The phenotypes of hybrids were highly variable, with six external morphotypes varying from intermediate to parental-like. Cranial morphometric analyses revealed a mosaic of parental traits in hybrids, although there were some transgressive traits, while molecular analyses indicate higher genetic diversity among hybrids relative to parental species. No clear geographical association was found in relation to hybrid distribution, with the hybrid haplotypes occurring randomly throughout Rio de Janeiro state. [ABSTRACT FROM AUTHOR]

Cancer therapy has advanced from tradition chemotherapy methods to targeted therapy, novel drug delivery mechanisms, combination therapies etc. Although several novel chemotherapy strategies have been introduced, chemoresistance still remains as one of the major barriers in cancer treatments. Chemoresistance can lead to relapse and hinder the development of improved clinical results for cancer patients, and this continues to be the major hurdle in cancer therapy. Anticancer drugs acquire chemoresistance through different mechanisms. Understanding these mechanisms is crucial to overcome and increase the efficiency of the cancer therapies that are employed. The potential molecular pathways behind chemoresistance include tumor heterogeneity, elevated drug efflux, multidrug resistance, interconnected signaling pathways, and other factors. To surpass this limitation, new clinical tactics are to be introduced. This review aims to compile the most recent information on the molecular pathways that regulate chemoresistance in cancers, which will aid in development of new therapeutic targets and strategies. [ABSTRACT FROM AUTHOR]

The tumor microenvironment (TME) plays a pivotal role in cancer development and progression. In this line, revealing the precise mechanisms of the TME and associated signaling pathways of tumor resistance could pave the road for cancer prevention and efficient treatment. The use of nanomedicine could be a step forward in overcoming the barriers in tumor-targeted therapy. Novel delivery systems benefit from enhanced permeability and retention effect, decreasing tumor resistance, reducing tumor hypoxia, and targeting tumor-associated factors, including immune cells, endothelial cells, and fibroblasts. Emerging evidence also indicates the engagement of multiple dysregulated mediators in the TME, such as matrix metalloproteinase, vascular endothelial growth factor, cytokines/chemokines, Wnt/β-catenin, Notch, Hedgehog, and related inflammatory and apoptotic pathways. Hence, investigating novel multitargeted agents using a novel delivery system could be a promising strategy for regulating TME and drug resistance. In recent years, small molecules from natural sources have shown favorable anticancer responses by targeting TME components. Nanoformulations of natural compounds are promising therapeutic agents in simultaneously targeting multiple dysregulated factors and mediators of TME, reducing tumor resistance mechanisms, overcoming interstitial fluid pressure and pericyte coverage, and involvement of basement membrane. The novel nanoformulations employ a vascular normalization strategy, stromal/matrix normalization, and stress alleviation mechanisms to exert higher efficacy and lower side effects. Accordingly, the nanoformulations of anticancer monoclonal antibodies and conventional chemotherapeutic agents also improved their efficacy and lessened the pharmacokinetic limitations. Additionally, the coadministration of nanoformulations of natural compounds along with conventional chemotherapeutic agents, monoclonal antibodies, and nanomedicine-based radiotherapy exhibits encouraging results. This critical review evaluates the current body of knowledge in targeting TME components by nanoformulation-based delivery systems of natural small molecules, monoclonal antibodies, conventional chemotherapeutic agents, and combination therapies in both preclinical and clinical settings. Current challenges, pitfalls, limitations, and future perspectives are also discussed. [ABSTRACT FROM AUTHOR]

Combination therapies have taken center stage for cancer treatment, however, there is a lack of a comprehensive portrait to quantitatively map the current clinical combination progress. This study aims to capture clinical combination therapies of the validated FDA-approved new oncology drugs by a macro data analysis and to summarize combination mechanisms and strategies in the context of the existing literature. A total of 72 new molecular entities or new therapeutic biological products for cancer treatment approved by the FDA from 2017 to 2021 were identified, and the data on their related 3334 trials were retrieved from the database of ClinicalTrials.gov. Moreover, these sampled clinical trials were refined by activity status and combination relevance and labeled with the relevant clinical arms and drug combinations, as well as drug targets and target pairs. Combination therapies are increasingly prevalent in clinical trials of new oncology drugs. From retrospective work, existing clinical combination therapies in oncology are driven by different patterns (i.e., rational design and industry trends). The former can be represented by mechanism-based or structure-based combinations, such as targeting different domains of HER2 protein or in-series co-targeting in RAF plus MEK inhibitors. The latter is an empirically driven strategy, including redundant combinations in hot targets, such as PD-1/PD-L1, PI3K, CDK4/6, and PARP. Because of an explosion in the number of clinical trials and the resultant shortage of available patients, it is essential to rationally design drug combinations. [ABSTRACT FROM AUTHOR]

Background: Breast cancer is the most common tumor among females globally. Its prevalence is growing around the world, and it is alleged to be the leading cause of cancer death. Approved anti-breast cancer drugs display several side effects and resistance during the early treatment stage. Hence, there is a need for the development of more effective and safer drugs. This research was aimed at designing more potent quinazolin-4(3H)-one molecules as breast cancer inhibitors using a ligand-based design approach, studying their modes of interaction with the target enzyme using molecular docking simulation, and predicting their pharmacological properties. Methods: The QSAR model was developed using a series of quinazoline-4(3H)-one derivatives by utilizing Material Studio v8.0 software and validated both internally and externally. Applicability domain virtual screening was utilized in selecting the template molecule, which was structurally modified to design more potent molecules. The inhibitive capacities of the design molecules were predicted using the developed model. Furthermore, molecular docking was performed with the EGFR target active site residues, which were obtained from the protein data bank online server (PDB ID: 2ITO) using Molegro Virtual Docker (MVD) software. SwissADME and pkCSM online sites were utilized in predicting the pharmacological properties of the designed molecules. Results: Four QSAR models were generated, and the first model was selected due to its excellent internal and external statistical parameters as follows: R2 = 0.919, R2adj = 0.898, Q2cv = 0.819, and R2pred = 0.7907. The robustness of the model was also confirmed by the result of the Y-scrambling test performed with cR2p = 0.7049. The selected model was employed to design seven molecules, with compound 4 (pIC50 = 5.18) adopted as the template. All the designed compounds exhibit better activities ranging from pIC50 = 5.43 to 5.91 compared to the template and Doruxybucin (pIC50 = 5.35). The results of molecular docking revealed better binding with the EGFR target compared with the template and Doruxybucin. The designed compounds exhibit encouraging therapeutic applicability, as evidenced by the findings of pharmacological property prediction. Conclusions: The designed derivatives could be utilized as novel anti-breast cancer agents. [ABSTRACT FROM AUTHOR]

Breast cancer is the second utmost common cancer among women. In this research study, two feature selection methods, namely Consistency first Search-Best First search (CFS-BFS) and Consistency-Best First Search (Consistency-BFS) are used to find out the significant biomarkers for breast cancer. The feature selection methods pick a small count of important and relevant genes providing a higher degree of accuracy. The count of biomarkers selected in Consistency-BFS is less in comparison to CFS-BFS method. Three common identified biomarkers' genes are recognised to help in diagnosis and prognosis of breast cancer, namely SLC39A6, ESR1, and CDC20 are selected on the basis of histologic-grade and molecular subtype of breast cancer. These three genes identified are even found in PAM50 and judged for survival variances using Kaplan-Meier Survival Model. The result suggested that overexpression of SLC39A6, ESR1, and CDC20 proves to be an influencing factor for the poor prognosis of patients suffering from breast cancer. The proposed method is successful in creating a prognostic gene signature in forecasting the survival likelihood of patients. [ABSTRACT FROM AUTHOR]

The human Bactericidal/Permeability-Increasing Fold containing family B, member 1 (BPIFB1), or also known as LPLUNC1, C20orf114, is a member of the BPI/LBP/PLUNC protein family. BPIFB1 differential expression patterns have been reported in several cancers such as nasopharyngeal carcinoma (NPC). However, in gastric cancer (GC) the role of BPIFB1 is not known, but the expression of the gene has been reported in the stomach co-expressing E-cadherin (CDH1) together with making mucin 5, tracheobronchial/gastric mucin type A and C (MUC5AC). To investigate the role of BPIFB1 in GC development and its interactions with CDH1 and MUC5AC, overexpression of the gene was induced in three different GC cell lines; AGS, HGC-27 and MKN-45. The present of BPIFB1 protein in a transfected GC cell line was detected through gel Lumio Green Detection. BPIFB1, CDH1 and MUC5AC expression were then performed via RT-PCR and quantitative Real-time PCR (qPCR) followed by statistical analysis (p ≤ 0.05). BPIFB1 expression was detected in all transfected cells with the highest in AGS with the p = 0.003 followed by MKN-45 with the p = 0.009 and HGC-27 with the p = 0.015. The expression of MUC5AC is upregulated in BPIFB1 transfected GC cells whereby the highest expression is observed in MKN-45 with the p = 0.05 followed by AGS with the p = 0.001 and HGC-27 with the p = 0.026. CDH1 expression is downregulated in all BPIFB1 transfected GC cells with the lowest expression found in HGC-27 with the p = 0.001 followed by AGS with the p = 0.003 and MKN-45 with the p = 0.004. Thus, induction of BPIFB1 overexpression in vitro in GC cells contributes to the decreased in CDH1 expression and increased in MUC5AC expression suggesting that BPIFB1 other than co-expressed in the gastric gland with the two genes also regulates gene expression. We found that the overexpression of BPIFB1 downregulated the expression of CDH1 and upregulated MUC5AC gene expression. This finding was supported by both RT-PCR and qPCR. Conclusion: Our findings suggest that BPIFB1 is differentially expressed in GC cell lines and regulate the expression of CDH1 and MUC5AC. [ABSTRACT FROM AUTHOR]

Comprehensive screenings to clarify indirect cell–cell interactions, such as those in the tumor microenvironment, especially comprehensive assessments of supporting cells' effects, are challenging. Therefore, in this study, indirect CRISPR screening for drug resistance with cell–cell interactions was invented. The photoconvertible fluorescent protein Dendra2 was inducted to supporting cells and explored the drug resistance responsible factors of supporting cells with CRISPR screenings. Random mutated supporting cells co-cultured with leukemic cells induced drug resistance with cell–cell interactions. Supporting cells responsible for drug resistance were isolated with green-to-red photoconversion, and 39 candidate genes were identified. Knocking out C9orf89, MAGI2, MLPH, or RHBDD2 in supporting cells reduced the ratio of apoptosis of cancer cells. In addition, the low expression of RHBDD2 in supporting cells, specifically fibroblasts, of clinical pancreatic cancer showed a shortened prognosis, and a negative correlation with CXCL12 was observed. Indirect CRISPR screening was established to isolate the responsible elements of cell–cell interactions. This screening method could reveal unknown mechanisms in all kinds of cell–cell interactions by revealing live phenotype-inducible cells, and it could be a platform for discovering new targets of drugs for conventional chemotherapies. An indirect CRISPR screening system based on the photoconvertible fluorescent protein, Dendra2, enables the discovery of elements responsible for drug resistance from cell–cell interactions. [ABSTRACT FROM AUTHOR]

Hepatocellular carcinoma (HCC) is the major life-threatening primary liver malignancy in both sexes all over the world. Unfortunately, the majority of patients are diagnosed at later stages because HCC does not elicit obvious symptoms during its early incidence. Consequently, most individuals escape the first-line HCC treatments and are treated with chemotherapy. Regrettably, the therapeutic outcomes for those patients are usually poor because of the development of multidrug resistance phenomena. Furthermore, most anti-HCC therapies cause severe undesired side effects that notably interfere with the life quality of such patients. Accordingly, there is an important need to search for an alternative therapeutic drug or adjuvant which is more efficient with safe or even minimal side effects for HCC treatment. Melatonin was recently reported to exert intrinsic antitumor activity in different cancers. However, the regulatory pathways underlying the antitumor activity of melatonin are poorly understood in resistant liver cells. Furthermore, a limited number of studies have addressed the therapeutic role of melatonin in HCC cells resistant to doxorubicin chemotherapy. In this study, we investigated the antitumor effects of melatonin in doxorubicin-resistant HepG2 cells and explored the regulatory pivotal targets underlying these effects. To achieve our aim, an MTT assay was used to calculate the 50% inhibitory concentration of melatonin and evaluate its antiproliferative effect on resistant cells. Additionally, qRT-PCR was used to quantify genes having a role in drug resistance phenotype (ABCB1, ABCC1, ABCC2, ABCC3, ABCC4, ABCC5, and ABCG2); apoptosis (caspases-3, and -7, Bcl2, Bax, and p53); anti-oxidation (NRF2); expression of melatonin receptors (MT1, MT2, and MT3); besides, programmed death receptor PD-1 gene. The active form of the caspase-3 enzyme was estimated by ELISA. A human inflammatory antibody membrane array was employed to quantify forty inflammatory factors expressed in treated cells. We observed that melatonin inhibited the proliferation of doxorubicin-resistant HepG2 cells in a dose-dependent manner after 24-h incubation time with a calculated IC50 greater than 10 mM (13.4 mM), the expression levels of genes involved in drug resistance response (ABCB1, ABCC1, ABCC5, and ABCG2) were downregulated. Also, the expression of caspase-3, Caspase-7, NRF2, and p53 genes were expressed at higher levels as compared to control (DMSO-treated cells). An active form of caspase-3 was confirmed by ELISA. Moreover, the anti-inflammatory effect of melatonin was detected through the calculated fold change to control which was reduced for various mediators that have a role in the inflammation pathway. The current findings introduce melatonin as a promising anti-cancer treatment for human-resistant HCC which could be used in combination with current chemotherapeutic regimens to improve the outcome and reduce the developed multidrug resistance. [ABSTRACT FROM AUTHOR]

Circular RNAs (circRNAs) are regulatory elements that are involved in orchestrating gene expression and protein functions and are implicated in various biological processes including cancer. Notably, breast cancer has a significant mortality rate and is one of the most common malignancies in women. CircRNAs have been demonstrated to contribute to the pathogenesis of breast cancer including its initiation, progression, metastasis, and resistance to drugs. By acting as miRNA sponges, circRNAs can indirectly influence gene expression by disrupting miRNA regulation of their target genes, ultimately altering the course of cancer development and progression. Additionally, circRNAs can interact with proteins and modulate their functions including signaling pathways involved in the initiation and development of cancer. Recently, circRNAs can encode peptides that play a role in the pathophysiology of breast cancer and other diseases and their potential as diagnostic biomarkers and therapeutic targets for various cancers including breast cancer. CircRNAs possess biomarkers that differentiate, such as stability, specificity, and sensitivity, and can be detected in several biological specimens such as blood, saliva, and urine. Moreover, circRNAs play an important role in various cellular processes including cell proliferation, differentiation, and apoptosis, all of which are integral factors in the development and progression of cancer. This review synthesizes the functions of circRNAs in breast cancer, scrutinizing their contributions to the onset and evolution of the disease through their interactions with exosomes and cancer-related intracellular pathways. It also delves into the potential use of circRNA as a biomarker and therapeutic target against breast cancer. It discusses various databases and online tools that offer crucial circRNA information and regulatory networks. Lastly, the challenges and prospects of utilizing circRNAs in clinical settings associated with breast cancer are explored. [ABSTRACT FROM AUTHOR]

Failure to achieve complete elimination of triple negative breast cancer (TNBC) stem cells after adjuvant therapy is associated with poor outcomes. Aldehyde dehydrogenase 1 (ALDH1) is a marker of breast cancer stem cells (BCSCs), and its enzymatic activity regulates tumor stemness. Identifying upstream targets to control ALDH+ cells may facilitate TNBC tumor suppression. Here, we show that KK-LC-1 determines the stemness of TNBC ALDH+ cells via binding with FAT1 and subsequently promoting its ubiquitination and degradation. This compromises the Hippo pathway and leads to nuclear translocation of YAP1 and ALDH1A1 transcription. These findings identify the KK-LC-1-FAT1-Hippo-ALDH1A1 pathway in TNBC ALDH+ cells as a therapeutic target. To reverse the malignancy due to KK-LC-1 expression, we employ a computational approach and discover Z839878730 (Z8) as an small-molecule inhibitor which may disrupt KK-LC-1 and FAT1 binding. We demonstrate that Z8 suppresses TNBC tumor growth via a mechanism that reactivates the Hippo pathway and decreases TNBC ALDH+ cell stemness and viability. The presence of breast cancer stem cells is associated with therapy resistance in patients with triple-negative breast cancer (TNBC). Here, the authors identify KK-LC-1-mediated YAP signaling as a driver of TNBC stemness and develop a therapeutic molecule to target this axis in preclinical models of TNBC. [ABSTRACT FROM AUTHOR]

The importance of the microenvironment is widely recognized as it regulates not only malignant cell behavior but also drug sensitivity. The cancer cell microenvironment is composed of biological, physical and chemical elements, and simultaneous reproduction of these three elements are important conditions investigated in cancer research. In the present study, we focused on the epidemiological and anatomical specificities of endometrioid carcinoma, obesity (biological), fluid flow (physical) and anticancer agents (chemical) to target the specific microenvironmental elements of endometrioid carcinoma. To elucidate the individual effects of these elements on endometrioid carcinoma and to investigate the relationships between these factors, we developed an adipose tissue fragments (ATFs)-embedded cell disc under a rotational culture method to generate carcinoma-stroma interactions and to create fluid flow. ATFs and fluid flow individually or synergistically influenced proliferative cellular behavior and the morphological changes underlying endometrioid carcinoma. ATFs and fluid flow also governed the expression of extracellular signal-regulated kinase and p38 signaling synergistically or individually, depending on the endometrioid carcinoma cell type. Adipose tissue induced chemoresistance to cis-diamminedichloro-platinum (CDDP) in endometrioid cancer, but the resistance effect was abolished by fluid flow. Thus, a simple reconstructed model was established to investigate three elements of the microenvironment of endometrioid carcinoma in vitro. This culture model unequivocally demonstrated the individual and synergistic effects of the three elements on endometrioid carcinoma. This new culture model is a promising tool for elucidating the mechanisms underlying endometrioid carcinoma and for developing further treatment strategies. [ABSTRACT FROM AUTHOR]

Identification of the signature molecular profiles involved in therapy resistance is of vital importance in developing new strategies for treatments and disease monitoring. Protein alpha-1 antitrypsin (AAT, encoded by SERPINA1 gene) is an acute-phase protein, and its high expression has been linked with unfavorable clinical outcome in different types of cancer; however, data on its involvement in therapy resistance are still insufficient. We analyzed SERPINA1 mRNA expression in three different multidrug-resistant (MDR) cell lines—U87-TxR, NCI-H460/R, and DLD1-TxR—and in U87 cells grown in alginate microfibers as a 3D cellular model of glioblastoma. Expression of IL-6 as a major modulator of SERPINA1 was also analyzed. Additionally, AAT protein expression in MDR cells was analyzed by immunofluorescence. SERPINA1 gene expression and AAT protein expression were significantly upregulated in all the tested MDR cell lines compared with their sensitive counterparts. Moreover, SERPINA1 was significantly upregulated in 3D models of glioblastoma, previously found to have upregulated drug-resistance-related gene expression compared with 2D cells. With the exception of NCI-H460/R, in all cell lines as well as in a 3D model of U87 cells, increase in SERPINA1 expression correlated with the increase in IL-6 expression. Our results indicate that AAT could be utilized as a biomarker of therapy resistance in cancer; however, further studies are needed to elucidate the mechanisms driving AAT upregulation in therapy resistance and its biological significance in this process. [ABSTRACT FROM AUTHOR]

Drug combinations can be the prime strategy for increasing the initial treatment options in cancer therapy. However, identifying the combinations through experimental approaches is very laborious and costly. Notably, in vitro and/or in vivo examination of all the possible combinations might not be plausible. This study presented a novel computational approach to predicting synergistic drug combinations. Specifically, the deep neural network-based binary classification was utilized to develop the model. Various physicochemical, genomic, protein–protein interaction and protein-metabolite interaction information were used to predict the synergy effects of the combinations of different drugs. The performance of the constructed model was compared with shallow neural network (SNN), k-nearest neighbors (KNN), random forest (RF), support vector machines (SVMs), and gradient boosting classifiers (GBC). Based on our findings, the proposed deep neural network model was found to be capable of predicting synergistic drug combinations with high accuracy. The prediction accuracy and AUC metrics for this model were 92.21% and 97.32% in tenfold cross-validation. According to the results, the integration of different types of physicochemical and genomics features leads to more accurate prediction of synergy in cancer drugs. [ABSTRACT FROM AUTHOR]