A comprehensive pathway map of epidermal growth factor receptor signaling

Expression of an epidermal growth factor-transdermal peptide fusion protein in Arabidopsis thaliana and its therapeutic effects on skin barrier repair

Epidermal growth factor (EGF) is recognized for its role in regulating keratinocyte proliferation and differentiation, thereby facilitating the restoration of impaired skin barriers. Nevertheless, challenges related to the penetration and safety of EGF remain to be resolved. In this study, we evaluated the efficacy of TDP1, a transdermal peptide, in enhancing the penetration of EGF through murine skin, utilizing EGF expressed in A. thaliana. The coding sequences of the TDP1 and EGF genes were cloned as a fusion construct into a plant expression vector. The resulting plasmid, pGM3301-TDP1-EGF, was introduced into A. thaliana via the floral dip method. Positive clones were identified using polymerase chain reaction (PCR). High-expression strains were selected through Western-blot analysis and enzyme-linked immunosorbent assay (ELISA). Homozygotes plants were obtained through self-pollination. The impact of the TDP1-EGF fusion protein on the restoration of a compromised epidermal barrier was assessed using dermatoscopy. Keratinocyte (KC) proliferation was examined via hematoxylin and eosin (H&E) staining, while KC differentiation, lipid synthesis, and inflammatory factors were analyzed using reverse transcription quantitative PCR (RT-qPCR) and immunohistochemistry. Compared to other expression systems, the A. thaliana system utilized for TDP1-EGF expression offers the advantages of being devoid of toxicity from endogenous plant substances, rendering it both safe and suitable for scalable production of the recombinant protein. The yield of the TDP1-EGF fusion protein expressed in A. thaliana accounted for 0.0166% of the total soluble protein. EGF conjugated with TDP1 displayed enhanced transdermal activity compared to unconjugated EGF, as evidenced by the Franz diffusion cell assay. Furthermore, the biological efficacy of the TDP1-EGF fusion protein surpassed that of EGF alone in ameliorating epidermal barrier damage in a murine skin injury model. This research has the potential to revolutionize the development and delivery of skincare products and establishes a foundation for the application of molecular farming in skin health.

An Attention-Aware Multi-Task Learning Framework Identifies Candidate Targets for Drug Repurposing in Sarcopenia

BACKGROUND

Sarcopenia presents a pressing public health concern due to its association with age-related muscle mass decline, strength loss and reduced physical performance, particularly in the growing older population. Given the absence of approved pharmacological therapies for sarcopenia, the need to discover effective pharmacological interventions has become critical.

METHODS

To address this challenge and discover new therapies, we developed a novel Multi-Task Attention-aware method for Multi-Omics data (MTA-MO) to extract complex biological insights from various biomedical data sources, including transcriptome, methylome and genome data to identify drug targets and discover new therapies. Additionally, MTA-MO integrates human protein-protein interaction (PPI) networks and drug-target networks to improve target identification. The novel method is applied to a multi-omics dataset that included 1055 participants aged 20-50 (mean (± SD) age 36.88 (± 8.64)), comprising 37.82% African-American and 62.18% Caucasian/White individuals. Physical activity levels were self-reported and categorized into three groups: ≥ 3 times/week, < 3 times/week and no regular exercise. Mean (± SD) measures for grip strength, appendicular lean mass (ALM), exercise frequency and smoking status (no/yes, n (%)) were 38.72 (± 8.93) kg, 28.65 (± 4.63) kg, 4.31 (± 1.79) and 30.81%/69.19%, respectively. Significant differences (p < 0.05) were found between groups in age, ALM, smoking, and consumption of milk, alcohol, beer and wine.

RESULTS

Using the MTA-MO method, we identified 639 gene targets, and by analysing PPIs and querying public databases, we narrowed this list down to seven potential hub genes associated with sarcopenia (ESR1, ATM, CDC42, EP300, PIK3CA, EGF and PTK2B). These findings were further validated through diverse levels of pathobiological evidence associated with sarcopenia. Gene Ontology and KEGG pathways analysis highlighted five key functions and signalling pathways relevant to skeletal muscle. The interaction network analysis identified three transcriptional factors (GATA2, JUN and FOXC1) as the key transcriptional regulators of the seven potential genes. In silico analysis of 1940 drug candidates identified canagliflozin as a promising candidate for repurposing in sarcopenia, demonstrating the strongest binding affinity to the PTK2B protein (inhibition constant 6.97 μM). This binding is stabilized by hydrophobic bonds, Van der Waals forces, pi-alkyl interactions and pi-anion interactions around PTK2B's active residues, suggesting its potential as a therapeutic option.

CONCLUSIONS

Our novel approach effectively integrates multi-omics data to identify potential treatments for sarcopenia. The findings suggest that canagliflozin could be a promising therapeutic candidate for sarcopenia.

Luteolin inhibits inflammation and M1 macrophage polarization in the treatment of Pseudomonas aeruginosa-induced acute pneumonia through suppressing EGFR/PI3K/AKT/NF-κB and EGFR/ERK/AP-1 signaling pathways

BACKGROUND

The opportunistic pathogen Pseudomonas aeruginosa primarily causes infections in immunocompromised individuals. Luteolin, a natural flavonoid, is widely present in plants, which exerts various pharmacological activities, including anti-inflammatory and antimicrobial activities.

PURPOSE

This study aimed to explore the therapeutic efficacy of luteolin and the underlying molecular mechanisms in treating the P. aeruginosa-induced acute pneumonia.

METHODS

Network pharmacology was utilized to identify the core targets of luteolin for treating acute P. aeruginosa pneumonia. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed to dissect the potential effects of luteolin and the involved signaling pathways. Surface plasmon resonance (SPR) assay and molecular docking were employed for studying the binding affinities of luteolin with the key targets. Furthermore, we applied a mouse model of bacterial pneumonia for assessing the therapeutic effects of luteolin in vivo, and an in vitro infection model for specifically investigating the effects of luteolin on macrophages as well as the underlying mechanisms upon P. aeruginosa infection.

RESULTS

Network pharmacology identified TNF, IL-6, EGFR and AKT1 as the key targets of luteolin for treating acute P. aeruginosa pneumonia. Moreover, as revealed by GO and KEGG enrichment analysis, EGFR, MAPK and PI3K/AKT pathways were the potential pathways regulated the P. aeruginosa-induced inflammatory response. According to the in vivo results, luteolin effectively mitigated the P. aeruginosa-induced acute lung injury through reducing the pulmonary permeability, neutrophil infiltration, proinflammatory cytokine production (IL-1β, IL-6, TNF and MIP-2) and bacterial burden in lung tissues, which led to increased survival rate of mice. Furthermore, the luteolin-treated mice had diminished EGFR, PI3K, AKT, IκBα, NF-κB p65, ERK, c-Jun and c-Fos phosphorylation, down-regulated M1 macrophage marker levels (iNOS, CD86 and IL-1β) but up-regulated M2 macrophage marker levels (Ym1, CD206 and Arg1) in lung tissues. Consistently, the luteolin-pretreated macrophages exhibited reduced phosphorylation of these regulatory proteins, diminished proinflammatory cytokine production, and down-regulated expression of M1 macrophage markers, but up-regulated expression of IL-10 and M2 macrophage markers.

CONCLUSION

luteolin effectively suppressed the inflammatory responses and M1 macrophage polarization through inhibiting EGFR/PI3K/AKT/NF-κB and EGFR/ERK/AP-1 signaling pathways in the treatment of acute P. aeruginosa pneumonia. This study suggests that luteolin could be a promising candidate for development as a therapeutic agent for acute bacterial pneumonia.

Effect of human chorionic gonadotropin on oocyte maturation and developmental competence in buffalo

We hypothesized that human chorionic gonadotropic (hCG) could replace LH in the maturation media for buffalo oocytes, and hCG administration before ovum pick-up (OPU) enhances in-vitro development of buffalo oocytes. Objectives were 1) to investigate the effect of hCG supplementation on nuclear maturation, oocyte development, and granulosa cell mRNA abundance of genes related to growth and antioxidant pathways and 2) to determine the effect of hCG administration before OPU on in-vitro oocyte development. In Experiment 1, buffalo oocytes retrieved from slaughterhouse ovaries were maturated in the media supplemented with 0.5 μg of LH or 2 IU of hCG. After fertilization, cleavage and embryo were assessed on 48 h and 7 d of the culture, respectively. The nuclear maturation of the oocytes and granulosa cells mRNA abundance of genes (AREG,EREG,NRG1,CYP19A1,GDF9,CASP9,SOD1) were assessed after maturation. In Experiment 2, buffaloes were synchronized and superstimulated with FSH and 6 h before OPU, randomly assigned to either receive saline (CON, n = 4) or 1500 IU of hCG (hCG, n = 6). Four OPU sessions per buffalo were conducted at weekly intervals and retrieved oocytes were maturated and fertilized in-vitro. In Experiment 1, nuclear maturation, cleavage, embryo production, and mRNA abundance of the genes related to growth and steroidogenesis did not differ between treatments but SOD1 gene expression tended (P = 0.10) to lower in hCG treatment as compared with LH. In Experiment 2, oocytes retrieved from hCG-treated buffaloes resulted in a higher proportion of cleavage (84.0 vs. 42.5 ± 8.9 %, P = 0.02) and embryo (84.0 vs 24.0 ± 7.3, P < 0.01) than CON. In conclusion, hCG supplementation in the maturation media yielded comparable outcomes to that of LH, and hCG administration 6 h before OPU enhanced the in-vitro developmental competency of the buffalo oocytes.

Principles and Design of Molecular Tools for Sensing and Perturbing Cell Surface Receptor Activity

Cell-surface receptors are vital for controlling numerous cellular processes with their dysregulation being linked to disease states. Therefore, it is necessary to develop tools to study receptors and the signaling pathways they control. This Review broadly describes molecular approaches that enable 1) the visualization of receptors to determine their localization and distribution; 2) sensing receptor activation with permanent readouts as well as readouts in real time; and 3) perturbing receptor activity and mimicking receptor-controlled processes to learn more about these processes. Together, these tools have provided valuable insight into fundamental receptor biology and helped to characterize therapeutics that target receptors.

Regulation of epithelial growth factor receptors by the oncoprotein E5 during the HPV16 differentiation-dependent life cycle

Human papillomavirus (HPV) 16 infection initiates upon viral entry into the basal cells of the epithelium. The virus manipulates signaling pathways to complete its life cycle, which depends on cellular differentiation. The virus expresses the oncoproteins E5, E6, and E7 to promote immune evasion, cell cycle progression, apoptosis inhibition, and viral replication. The least studied viral oncoprotein is E5 (16E5), which can regulate epithelial growth factor receptor (GFR) signaling pathways. GFRs such as transforming growth factor-beta receptor (TGFBR), epidermal growth factor receptor (EGFR), and keratinocyte growth factor receptor (KGFR) have essential roles in cell growth, differentiation, and proliferation. These receptors obtain their ligands from the microenvironment, and once activated, regulate cellular behavior in the epithelium. GFRs therefore represent valuable targets for the virus to establish and maintain a cellular environment supportive of infection. The ability of 16E5 to regulate proliferation and differentiation varies through the differentiating epithelium, making it necessary to adequately describe the association between 16E5 and GFRs. Here we summarize the regulation of GFR signaling pathways by 16E5, discuss the roles of stromal growth factors, and outline unresolved questions over cellular differentiation and proliferation during the HPV life cycle.

PYCR1 Promotes Esophageal Squamous Cell Carcinoma by Interacting With EGFR to Affecting the PI3K/Akt/mTOR Signaling Pathway

BACKGROUND

The expression and functional role of pyrroline-5-carboxylate reductase 1 (PYCR1) in esophageal squamous cell carcinoma (ESCC) remain poorly understood. This study aimed to elucidate the role and underlying mechanisms of PYCR1 in ESCC.

METHODS

We utilized an ESCC tissue microarray coupled with immunohistochemical staining to assess variability in PYCR1 protein expression among ESCC patients and evaluate its clinical relevance. PYCR1 was silenced in ESCC cell lines with short hairpin RNA (shRNA), followed by functional assays (colony formation, caspase 3/7 activity, methylthiazol tetrazolium, wound healing, and migration/invasion assays) to evaluate its role in ESCC progression. In vivo, mouse tumor xenograft models were used to examine PYCR1's impact on tumor growth. To identify downstream targets and pathways, we conducted coimmunoprecipitation, mass spectrometry, immunofluorescence, and proteomic analyses, validated by western blotting and rescue experiments.

RESULTS

Our findings demonstrated a consistent upregulation of PYCR1 in ESCC tissues. Both in vitro and in vivo studies revealed that PYCR1 suppression significantly inhibited ESCC progression, impacting key processes such as proliferation, apoptosis, migration, and invasion. Mechanistically, PYCR1 was shown to interact with EGFR, promoting ESCC progression and metastasis by activating the PI3K/AKT/mTOR signaling pathways, which are integral to the aggressive behavior of the disease. Rescue experiments further confirmed that EGFR overexpression effectively reversed the inhibitory effects of PYCR1 knockdown in ESCC cells.

CONCLUSION

This study highlights the critical role of PYCR1 in driving ESCC progression and metastasis, underscoring its potential as a promising therapeutic target for managing this malignancy.

Phytochemical strategies in glioblastoma therapy: Mechanisms, efficacy, and future perspectives

Glioblastoma (GBM) is foremost the most aggressive primary brain tumor, presenting extensive therapeutic challenges due to its high invasiveness, genetic complexity, and resistance to established treatments. Despite substantial advances in surgical and chemotherapeutic interventions, the median survival rate for patients is only 14.6 months, and the prognosis remains poor. This review focuses on the molecular hallmarks of GBM, including the activation of the PI3K/Akt pathway, genomic instability, and the deregulation of epidermal growth factor receptor (EGFR), all of which contribute to the tumor's aggressive behavior. Current therapies, such as Temozolomide and Bevacizumab, have limitations, highlighting the need for novel treatment strategies. Phytochemicals, bioactive compounds found in plants, have emerged as potential therapeutic agents by targeting multiple cellular pathways involved in GBM progression. This review provides an overview of key phytochemicals, including quercetin, curcumin, apigenin, and resveratrol. These compounds have shown promise in preclinical studies, with their anti-invasive, anti- angiogenic, pro-apoptotic, and anti-proliferative properties positioning them as strong candidates for GBM therapy. While phytochemicals offer a promising avenue for GBM treatment, further research is required to fully understand their mechanisms of action and to evaluate their efficiency in clinical settings. Developing multi-targeted, safer, and cost-effective anti-GBM therapies could significantly improve patient outcomes.

Advancing Targeted Therapies in Pancreatic Cancer: Leveraging Molecular Aberrations for Therapeutic Success

Pancreatic cancer is one of the most deadly with poor prognosis and overall survival rate due to the dense stroma in the tumors which often is challenging for the delivery of drug to penetrate deep inside the tumor bed and usually results in the progression of cancer. The conventional treatment such as chemotherapy, radiotherapy or surgery shows a minimal benefit in the survival due to the drug resistance, poor penetration, less radiosensitivity or recurrence of tumor. There is an urgent demand to develop molecular- level targeted therapies to achieve therapeutic efficacy in the pancreatic ductal adenocarcinoma (PDAC) patients. The precision oncology focuses on the unique attributes of the patient such as epigenome, proteome, genome, microbiome, lifestyle and diet habits which contributes to promote oncogenesis. The targeted therapy helps to target the mutated proteins responsible for controlling growth, division and metastasis of tumor in the cancer cells. It is very important to consider all the attributes of the patient to provide the suitable personalized treatment to avoid any severe side effects. In this review, we have laid emphasis on the precision medicine; the utmost priority is to improve the survival of cancer patients by targeting molecular mutations through transmembrane proteins, inhibitors, signaling pathways, immunotherapy, gene therapy or the use of nanocarriers for the delivery at the tumor site. It will become beneficial therapeutic window to be considered for the advanced stage pancreatic cancer patients to prolong their survival rate.

Targeted therapy and immunotherapy for gastric cancer: rational strategies, novel advancements, challenges, and future perspectives

Gastric cancer (GC) is one of the most common malignant tumors worldwide, and its treatment has been a focus of medical research. Herein we systematically review the current status of and advancements in targeted therapy and immunotherapy for GC, which have emerged as important treatment strategies in recent years with great potential, and summarize the efficacy and safety of such treatments. Targeted therapies against key targets in GC, including epidermal growth factor receptor (EGFR), human epidermal growth factor receptor 2 (HER2), and vascular endothelial growth factor (VEGF)/VEGF receptor (VEGFR), have shown remarkable therapeutic efficacies by inhibiting tumor progression and/or blood supply. In particular, markable breakthroughs have been made in HER2-targeting drugs for HER2-positive GC patients. To address intrinsic and acquired resistances to HER2-targeting drugs, novel therapeutic agents including bispecific antibodies and antibody-drug conjugates (ADC) targeting HER2 have been developed. Immunotherapy enhances the recognition and elimination of cancer cells by activating body anticancer immune system. Programmed cell death protein 1 (PD-1) and programmed cell death-ligand 1 (PD-L1) antibodies are the most commonly used immunotherapeutic agents and have been used with some success in GC treatment. Innovative immunotherapy modalities, including adoptive immune cell therapy, tumor vaccines, and non-specific immunomodulators therapy, and oncolytic viruses have shown promise in early-stage clinical trials for GC. Clinical trials have supported that targeted therapy and immunotherapy can significantly improve the survival and quality of life of GC patients. However, the effects of such therapies need to be further improved and more personalized, with advancement in researches on tumor immune microenvironment. Further studies remain needed to address the issues of drug resistance and adverse events pertaining to such therapies for GC. The combined application of such therapies and individualized treatment strategies should be further explored with novel drugs developed, to provide more effective treatments for GC patients.

Growth factors IGF-1 and KGF and adipose-derived stem cells promote migration and viability of primary human keratinocytes in an in vitro wound model

Introduction

In the field of plastic surgery, epidermal transplantation is a potential treatment for chronic wounds that results in only minor donor site morbidity. Improving the regenerative capacities of epidermal grafts or single-cell suspensions and therefore accelerating healing processes would be of significant interest.

Methods

In the present study, we analyzed the effects of growth factors and adipose-derived stem cells (ADSCs) on keratinocyte properties. For optimum translation into the clinical setting, primary human keratinocytes and patient-matched ADSCs were isolated and used in an in vitro wound model.

Results

The keratinocyte migration and viability increased after treatment with the growth factors insulin-like growth factor 1 (IGF-1) and keratinocyte growth factor (KGF). A similar effect was observed with the use of a concentrated ADSC-conditioned medium (ADSC-CM). It was further possible to isolate the keratinocytes in a xenogen-free medium, which is essential for clinical translation. Importantly, a patient-dependent influence on the effects of the growth factors and ADSC-CM was observed.

Discussion

This study provides potential for the improvement of epidermal transplantation in the treatment of chronic wounds using xenogen-free isolated and cultivated keratinocytes, growth factors, and ADSC. Translating these results into clinical application may help accelerate wound healing and shorten the time until patients can return to everyday life.

Applications of liposomes and lipid nanoparticles in cancer therapy: current advances and prospects

Liposomes and lipid nanoparticles are common lipid-based drug delivery systems and play important roles in cancer treatment and vaccine manufacture. Although significant progress has been made with these lipid-based nanocarriers in recent years, efficient clinical translation of active targeted liposomal nanocarriers remains extremely challenging. In this review, we focus on targeted liposomes, stimuli-responsive strategy and combined therapy in cancer treatment. We also summarize advances of liposome and lipid nanoparticle applications in nucleic acid delivery and tumor vaccination. In addition, we discuss limitations and challenges in the clinical translation of these lipid nanomaterials and make recommendations for the future research in cancer therapy.

In Silico Born Designed Anti-EGFR Aptamer Gol1 Has Anti-Proliferative Potential for Patient Glioblastoma Cells

The epidermal growth factor receptor (EGFR) is one of the key oncomarkers in glioblastoma (GB) biomedical research. High levels of EGFR expression and mutations have been found in many GB patients, making the EGFR an attractive target for therapeutic treatment. The EGFRvIII mutant is the most studied, it is not found in normal cells and is positively associated with tumor cell aggressiveness and poor patient prognosis, not to mention there is a possibility of it being a tumor stem cell marker. Some anti-EGFR DNA aptamers have already been selected, including the aptamer U2. The goal of this study was to construct a more stable derivative of the aptamer U2, while not ruining its functional potential toward cell cultures from GB patients. A multiloop motif in a putative secondary structure of the aptamer U2 was taken as a key feature to design a novel minimal aptamer, Gol1, using molecular dynamics simulations for predicted 3D models. It turned out that the aptamer Gol1 has a similar putative secondary structure, with G-C base pairs providing its stability. The anti-proliferative activities of the aptamer Gol1 were assessed using patient-derived GB continuous cell cultures, G01 and BU881, with different abundances of EGFR and EGFRvIII. The transcriptome data for the cell culture G01, after aptamer Gol1 treatment, revealed significant changes in gene expression; it induced the transcription of genes associated with neurogenesis and cell differentiation, and it decreased the transcription of genes mediating key nuclear processes. There were significant changes in the gene transcription of key pro-oncogenic signaling pathways mediated by the EGFR. Therefore, the aptamer Gol1 could potentially be an efficient molecule for translation into biomedicine, in order to develop targeted therapy for GB patients.

MET Activation in Lung Cancer and Response to Targeted Therapies

The hepatocyte growth factor receptor (MET) is a receptor tyrosine kinase (RTK) that mediates the activity of a variety of downstream pathways upon its activation. These pathways regulate various physiological processes within the cell, including growth, survival, proliferation, and motility. Under normal physiological conditions, this allows MET to regulate various development and regenerative processes; however, mutations resulting in aberrant MET activity and the consequent dysregulation of downstream signaling can contribute to cellular pathophysiology. Mutations within MET have been identified in a variety of cancers and have been shown to mediate tumorigenesis by increasing RTK activity and downstream signaling. In lung cancer specifically, a number of patients have been identified as possessing MET alterations, commonly receptor amplification (METamp) or splice site mutations resulting in loss of exon 14 (METex14). Due to MET's role in mediating oncogenesis, it has become an attractive clinical target and has led to the development of various targeted therapies, including MET tyrosine kinase inhibitors (TKIs). Unfortunately, these TKIs have demonstrated limited clinical efficacy, as patients often present with either primary or acquired resistance to these therapies. Mechanisms of resistance vary but often occur through off-target or bypass mechanisms that render downstream signaling pathways insensitive to MET inhibition. This review provides an overview of the therapeutic landscape for MET-positive cancers and explores the various mechanisms that contribute to therapeutic resistance in these cases.

Lingo1 in the hippocampus contributes to cognitive dysfunction after anesthesia and surgery in aged mice

Cognitive impairment caused by anesthesia and surgery is one of the most common complications with multiple etiologies that occurs in elderly patients. The underlying mechanisms are not fully understood, and there is a lack of therapeutic strategies. Increasing evidence has demonstrated that myelin loss, abnormal phosphorylation of the tau protein and neuronal apoptosis are substantial driving factors of cognitive deficits. However, the key regulatory factors involved in the pathology of postoperative cognitive dysfunction require further investigation. Herein, we identified a key regulator, Lingo1, whose expression significantly increased in hippocampal neurons after aged mice underwent unilateral nephrectomy. Elevated Lingo1 expression markedly activated the RhoA/ROCK1 signaling pathway through interactions with NgR and p75NTR, subsequently promoting myelin loss and abnormal phosphorylation of the tau protein. Moreover, the upregulation of Lingo1 in hippocampal neurons further inhibited the EGFR/PI3K/Akt pathway, which may increase neuronal apoptosis. These pathological changes ultimately lead to cognitive impairment in aged mice after surgery. Notably, Lingo1 knockdown significantly reversed pathological changes in the hippocampus and attenuated cognitive decline. In conclusion, our findings highlight that Lingo1 upregulation in hippocampal neurons promotes the occurrence and development of postoperative cognitive dysfunction by regulating myelin loss, abnormal tau phosphorylation and neuronal apoptosis, suggesting that Lingo1 might be a potential target for treating postoperative cognitive dysfunction.

Furopyridine Derivatives as Potent Inhibitors of the Wild Type, L858R/T790M, and L858R/T790M/C797S EGFR

The treatment of patients with nonsmall cell lung cancer (NSCLC) using epidermal growth factor receptor (EGFR) inhibitors is complicated by drug-sensitive activating L858R/T790M and L858R/T790M/C797S mutations. To overcome drug resistance, a series of furopyridine (PD) compounds were virtually screened to identify potent EGFR inhibitors using molecular docking and molecular dynamics (MD) simulations based on the solvated interaction energy (SIE) method. Several PD compounds identified from virtual screening demonstrated the potential to suppress both wild-type and mutant forms of EGFR, with IC50 values in the nanomolar range. Among these, PD18 and PD56 exhibited highly potent inhibitory activity against both wild-type and mutant forms of EGFR, surpassing the efficacy of known drugs. Additionally, both PD compounds were cytotoxic to NSCLC cell lines (A549 and H1975) while being nontoxic to normal cell lines (Vero). The interaction mechanisms of both PD compounds complexed with wild-type and mutant forms of EGFR were elucidated through 500 ns molecular dynamics simulations. The predicted binding affinity from molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) correlated well with the experimental binding affinity derived from IC50 values. Furthermore, it was observed that van der Waals interactions, rather than electrostatic interactions, played a significant role in interacting with EGFR's active site. The strong inhibitory activity against EGFR was attributed to two key residues, M793 and S797, via hydrogen bonding, corresponding with lower solvent accessibility and a higher number of atomic contacts. Therefore, these potent compounds could be developed as promising drugs targeting both wild-type and mutant EGFR for the treatment of NSCLC.

Pax6 expressing neuroectodermal and ocular stem cells: Its role from a developmental biology perspective

Pax-6 emerges as a critical transcription factor that guides the fate of stem cells towards neural lineages. Its expression influences the differentiation of neural progenitors into diverse neuronal subtypes, glial cells, and other neural cell types. Pax-6 operates with other regulatory factors to ensure the precise patterning and organization of the developing nervous system. The intricate interplay between Pax-6 and other signaling pathways, transcription factors, and epigenetic modifiers underpins the complicated balance between stem cell maintenance, proliferation, and differentiation in neuroectodermal and ocular contexts. Dysfunction of Pax-6 can lead to a spectrum of developmental anomalies, underscoring its importance in these processes. This review highlights the essential role of Pax-6 expression in neuroectodermal and ocular stem cells, shedding light on its significance in orchestrating the intricate journey from stem cell fate determination to the emergence of diverse neural and ocular cell types. The comprehensive understanding of Pax-6 function gained from a developmental biology perspective offers valuable insights into normal development and potential therapeutic avenues for neuroectodermal and ocular disorders.

Exploration of drug repurposing for Mpox outbreaks targeting gene signatures and host-pathogen interactions

Monkeypox (Mpox) is a growing public health concern, with complex interactions within host systems contributing to its impact. This study employs multi-omics approaches to uncover therapeutic targets and potential drug repurposing opportunities to better understand Mpox's molecular pathogenesis. We developed an in silico host-pathogen interaction (HPI) network and applied weighted gene co-expression network analysis (WGCNA) to explore interactions between Mpox and host proteins. Subtype-specific host-pathogen protein-protein interaction networks were constructed, and key modules from the HPI and WGCNA were integrated to identify significant host proteins. To predict upstream signaling pathways and transcription factors, we used eXpression2Kinases and ChIP-X Enrichment Analysis. The multi-Steiner trees method was applied to compare our findings with those from FDA-approved antiviral drugs. Analysis of 55 differentially expressed genes in Mpox infection revealed 11 kinases and 15 transcription factors as key regulators. We identified 16 potential drug targets, categorized into 8 proviral genes (ESR2, ERK1, ERK2, P38, JNK1, CDK4, GSK3B, STAT3) designated for inhibition, and 8 antiviral genes (IKKA, HDAC1, HIPK2, TF65, CSK21, HIPK2, ESR2, GSK3B) designated for activation. Proviral genes are involved in the AKT, Wnt, and STAT3 pathways, while antiviral genes impact the AP-1, NF-κB, apoptosis, and IFN pathways. Promising FDA-approved candidates were identified, including kinase inhibitors, steroid hormone receptor agonists, STAT3 inhibitors, and notably Niclosamide. This study enhances our understanding of Mpox by identifying key therapeutic targets and potential repurposable drugs, providing a valuable framework for developing new treatments.

Nuclear epidermal growth factor receptor (nEGFR) in clinical treatment

The epidermal growth factor receptor (EGFR) is a recognized target in tumor treatment. While there is significant focus on inhibiting membrane EGFR and its downstream signaling activation, the ectopic accumulation of EGFR, particularly nuclear EGFR (nEGFR), has been implicated in tumor-associated activities and associated with poor prognosis. Within the nucleus, nEGFR functions as a transcriptional regulator to modulate transcriptional landscape and exerts tyrosine kinase activity to phosphorylate nuclear proteins and subsequently influences DNA repair, cell cycle, proliferation, and resistance to radiotherapy and chemotherapy. The nuclear localization of EGFR involves the internalization, subcellular trafficking, and nuclear envelope shuttling of membrane EGFR. Given the challenges of delivering drugs to the nucleus for targeting nEGFR, understanding the molecules affecting the translocation process is crucial for novel insights. This review initially explores the association between nEGFR expression and clinical outcomes and then elucidates how nEGFR fulfills its regulatory role within the nucleus. Subsequently, the mechanisms governing EGFR nuclear translocation and potential therapeutic targets during this process are summarized, highlighting avenues to target nEGFR as an innovative strategy in tumor treatment.

Transactivation of the EGF receptor as a novel desensitization mechanism for G protein-coupled receptors, illustrated by dopamine D2-like and β2 adrenergic receptors

Transactivation of epidermal growth factor receptors (EGFR) provides intricate control over multiple regulatory cellular processes that merge the diversity of G protein-coupled receptors (GPCRs) with the robust signaling capacities of receptor tyrosine kinases. Contrary to the typical assertions, our findings demonstrate that EGFR transactivation contributes to the desensitization of GPCRs. Repeated agonist stimulation of certain GPCRs enhanced EGFR transactivation, triggering a series of cellular events associated with GPCR desensitization. This effect was observed in receptors undergoing desensitization (D3R, K149C-D2R, β2AR) but not in those resistant to desensitization (D2R, C147K-D3R, D4R, β2AR mutants lacking GRK2 or GRK6 phosphorylation sites). The EGFR inhibitor AG1478 prevented both desensitization and the associated cellular events. Similarly, these cellular events were also observed when cells were treated with EGF, but only in GPCRs that undergo desensitization. These findings suggest that EGFR transactivation diversifies pathways involved in ERK activation through the EGFR signaling system and also mediates GPCR desensitization. Alongside the widely accepted steric hindrance model, these findings offer new insights into understanding the mechanisms of GPCR desensitization, which occurs through complex cellular processes.

Treatment of a mutant KRAS lung cancer cell line with polyisoprenylated cysteinyl amide inhibitors activates the MAPK pathway, inhibits cell migration and induces apoptosis

KRAS mutations are the most common oncogenic mutations in lung adenocarcinoma in Black Americans. Polyisoprenylated Cysteinyl amide Inhibitors (PCAIs) constitute a group of potential cancer therapy agents that we designed to specifically disrupt and suppress hyperactive G-protein signaling, such as that caused by mutated RAS proteins. Here we determine the effects of PCAIs on the viability, G-protein levels, downstream mediators, and apoptosis-related proteins on the KRAS-mutated, Black American-derived lung adenocarcinoma cell line, NCI-H23. Of the 17 PCAIs tested, compounds NSL-YHJ-2-27 and NSL-YHJ-2-46 showed the most potency with EC50 values of 2.7 and 3.3 μM, respectively. Western blotting was used to determine the effect of the PCAIs on the phosphorylation levels of MAPK pathway enzymes. After 48 h exposure to 5 μM of the PCAIs, NSL-YHJ-2-46, the MAPK proteins BRAF, MEK1/2, ERK1/2, and p90RSK were activated through phosphorylation by 90, 190, 150 and 120%, respectively. However, CRAF/RAF1 phosphorylation decreased by 40%, suggesting significant changes in the KRAS/MAPK signaling patterns. Furthermore, 5 μM of NSL-YHJ-2-27 depleted the singly polyisoprenylated monomeric G-proteins RAC 1/2/3 and CDC42 by 77 and 76%, respectively. The depletion of these key cytoskeletal proteins may account for the observed inhibition of cell migration and invasion, and spheroid invasion observed on exposure to NSL-YHJ-2-27 and NSL-YHJ-2-46. Treatment with 5 μM of NSL-YHJ-2-27 suppressed full-length inactive caspase 3 and 7 levels by 72 and 91%, respectively. An analysis of cells treated with the fluorescently labeled active caspase 3/7 irreversible inhibitor, CaspaTagTM Caspase-3/7 in situ reagent revealed a 124% increase in active caspase at 3 μM over controls. These findings clearly show the direct effects of the PCAIs on the RAS signaling pathway. Given the profound increases observed in RPS6KA1/p90RSK phosphorylation, future work will involve a determination whether the proapoptotic isoforms of RPS6KA1/p90RSK are phosphorylated due to the PCAIs treatments. These results support the potential use of the PCAIs as targeted therapies against cancers with KRAS mutations.

SMEK1 promotes clear cell renal cell carcinoma progression via EGFR tyrosine-kinase dependent pathway

Studying the mechanisms underlying clear cell renal cell carcinoma (ccRCC), the most common subtype of kidney cancer, may address an unmet need in ccRCC-targeted drug research. Growing evidences indicate that protein phosphatase 4 (PP4) plays an important role in cancer biology. Here, we characterized the upregulation of PP4 core component SMEK1 in ccRCC using tissue microarrays and revealed that its high expression is closely associated with reduced patient survival. We then conducted cell function experiments and animal experiments to prove the tumor-promoting effect of SMEK1. Next, RNA-seq was performed to explore its underlying mechanism, and the results revealed that SMEK1-regulated genes were extensively involved in cell motility, and the canonical tyrosine kinase receptor EGFR was one of its targets. Moreover, we verified the regulatory effect of SMEK1 on EGFR and its downstream MAPK and AKT pathway through molecular experiments, in which erlotinib, a tyrosine kinase inhibitor, can partially block this regulation, demonstrating that SMEK1 mediates its effects dependent on the tyrosine kinase activity of EGFR. Mechanistically, SMEK1 bond to PRMT5 and facilitated PRMT5-mediated histone methylation to promote the transcription of EGFR. Furthermore, we studied the upstream regulators of SMEK1 and demonstrated that the transcription factor E2F1 could directly bind to the SMEK1 promoter by chromatin immunoprecipitation. Functionally, E2F1 could also induce ccRCC progression by manipulating the expression of SMEK1. Collectively, our findings demonstrate the overexpression of SMEK1 in ccRCC, and reveal a novel E2F1/SMEK1/PRMT5/EGFR-tyrosine-kinase-dependent pathway for ccRCC progression.

Mathematical Modeling and Inference of Epidermal Growth Factor-Induced Mitogen-Activated Protein Kinase Cell Signaling Pathways

The mitogen-activated protein kinase (MAPK) pathway is an important intracellular signaling cascade that plays a key role in various cellular processes. Understanding the regulatory mechanisms of this pathway is essential for developing effective interventions and targeted therapies for related diseases. Recent advances in single-cell proteomic technologies have provided unprecedented opportunities to investigate the heterogeneity and noise within complex, multi-signaling networks across diverse cells and cell types. Mathematical modeling has become a powerful interdisciplinary tool that bridges mathematics and experimental biology, providing valuable insights into these intricate cellular processes. In addition, statistical methods have been developed to infer pathway topologies and estimate unknown parameters within dynamic models. This review presents a comprehensive analysis of how mathematical modeling of the MAPK pathway deepens our understanding of its regulatory mechanisms, enhances the prediction of system behavior, and informs experimental research, with a particular focus on recent advances in modeling and inference using single-cell proteomic data.

Contribution of Keratinocytes in Skin Cancer Initiation and Progression

Keratinocytes are major cellular components of the skin and are strongly involved in its homeostasis. Oncogenic events, starting mainly from excessive sun exposure, lead to the dysregulation of their proliferation and differentiation programs and promote the initiation and progression of non-melanoma skin cancers (NMSCs). Primary melanomas, which originate from melanocytes, initiate and develop in close interaction with keratinocytes, whose role in melanoma initiation, progression, and immune escape is currently being explored. Recent studies highlighted, in particular, unexpected modes of communication between melanocytic cells and keratinocytes, which may be of interest as sources of new biomarkers in melanomagenesis or potential therapeutic targets. This review aims at reporting the various contributions of keratinocytes in skin basal cell carcinoma (BCC), cutaneous squamous cell carcinoma (cSCC), and melanoma, with a greater focus on the latter in order to highlight some recent breakthrough findings. The readers are referred to recent reviews when contextual information is needed.

A Bioinformatic Analysis Predicts That Cannabidiol Could Function as a Potential Inhibitor of the MAPK Pathway in Colorectal Cancer

Colorectal cancer (CRC), found in the intestinal tract, is initiated and progresses through various mechanisms, including the dysregulation of signaling pathways. Several signaling pathways, such as EGFR and MAPK, involved in cell proliferation, migration, and apoptosis, are often dysregulated in CRC. Although cannabidiol (CBD) has previously induced apoptosis and cell cycle arrest in vitro in CRC cell lines, its effects on signaling pathways have not yet been determined. An in silico analysis was used here to assess partner proteins that can bind to CBD, and docking simulations were used to predict precisely where CBD would bind to these selected proteins. A survey of the current literature was used to hypothesize the effect of CBD binding on such proteins. The results predict that CBD could interact with EGFR, RAS/RAF isoforms, MEK1/2, and ERK1/2. The predicted CBD-induced inhibition might be due to CBD binding to the ATP binding site of the target proteins. This prevents the required phosphoryl transfer to activate substrate proteins and/or CBD binding to the DFG motif from taking place, thus reducing catalytic activity.

Development of a genome atlas for discriminating benign, preinvasive, and invasive lung nodules

To tackle misdiagnosis in lung cancer screening with low-dose computed tomography (LDCT), we aimed to compile a genome atlas for differentiating benign, preinvasive, and invasive lung nodules and characterize their molecular pathogenesis. We collected 432 lung nodule tissue samples from Chinese patients, spanning benign, atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (IA). We performed comprehensive sequencing, examining somatic variants, gene expressions, and methylation levels. Our findings uncovered EGFR and TP53 mutations as key drivers in - early lung cancer development, with EGFR mutation frequency increasing with disease progression. Both EGFR mutations and EGF/EGFR hypo-methylation activated the EGFR pathway, fueling cancer growth. Transcriptome analysis identified four lung nodule subtypes (G1-4) with distinct molecular features and immune cell infiltrations: EGFR-driven G1, EGFR/TP53 co-mutation G2, inflamed G3, stem-like G4. Estrogen/androgen response was associated with the EGFR pathway, proposing a new therapy combining tyrosine kinase inhibitors with antiestrogens. Preinvasive nodules exhibited stem cell pathway enrichment, potentially hindering invasion. Epigenetic regulation of various genes was essential for lung cancer initiation and development. This study provides insights into the molecular mechanism of neoplastic progression and identifies potential diagnostic biomarkers and therapeutic targets for lung cancer.

miR-107 reverses the multidrug resistance of gastric cancer by targeting the CGA/EGFR/GATA2 positive feedback circuit

Chemotherapy is still the main therapeutic strategy for gastric cancer (GC). However, most patients eventually acquire multidrug resistance (MDR). Hyperactivation of the EGFR signaling pathway contributes to MDR by promoting cancer cell proliferation and inhibiting apoptosis. We previously identified the secreted protein CGA as a novel ligand of EGFR and revealed a CGA/EGFR/GATA2 positive feedback circuit that confers MDR in GC. Herein, we outline a microRNA-based treatment approach for MDR reversal that targets both CGA and GATA2. We observed increased expression of CGA and GATA2 and increased activation of EGFR in GC samples. Bioinformatic analysis revealed that miR-107 could simultaneously target CGA and GATA2, and the low expression of miR-107 was correlated with poor prognosis in GC patients. The direct interactions between miR-107 and CGA or GATA2 were validated by luciferase reporter assays and Western blot analysis. Overexpression of miR-107 in MDR GC cells increased their susceptibility to chemotherapeutic agents, including fluorouracil, adriamycin, and vincristine, in vitro. Notably, intratumor injection of the miR-107 prodrug enhanced MDR xenograft sensitivity to chemotherapies in vivo. Molecularly, targeting CGA and GATA2 with miR-107 inhibited EGFR downstream signaling, as evidenced by the reduced phosphorylation of ERK and AKT. These results suggest that miR-107 may contribute to the development of a promising therapeutic approach for the treatment of MDR in GC.

Current Landscape of Antibody-Drug Conjugate Development in Head and Neck Cancer

Antibody-drug conjugates (ADCs) are fusions of therapeutic drugs and antibodies conjugated by a linker, designed to deliver a therapeutic payload to cells expressing the target antigen. By delivering the highly cytotoxic agent directly to cancer cells, ADCs are designed to enhance safety and broaden the therapeutic window. Recently, ADCs have demonstrated promising efficacy in various solid tumors and are rapidly expanding their indications. The prognosis of patients with advanced head and neck squamous cell carcinoma (HNSCC) remains poor, with no new therapeutics since the advent of anti-PD-1 antibodies in 2016, highlighting a critical need for innovative therapies. Recent preliminary results suggest that ADCs could be promising treatment options for HNSCC as they explore a variety of target antigens, payloads, and linkers. However, for successful adaptation of ADCs in the treatment of HNSCC, addressing key challenges such as payload toxicities, antigen heterogeneity, and adaptive resistance will be essential. Current research focused on new ADC structures, including multispecific antibodies and noncytotoxic payloads, and diverse combination approaches, show promise for future advancements.

Therapeutic targeting of voltage-gated sodium channel NaV1.7 for cancer metastasis

This review focuses on the expression and function of voltage-gated sodium channel subtype NaV1.7 in various cancers and explores its impact on the metastasis driving cell functions such as proliferation, migration, and invasiveness. An overview of its structural characteristics, drug binding sites, inhibitors and their likely mechanisms of action are presented. Despite the lack of clarity on the precise mechanism by which NaV1.7 contributes to cancer progression and metastasis; many studies have suggested a connection between NaV1.7 and proteins involved in multiple signaling pathways such as PKA and EGF/EGFR-ERK1/2. Moreover, the functional activity of NaV1.7 appears to elevate the expression levels of MACC1 and NHE-1, which are controlled by p38 MAPK activity, HGF/c-MET signaling and c-Jun activity. This cascade potentially enhances the secretion of extracellular matrix proteases, such as MMPs which play critical roles in cell migration and invasion activities. Furthermore, the NaV1.7 activity may indirectly upregulate Rho GTPases Rac activity, which is critical for cytoskeleton reorganization, cell adhesion, and actin polymerization. The relationship between NaV1.7 and cancer progression has prompted researchers to investigate the therapeutic potential of targeting NaV1.7 using inhibitors. The positive outcome of such studies resulted in the discovery of several inhibitors with the ability to reduce cancer cell migration, invasion, and tumor growth underscoring the significance of NaV1.7 as a promising pharmacological target for attenuating cancer cell proliferation and metastasis. The research findings summarized in this review suggest that the regulation of NaV1.7 expression and function by small molecules and/or by genetic engineering is a viable approach to discover novel therapeutics for the prevention and treatment of metastasis of cancers with elevated NaV1.7 expression.

Role of vaccinia virus growth factor in stimulating the mTORC1-CAD axis of the de novo pyrimidine pathway under different nutritional cues

Vaccinia virus (VACV), the prototype poxvirus, actively reprograms host cell metabolism upon infection. However, the nature and molecular mechanisms remain largely elusive. Given the diverse nutritional exposures of cells in different physiological contexts, it is essential to understand how VACV may alter various metabolic pathways in different nutritional conditions. In this study, we established the importance of de novo pyrimidine biosynthesis in VACV infection. We elucidated the significance of vaccinia growth factor (VGF), a viral early protein and a homolog of cellular epidermal growth factor, in enabling VACV to phosphorylate the key enzyme CAD of the de novo pyrimidine pathway at serine 1859, a site known to positively regulate CAD activity. While nutrient-poor conditions typically inhibit mTORC1 activation, VACV activates CAD via mTORC1-S6K1 signaling axis, in conditions where glutamine and asparagine are absent. However, unlike its cellular homolog, epidermal growth factor (EGF), VGF peptide alone in the absence of VACV infection has minimal ability to activate CAD, suggestive of the involvement of other viral factor(s) and differential functions to EGF acquired during poxvirus evolution. Our research provides a foundation for understanding the regulation of a significant metabolic pathway, namely, de novo pyrimidine synthesis during VACV infection, shedding new light on viral regulation under distinct nutritional environments. This study not only has the potential to contribute to the advancement of antiviral treatments but also improve the development of VACV as an oncolytic agent and vaccine vector.

The therapeutic impact of programmed death - 1 in the treatment of colorectal cancer

Colorectal cancer (CRC) is the most common type of newly diagnosed cancer. Metastatic spread and multifactorial chemoresistance have limited the benefits of current therapies. Hence, it is imperative to identify new therapeutic agents to increase treatment efficacy. One of CRC's most promising immunotherapeutic targets is programmed death-1 (PD-1), a cell surface receptor that regulates immune responses. In this paper, we provide an overview of the therapeutic impact of PD-1 in the treatment of CRC. Cancer cells can exploit the PD-1 pathway by upregulating its programmed death-ligand 1 (PD-L1) ligand to evade immune surveillance. The binding of PD-L1 to PD-1 inhibits T cell function, leading to tumor immune escape. PD-1 inhibitors, such as pembrolizumab and nivolumab, block the PD-1/PD-L1 interaction. Clinical trials evaluating PD-1 inhibitors in advanced CRC have shown promising results. In patients with microsatellite instability-high (MSI-H) or mismatch repair-deficient (dMMR) tumors characterized by high mutation rates and increased immunogenicity, PD-1 blockade has demonstrated remarkable efficacy. As a result, pembrolizumab and nivolumab have received accelerated approval by regulatory authorities for the treatment of MSI-H/dMMR metastatic CRC. Additionally, combination approaches, such as combining PD-1 inhibitors with other immunotherapies or targeted agents, are being explored. Despite the success of PD-1 inhibitors in CRC, challenges still exist. Immune-related adverse events can occur and require close monitoring. In conclusion, PD-1 inhibitors have demonstrated significant therapeutic impact, particularly in patients with MSI-H/dMMR tumors.

Revisiting the evolution of bow-tie architecture in signaling networks

Bow-tie architecture is a layered network structure that has a narrow middle layer with multiple inputs and outputs. Such structures are widely seen in the molecular networks in cells, suggesting that a universal evolutionary mechanism underlies the emergence of bow-tie architecture. The previous theoretical studies have implemented evolutionary simulations of the feedforward network to satisfy a given input-output goal and proposed that the bow-tie architecture emerges when the ideal input-output relation is given as a rank-deficient matrix with mutations in network link intensities in a multiplicative manner. Here, we report that the bow-tie network inevitably appears when the link intensities representing molecular interactions are small at the initial condition of the evolutionary simulation, regardless of the rank of the goal matrix. Our dynamical system analysis clarifies the mechanisms underlying the emergence of the bow-tie structure. Further, we demonstrate that the increase in the input-output matrix reduces the width of the middle layer, resulting in the emergence of bow-tie architecture, even when evolution starts from large link intensities. Our data suggest that bow-tie architecture emerges as a side effect of evolution rather than as a result of evolutionary adaptation.

Tumor-Agnostic Therapy-The Final Step Forward in the Cure for Human Neoplasms?

Cancer accounted for 10 million deaths in 2020, nearly one in every six deaths annually. Despite advancements, the contemporary clinical management of human neoplasms faces a number of challenges. Surgical removal of tumor tissues is often not possible technically, while radiation and chemotherapy pose the risk of damaging healthy cells, tissues, and organs, presenting complex clinical challenges. These require a paradigm shift in developing new therapeutic modalities moving towards a more personalized and targeted approach. The tumor-agnostic philosophy, one of these new modalities, focuses on characteristic molecular signatures of transformed cells independently of their traditional histopathological classification. These include commonly occurring DNA aberrations in cancer cells, shared metabolic features of their homeostasis or immune evasion measures of the tumor tissues. The first dedicated, FDA-approved tumor-agnostic agent's profound progression-free survival of 78% in mismatch repair-deficient colorectal cancer paved the way for the accelerated FDA approvals of novel tumor-agnostic therapeutic compounds. Here, we review the historical background, current status, and future perspectives of this new era of clinical oncology.

Circadian patterns of growth factor receptor-dependent signaling and implications for carcinogenesis

Several different signaling pathways that regulate cell proliferation and differentiation are initiated by binding of ligands to cell-surface and membrane-bound enzyme-linked receptors, such as receptor tyrosine kinases and serine-threonine kinases. They prompt phosphorylation of tyrosine and serine-threonine residues and initiate downstream signaling pathways and priming of intracellular molecules that convey the signal in the cytoplasm and nucleus, with transcriptional activation of specific genes enriching cell growth and survival-related cascades. These cell processes are rhythmically driven by molecular clockworks endowed in every cell type and when deregulated play a crucial role in cancer onset and progression. Growth factors and their matching receptor-dependent signaling are frequently overexpressed and/or dysregulated in many cancer types. In this review we focus on the interplay between biological clocks and Growth Factor Receptor-dependent signaling in the context of carcinogenesis.

Growth factor-dependent phosphorylation of Gαi shapes canonical signaling by G protein-coupled receptors

A long-standing question in the field of signal transduction is how distinct signaling pathways interact with each other to control cell behavior. Growth factor receptors and G protein-coupled receptors (GPCRs) are the two major signaling hubs in eukaryotes. Given that the mechanisms by which they signal independently have been extensively characterized, we investigated how they may cross-talk with each other. Using linear ion trap mass spectrometry and cell-based biophysical, biochemical, and phenotypic assays, we found at least three distinct ways in which epidermal growth factor affected canonical G protein signaling by the Gi-coupled GPCR CXCR4 through the phosphorylation of Gαi. Phosphomimicking mutations in two residues in the αE helix of Gαi (tyrosine-154/tyrosine-155) suppressed agonist-induced Gαi activation while promoting constitutive Gβγ signaling. Phosphomimicking mutations in the P loop (serine-44, serine-47, and threonine-48) suppressed Gi activation entirely, thus completely segregating growth factor and GPCR pathways. As expected, most of the phosphorylation events appeared to affect intrinsic properties of Gαi proteins, including conformational stability, nucleotide binding, and the ability to associate with and to release Gβγ. However, one phosphomimicking mutation, targeting the carboxyl-terminal residue tyrosine-320, promoted mislocalization of Gαi from the plasma membrane, a previously uncharacterized mechanism of suppressing GPCR signaling through G protein subcellular compartmentalization. Together, these findings elucidate not only how growth factor and chemokine signals cross-talk through the phosphorylation-dependent modulation of Gαi but also how such cross-talk may generate signal diversity.

Applications of model simulation in pharmacological fields and the problems of theoretical reliability

The use of mathematical models has become increasingly prevalent in pharmacological fields, particularly in drug development processes. These models are instrumental in tasks such as designing clinical trials and assessing factors like efficacy, toxicity, and clinical practice. Various types of models have been developed and documented. Nevertheless, emphasizing the reliability of parameter values is crucial, as they play a pivotal role in shaping the behavior of the system. In some instances, parameter values reported previously are treated as fixed values, which can lead to convergence towards values that deviate substantially from those found in actual biological systems. This is especially true when parameter values are determined through fitting to limited observations. To mitigate this risk, the reuse of parameter values from previous reports should be approached with a critical evaluation of their validity. Currently, there is a proposal for a simultaneous search for plausible values for all parameters using comprehensive search algorithms in both pharmacokinetic and pharmacodynamic or systems pharmacological models. Implementing these methodologies can help address issues related to parameter determination. Furthermore, integrating these approaches with methods developed in the field of machine-learning field has the potential to enhance the reliability of parameter values and the resulting model outputs.

HER2 puzzle pieces: Non-Coding RNAs as keys to mechanisms, chemoresistance, and clinical outcomes in Ovarian cancer

Ovarian cancer (OC) presents significant challenges, characterized by limited treatment options and therapy resistance often attributed to dysregulation of the HER2 signaling pathway. Non-coding RNAs (ncRNAs) have emerged as key players in regulating gene expression in OC. This comprehensive review underscores the pivotal role of ncRNAs in modulating HER2 signaling, with a specific focus on their mechanisms, impact on chemoresistance, and prognostic/diagnostic implications. MicroRNAs, long non-coding RNAs, and circular RNAs have been identified as essential regulators in the modulation of the HER2 pathway. By directly targeting key components of the HER2 axis, these ncRNAs influence its activation and downstream signaling cascades. Dysregulated ncRNAs have been closely associated with chemoresistance, leading to treatment failures and disease progression in OC. Furthermore, distinct expression profiles of ncRNAs hold promise as reliable prognostic and diagnostic markers, facilitating personalized treatment strategies and enhancing disease outcome assessments. A comprehensive understanding of how ncRNAs intricately modulate HER2 signaling is imperative for the development of targeted therapies and the improvement of patient outcomes. The integration of ncRNA profiles into clinical practice has the potential to enhance prognostic and diagnostic accuracy in the management of ovarian cancer. Further research efforts are essential to validate the clinical utility of ncRNAs and elucidate their precise roles in the regulation of HER2 signaling. In conclusion, ncRNAs play a crucial role in governing HER2 signaling in ovarian cancer, impacting chemoresistance and providing valuable prognostic and diagnostic insights. The exploration of ncRNA-mediated HER2 modulation offers promising avenues for the development of personalized treatment approaches, ultimately advancing patient care and outcomes in OC.

Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer

Breast cancer is one of the prevailing cancers globally, with a high mortality rate. Metastatic breast cancer (MBC) is an advanced stage of cancer, characterised by a highly nonlinear, heterogeneous process involving numerous singling pathways and regulatory interactions. Epithelial-mesenchymal transition (EMT) emerges as a key mechanism exploited by cancer cells. Transforming Growth Factor-β (TGFβ)-dependent signalling is attributed to promote EMT in advanced stages of breast cancer. A comprehensive regulatory map of TGFβ induced EMT was developed through an extensive literature survey. The network assembled comprises of 312 distinct species (proteins, genes, RNAs, complexes), and 426 reactions (state transitions, nuclear translocations, complex associations, and dissociations). The map was developed by following Systems Biology Graphical Notation (SBGN) using Cell Designer and made publicly available using MINERVA ( http://35.174.227.105:8080/minerva/?id=Metastatic_Breast_Cancer_1 ). While the complete molecular mechanism of MBC is still not known, the map captures the elaborate signalling interplay of TGFβ induced EMT-promoting MBC. Subsequently, the disease map assembled was translated into a Boolean model utilising CaSQ and analysed using Cell Collective. Simulations of these have captured the known experimental outcomes of TGFβ induced EMT in MBC. Hub regulators of the assembled map were identified, and their transcriptome-based analysis confirmed their role in cancer metastasis. Elaborate analysis of this map may help in gaining additional insights into the development and progression of metastatic breast cancer.

Understanding Gene Involvement in Hepatocellular Carcinoma: Implications for Gene Therapy and Personalized Medicine

Hepatocellular carcinoma (HCC) is the dominant type of liver cancers and is one of the deadliest health threats globally. The conventional therapeutic options for HCC are hampered by low efficiency and intolerable side effects. Gene therapy, however, now offers hope for the treatment of many disorders previously considered incurable, and gene therapy is beginning to address many of the shortcomings of conventional therapies. Herein, we summarize the involvement of genes in the pathogenesis and prognosis of HCC, with a special focus on dysregulated signaling pathways, genes involved in immune evasion, and non-coding RNAs as novel two-edged players, which collectively offer potential targets for the gene therapy of HCC. Herein, the opportunities and challenges of HCC gene therapy are discussed. These include innovative therapies such as genome editing and cell therapies. Moreover, advanced gene delivery technologies that recruit nanomedicines for use in gene therapy for HCC are highlighted. Finally, suggestions are offered for improved clinical translation and future directions in this area of endeavor.

Molecular modelling, docking and network analysis of phytochemicals from Haritaki churna: role of protein cross-talks for their action

Phytochemicals are bioactive agents present in medicinal plants with therapeutic values. Phytochemicals isolated from plants target multiple cellular processes. In the current work, we have used fractionation techniques to identify 13 bioactive polyphenols in ayurvedic medicine Haritaki Churna. Employing the advanced spectroscopic and fractionation, structure of bioactive polyphenols was determined. Blasting the phytochemical structure allow us to identify a total of 469 protein targets from Drug bank and Binding DB. Phytochemicals with their protein targets from Drug bank was used to create a phytochemical-protein network comprising of 394 nodes and 1023 edges. It highlights the extensive cross-talk between protein target corresponding to different phytochemicals. Analysis of protein targets from Binding data bank gives a network comprised of 143 nodes and 275 edges. Taking the data together from Drug bank and binding data, seven most prominent drug targets (HSP90AA1, c-Src kinase, EGFR, Akt1, EGFR, AR, and ESR-α) were found to be target of the phytochemicals. Molecular modelling and docking experiment indicate that phytochemicals are fitting nicely into active site of the target proteins. The binding energy of the phytochemicals were better than the inhibitors of these protein targets. The strength and stability of the protein ligand complexes were further confirmed using molecular dynamic simulation studies. Further, the ADMET profiles of phytochemicals extracted from HCAE suggests that they can be potential drug targets. The phytochemical cross-talk was further proven by choosing c-Src as a model. HCAE down regulated c-Src and its downstream protein targets such as Akt1, cyclin D1 and vimentin. Hence, network analysis followed by molecular docking, molecular dynamics simulation and in-vitro studies clearly highlight the role of protein network and subsequent selection of drug candidate based on network pharmacology.Communicated by Ramaswamy H. Sarma.

The anticancer activity of bovine lactoferrin is reduced by deglycosylation and it follows a different pathway in cervix and colon cancer cells

Bovine lactoferrin (bLF) is a glycosylated protein with purported beneficial properties. The aim of this work was to determine the role of bLF glycosylation in the adhesion, internalization, and growth inhibition of cancer cells. The viability of cervix (HeLa) and colon (Caco-2) cancer cells (MTT assay and epifluorescence microscopy) was inhibited by bLF, while deglycosylated bLF (bLFdeg) had no effect. Adhesion to cell surfaces was quantified by immunofluorescence assay and showed that bLF was able to bind more efficiently to both cell lines than bLFdeg. Microscopic observations indicated that bLF glycosylation favored bLF binding to epithelial cells and that it was endocytosed through caveolin-1-mediated internalization. In addition, the mechanism of action of bLF on cancer cell proliferation was investigated by determining the amount of phosphorylated intermediates of signaling pathways such as epidermal growth factor receptor (EGFR), extracellular signal-regulated kinase (ERK) and protein kinase B (known as Akt). Chemoluminescence immunoassay of phosphorylated intermediates showed that bLF inhibited Akt phosphorylation, consistent with its growth inhibiting activity. This assay also indicated that the bLF receptor/signaling pathways may be different in the two cell lines, Caco-2 and HeLa. This work confirmed the effect of glycosylated bLF in inhibiting cancer cell growth and that glycosylation is required for optimal surface adhesion, internalization, and inhibition of the ERK/Akt pathway of cell proliferation through glycosylated cell surface receptors.

CX3CL1 (Fractalkine)-CX3CR1 Axis in Inflammation-Induced Angiogenesis and Tumorigenesis

The chemotactic cytokine fractalkine (FKN, chemokine CX3CL1) has unique properties resulting from the combination of chemoattractants and adhesion molecules. The soluble form (sFKN) has chemotactic properties and strongly attracts T cells and monocytes. The membrane-bound form (mFKN) facilitates diapedesis and is responsible for cell-to-cell adhesion, especially by promoting the strong adhesion of leukocytes (monocytes) to activated endothelial cells with the subsequent formation of an extracellular matrix and angiogenesis. FKN signaling occurs via CX3CR1, which is the only known member of the CX3C chemokine receptor subfamily. Signaling within the FKN-CX3CR1 axis plays an important role in many processes related to inflammation and the immune response, which often occur simultaneously and overlap. FKN is strongly upregulated by hypoxia and/or inflammation-induced inflammatory cytokine release, and it may act locally as a key angiogenic factor in the highly hypoxic tumor microenvironment. The importance of the FKN/CX3CR1 signaling pathway in tumorigenesis and cancer metastasis results from its influence on cell adhesion, apoptosis, and cell migration. This review presents the role of the FKN signaling pathway in the context of angiogenesis in inflammation and cancer. The mechanisms determining the pro- or anti-tumor effects are presented, which are the cause of the seemingly contradictory results that create confusion regarding the therapeutic goals.

Immunotherapy guided precision medicine in solid tumors

Cancer is no longer recognized as a single disease but a collection of diseases each with its defining characteristics and behavior. Even within the same cancer type, there can be substantial heterogeneity at the molecular level. Cancer cells often accumulate various genetic mutations and epigenetic alterations over time, leading to a coexistence of distinct subpopulations of cells within the tumor. This tumor heterogeneity arises not only due to clonal outgrowth of cells with genetic mutations, but also due to interactions of tumor cells with the tumor microenvironment (TME). The latter is a dynamic ecosystem that includes cancer cells, immune cells, fibroblasts, endothelial cells, stromal cells, blood vessels, and extracellular matrix components, tumor-associated macrophages and secreted molecules. The complex interplay between tumor heterogeneity and the TME makes it difficult to develop one-size-fits-all treatments and is often the cause of therapeutic failure and resistance in solid cancers. Technological advances in the post-genomic era have given us cues regarding spatial and temporal tumor heterogeneity. Armed with this knowledge, oncologists are trying to target the unique genomic, epigenetic, and molecular landscape in the tumor cell that causes its oncogenic transformation in a particular patient. This has ushered in the era of personalized precision medicine (PPM). Immunotherapy, on the other hand, involves leveraging the body's immune system to recognize and attack cancer cells and spare healthy cells from the damage induced by radiation and chemotherapy. Combining PPM and immunotherapy represents a paradigm shift in cancer treatment and has emerged as a promising treatment modality for several solid cancers. In this chapter, we summarise major types of cancer immunotherapy and discuss how they are being used for precision medicine in different solid tumors.

Protein neddylation and its role in health and diseases

NEDD8 (Neural precursor cell expressed developmentally downregulated protein 8) is an ubiquitin-like protein that is covalently attached to a lysine residue of a protein substrate through a process known as neddylation, catalyzed by the enzyme cascade, namely NEDD8 activating enzyme (E1), NEDD8 conjugating enzyme (E2), and NEDD8 ligase (E3). The substrates of neddylation are categorized into cullins and non-cullin proteins. Neddylation of cullins activates CRLs (cullin RING ligases), the largest family of E3 ligases, whereas neddylation of non-cullin substrates alters their stability and activity, as well as subcellular localization. Significantly, the neddylation pathway and/or many neddylation substrates are abnormally activated or over-expressed in various human diseases, such as metabolic disorders, liver dysfunction, neurodegenerative disorders, and cancers, among others. Thus, targeting neddylation becomes an attractive strategy for the treatment of these diseases. In this review, we first provide a general introduction on the neddylation cascade, its biochemical process and regulation, and the crystal structures of neddylation enzymes in complex with cullin substrates; then discuss how neddylation governs various key biological processes via the modification of cullins and non-cullin substrates. We further review the literature data on dysregulated neddylation in several human diseases, particularly cancer, followed by an outline of current efforts in the discovery of small molecule inhibitors of neddylation as a promising therapeutic approach. Finally, few perspectives were proposed for extensive future investigations.

Dysregulation of cellular membrane homeostasis as a crucial modulator of cancer risk

Cellular membranes serve as an epicentre combining extracellular and cytosolic components with membranous effectors, which together support numerous fundamental cellular signalling pathways that mediate biological responses. To execute their functions, membrane proteins, lipids and carbohydrates arrange, in a highly coordinated manner, into well-defined assemblies displaying diverse biological and biophysical characteristics that modulate several signalling events. The loss of membrane homeostasis can trigger oncogenic signalling. More recently, it has been documented that select membrane active dietaries (MADs) can reshape biological membranes and subsequently decrease cancer risk. In this review, we emphasize the significance of membrane domain structure, organization and their signalling functionalities as well as how loss of membrane homeostasis can steer aberrant signalling. Moreover, we describe in detail the complexities associated with the examination of these membrane domains and their association with cancer. Finally, we summarize the current literature on MADs and their effects on cellular membranes, including various mechanisms of dietary chemoprevention/interception and the functional links between nutritional bioactives, membrane homeostasis and cancer biology.

The potential of phytochemicals against epidermal growth factor receptor tyrosine kinase (EGFRK): an insight from molecular dynamic simulations

Cancer is an umbrella term used to define various diseases with abnormal cell proliferation at the focal point. According to the WHO, cancer is the leading cause of death worldwide, with lung cancer being the second most common perpetrator after breast cancer. There are several proteins acting in harmony that lead to cancer. EGFR has been identified as one of the proteins that is linked to cell division, even when it is cancerous in nature. Cancer can be treated using therapeutic agents that target EGFR or their signaling networks. Available drugs that could inhibit EGFR have acquired resistance in most cases and multiple side effects on the human body. That is why phytochemicals are being studied for their role in this case. Around 8000 compounds were retrieved from our previously created phytochemdb database for their drug activity, and the 3D protein structure was collected from the protein data bank. The selected dataset of ligands was virtually screened through HTVS, SP, and XP to retain the top 4 hits. Molecular dynamics revealed the stability and flexibility of protein-(selected)ligand interactions. The non-bond interactions of each of the compounds with EGFR, such as Gossypetin interacting with active site MET769 and ASP831; Muxiangrine III interacting with MET769 and ASP831; Quercetagetin showing non-bonded interactions with GLU738, GLN767, and MET769 for >100% of the simulation timeframe These findings suggest further research into these compounds, which can yield a potential phytochemical drug against cancer.Communicated by Ramaswamy H. Sarma.

Crosstalk between KDEL receptor and EGF receptor mediates cell proliferation and migration via STAT3 signaling

Hostile microenvironment of cancer cells provoke a stressful condition for endoplasmic reticulum (ER) and stimulate the expression and secretion of ER chaperones, leading to tumorigenic effects. However, the molecular mechanism underlying these effects is largely unknown. In this study, we reveal that the last four residues of ER chaperones, which are recognized by KDEL receptor (KDELR), is required for cell proliferation and migration induced by secreted chaperones. By combining proximity-based mass spectrometry analysis, split venus imaging and membrane yeast two hybrid assay, we present that EGF receptor (EGFR) may be a co-receptor for KDELR on the surface. Prior to ligand addition, KDELR spontaneously oligomerizes and constantly undergoes recycling near the plasma membrane. Upon KDEL ligand binding, the interactions of KDELR with itself and with EGFR increase rapidly, leading to augmented internalization of KDELR and tyrosine phosphorylation in the C-terminus of EGFR. STAT3, which binds the phosphorylated tyrosine motif on EGFR, is subsequently activated by EGFR and mediates cell growth and migration. Taken together, our results suggest that KDELR serves as a bona fide cell surface receptor for secreted ER chaperones and transactivates EGFR-STAT3 signaling pathway.

Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks

Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods that encompass multiple omics data. Visualization in 2.5 dimension (2.5D visualization), which is an isometric view of stacked X-Y planes, is a convenient way to interpret multi-omics/trans-omics data in the context of the conventional layouts of biochemical networks drawn on each of the stacked omics layers. However, 2.5D visualization of trans-omics networks is a state-of-the-art method that primarily relies on time-consuming human efforts involving manual drawing. Here, we present an R Bioconductor package 'transomics2cytoscape' for automated visualization of 2.5D trans-omics networks. We confirmed that transomics2cytoscape could be used for rapid visualization of trans-omics networks presented in published papers within a few minutes. Transomics2cytoscape allows for frequent update/redrawing of trans-omics networks in line with the progress in multi-omics/trans-omics data analysis, thereby enabling network-based interpretation of multi-omics data at each research step. The transomics2cytoscape source code is available at https://github.com/ecell/transomics2cytoscape .

Epidermal Growth Factor Receptor Inhibition With Erlotinib in Liver: Dose De-Escalation Pilot Trial as an Initial Step in a Chemoprevention Strategy

Background and Aims

Effective approaches for prevention of hepatocellular carcinoma (HCC) will have a significant impact on HCC-related mortality. There are strong preclinical data and rationale to support targeting epidermal growth factor receptor (EGFR) for HCC chemoprevention. Small molecule inhibitors of EGFR have been Food and Drug Administration-approved for cancer therapy, which provides an opportunity to repurpose one of these drugs for chemoprevention of HCC. Unfortunately, the frequency of side effects associated with administration of these drugs at oncology doses renders them ineffective for chemoprevention. This clinical trial assesses whether lower doses of one of these inhibitors, erlotinib, still engages EGFR in the liver to block signaling (eg, EGFR phosphorylation). The objective of this clinical trial was determination of a safe and minimum effective dose of erlorinib for which ≥ 50% reduction phospho-EGFR immunohistochemical staining in the liver was observed.

Methods

Forty six participants were preregistered and 25 participants were registered in this multicenter trial. By dose de-escalation trial design, cohorts of participants received a 7-day course of erlotinib 75 mg/day, 50 mg/day or 25 mg/day with liver tissue acquisition prior to and after erlotinib.

Results

A ≥50% reduction phospho-EGFR immunohistochemical staining in the liver was observed in a minimum of 40% of participants (predetermined threshhold) at each of the dose levels. Erlotinib was very well tolerated with few side effects observed, particularly at the dose of 25 mg/day. Favorable modulation of the Prognostic Liver Signature was observed in participants who received erlotinib.

Conclusion

These data support the selection of erlotinib doses as low as 25 mg/day of for a longer intervention to assess for evidence of efficacy as an HCC chemoprevention drug (ClinicalTrials.govNCT02273362).