Focal Adhesion Signaling Research Articles

Abstract 4745: A novel combination therapy targeting RAF, MEK and FAK to overcome skin cutaneous melanoma treatment resistance

Abstract Metastatic melanoma is the most aggressive malignancy of the skin and BRAFV600E mutation is the most common genetic alteration in skin cutaneous melanoma (SKCM). Despite the advent of immune checkpoint inhibition (ICI) immunotherapy, only 40% of patients show long-term responses. As such, combined therapy with BRAF and MEK inhibitors (BRAFi + MEKi) remains the standard of care for BRAFV600E+ SKCM. In the present study, transcriptome analysis of BRAFV600E+ SKCM tumors derived from patients revealed that activation of extracellular matrix signaling, including focal adhesion signaling, is highly enriched in patients who experienced disease progression on BRAFi + MEKi therapy. Consistent with these results, we found increased activation of focal adhesion kinase (FAK) in human BRAFV600E+ SKCM A375 cells treated with BRAFi, MEKi or the RAF/MEK clamp avutometinib. Mechanistically, we discovered that avutometinib-mediated inhibition of the RAF/MEK/ERK pathway decreased RhoE/Rnd3 expression, thereby unleashing RhoA/FAK/AKT signaling. Thus, we hypothesized that FAK activation represents a resistance mechanism to BRAFi + MEKi and that FAK inhibition (FAKi) might overcome resistance to BRAFi/MEKi. Indeed, avutometinib demonstrated synergistic antiproliferative and proapoptotic activity when combined with FAKi in human BRAFV600E+ SKCM A375 cells. Importantly, we found that the combination of FAKi + avutometinib overcame resistance to BRAFi + MEKi in SKCM xenografts and patient-derived cells from SKCM-resistant lesions. Finally, we showed that while BRAFV600E+ SKCM YUMM 1.7 syngeneic tumors failed to respond to ICI therapy, avutometinib ± FAKi inhibited tumor growth. We observed that tumors treated with avutometinib as single agent eventually developed resistance and escaped growth inhibition, but those treated with combined avutometinib and FAKi displayed durable treatment responses, often with complete tumor regression. These findings provide a rationale for the clinical development of avutometinib with defactinib (FAKi) in patients with BRAFV600E+ cutaneous melanoma following progression on BRAFi + MEKi and/or ICI therapy. Citation Format: Simone Lubrano, Farhoud Faraji, Rodolfo Daniel Cervantes-Villagrana, Sydney Ramirez, Nadia Arang, Adam Officer, Damiano C. Rigiracciolo, Paola Y. Anguiano Quiroz, Antonieta Bacchiocchi, Ruth Halaban, Silvia Coma, Sheri Holmen, Claudia Martini, Jonathan Pachter, Andrew Aplin, J. Silvio Gutkind. A novel combination therapy targeting RAF, MEK and FAK to overcome skin cutaneous melanoma treatment resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4745.

Mechanisms underlying morphological and functional changes of cilia in fibroblasts derived from patients bearing ARL3T31A and ARL3T31A/C118F mutations.

ARL3 is essential for cilia development, and mutations in ARL3 are closely associated with ciliopathies. In a previous study, we observed distinct phenotypes of retinal dystrophy in patients with heterozygous ARL3T31A and compound heterozygous ARL3T31A/C118F mutations, indicating that different mutation types may exert diverse effects on their functions. Here, we generated transformed immortal fibroblast cells from patients carrying heterozygous ARL3T31A and compound heterozygous ARL3T31A/C118F mutations, and systematically evaluated their cilia morphology and function, which were further validated in ARPE-19 cells. Results showed that both ARL3T31A and ARL3T31A/C118F mutations led to a decrease in cilium formation. The ARL3T31A/C118F mutations caused significantly elongated cilia and impaired retrograde transport, whereas the ARL3T31A mutation did not induce significant changes in fibroblasts. RNA-sequencing results indicated that compared to ARL3T31A , ARL3T31A/C118F fibroblasts exhibited a higher enrichment of biological processes related to neuron projection development, tissue morphogenesis, and extracellular matrix (ECM) organization, with noticeable alterations in pathways such as ECM-receptor interaction, focal adhesion, and TGF-β signaling. Similar changes were observed in the proteomic results in ARPE-19 cells. Core regulated genes including IQUB, UNC13D, RAB3IP, and GRIP1 were specifically downregulated in the ARL3T31A/C118F group, and expressions of IQUB, NPM2, and SLC38A4 were further validated. Additionally, IQUB showed a rescuing effect on the overlong cilia observed in ARL3T31A/C118F fibroblasts. Our results not only enhance our understanding of ARL3-related diseases but also provide new insights into the analysis of heterozygous and compound heterozygous mutations in genetics.

Mechanisms of imbalanced testicular homeostasis in infancy due to aberrant histone acetylation in undifferentiated spermatogonia under different concentrations of Di(2-ethylhexyl) phthalate (DEHP) exposure

Di (2-ethylhexyl) phthalate (DEHP), identified as an endocrine-disrupting chemical, is associated with reproductive toxicity. This association is particularly noteworthy in newborns with incompletely developed metabolic functions, as exposure to DEHP can induce enduring damage to the reproductive system, potentially influencing adult reproductive health. In this study, we continuously administered 40 μg/kg and 80 μg/kg DEHP to postnatal day 5 (PD5) mice for ten days to simulate low and high doses of DEHP exposure during infancy. Utilizing single-cell RNA sequencing (scRNA-seq), our analysis revealed that varying concentrations of DEHP exposure during infancy induced distinct DNA damage response characteristics in testicular Undifferentiated spermatogonia (Undiff SPG). Specifically, DNA damage triggered mitochondrial dysfunction, leading to acetyl-CoA content alterations. Subsequently, this disruption caused aberrations in histone acetylation patterns, ultimately resulting in apoptosis of Undiff SPG in the 40 μg/kg DEHP group and autophagy in the 80 μg/kg DEHP group. Furthermore, we found that DEHP exposure impacts the development and functionality of Sertoli and Leydig cells through the focal adhesion and PPAR signaling pathways, respectively. We also revealed that Leydig cells regulate the metabolic environment of Undiff SPG via Ptn-Sdc4 and Mdk-Sdc4 after DEHP exposure. Finally, our study provided pioneering evidence that disruptions in testicular homeostasis induced by DEHP exposure during infancy endure into adulthood. In summary, this study elucidates the molecular mechanisms through which DEHP exposure during infancy influences the development of testicular cell populations.

Signaling pathways and regulatory networks in quail skeletal muscle development: insights from whole transcriptome sequencing

Quail, as an advantageous avian model organism due to its compact size and short reproductive cycle, holds substantial potential for enhancing our understanding of skeletal muscle development. The quantity of skeletal muscle represents a vital economic trait in poultry production. Unraveling the molecular mechanisms governing quail skeletal muscle development is of paramount importance for optimizing meat and egg yield through selective breeding programs. However, a comprehensive characterization of the regulatory dynamics and molecular control underpinning quail skeletal muscle development remains elusive. In this study, through the application of HE staining on quail leg muscle sections, coupled with preceding fluorescence quantification PCR of markers indicative of skeletal muscle differentiation, we have delineated embryonic day 9 (E9) and embryonic day 14 (E14) as the start and ending points, respectively, of quail skeletal muscle differentiation. Then, we employed whole transcriptome sequencing to investigate the temporal expression profiles of leg muscles in quail embryos at the initiation of differentiation (E9) and upon completion of differentiation (E14). Our analysis revealed the expression patterns of 12,012 genes, 625 lncRNAs, 14,457 circRNAs, and 969 miRNAs in quail skeletal muscle samples. Differential expression analysis between the E14 and E9 groups uncovered 3,479 differentially expressed mRNAs, 124 lncRNAs, 292 circRNAs, and 154 miRNAs. Furthermore, enrichment analysis highlighted the heightened activity of signaling pathways related to skeletal muscle metabolism and intermuscular fat formation, such as the ECM-receptor interaction, focal adhesion, and PPAR signaling pathway during E14 skeletal muscle development. Conversely, the E9 stage exhibited a prevalence of pathways associated with myoblast proliferation, exemplified by cell cycle processes. Additionally, we constructed regulatory networks encompassing lncRNA‒mRNA, miRNA‒mRNA, lncRNA‒miRNA-mRNA, and circRNA-miRNA‒mRNA interactions, thus shedding light on their putative roles within quail skeletal muscle. Collectively, our findings illuminate the gene and non-coding RNA expression characteristics during quail skeletal muscle development, serving as a foundation for future investigations into the regulatory mechanisms governing non-coding RNA and quail skeletal muscle development in poultry production.

Curcumin suppresses metastasis of triple-negative breast cancer cells by modulating EMT signaling pathways: An integrated study of bioinformatics analysis.

This study aimed to use bioinformatics approaches for predicting the anticancer mechanisms of curcumin on triple-negative breast cancer (TNBC) and to verify these predictions through in vitro experiments. Initially, the Cell Counting Kit-8 (CCK8) assay was employed to rigorously investigate the influence of curcumin on the proliferative capacity of TNBC cells. Subsequently, flow cytometry was employed to meticulously assess the impact of curcumin on cellular apoptosis and the cell cycle regulation. Transwell assays were employed to meticulously evaluate the effect of curcumin on the motility of TNBC cells. RNA sequencing was conducted, followed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of differentially expressed genes, aiming to elucidate the potential anticancer mechanisms underlying curcumin's effects. To thoroughly elucidate the interactions among multiple proteins, we constructed a protein-protein interaction (PPI) network. Finally, the expression levels of several key proteins, including fibronectin, mTOR, β-Catenin, p-Akt, Akt, N-Cadherin, p-S6, and S6, were assessed using the western blot. The CCK8 assay results showed that curcumin significantly inhibited the proliferation of Hs578T and MDA-MB-231 cells. Flow cytometry results showed that curcumin induced apoptosis in these cells and arrested the cell cycle at the G2/M phase. Additionally, Transwell assay results showed that curcumin effectively reduced the motility of Hs578T and MDA-MB-231 cells. Enrichment analysis of RNA sequencing data showed that the mechanism of action of curcumin was significantly associated with signaling pathways such as pathways in cancer, focal adhesion, and PI3K-Akt signaling pathways. Subsequently, we constructed a protein-protein interaction network to elucidate the interactions among multiple proteins. Finally, Western blotting analysis showed that curcumin significantly decreased the expression levels of key proteins including Fibronectin, mTOR, β-Catenin, p-Akt, Akt, N-Cadherin, p-S6, and S6. Curcumin exhibits its therapeutic potential in TNBC by modulating multiple signaling pathways. It may inhibit the epithelial-mesenchymal transition process by downregulating the expression of proteins involved in the mTOR and PI3K-Akt signaling pathways, thereby suppressing the motility of TNBC cells. These findings provide experimental evidence for considering curcumin as a potential therapeutic strategy in the treatment of TNBC.

Filamin C Deficiency Impairs Sarcomere Stability and Activates Focal Adhesion Kinase through PDGFRA Signaling in Induced Pluripotent Stem Cell-Derived Cardiomyocytes.

Truncating mutations in filamin C (FLNC) are associated with dilated cardiomyopathy and arrhythmogenic cardiomyopathy. FLNC is an actin-binding protein and is known to interact with transmembrane and structural proteins; hence, the ablation of FLNC in cardiomyocytes is expected to dysregulate cell adhesion, cytoskeletal organization, sarcomere structural integrity, and likely nuclear function. Our previous study showed that the transcriptional profiles of FLNC homozygous deletions in human pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are highly comparable to the transcriptome profiles of hiPSC-CMs from patients with FLNC truncating mutations. Therefore, in this study, we used CRISPR-Cas-engineered hiPSC-derived FLNC knockout cardiac myocytes as a model of FLNC cardiomyopathy to determine pathogenic mechanisms and to examine structural changes caused by FLNC deficiency. RNA sequencing data indicated the significant upregulation of focal adhesion signaling and the dysregulation of thin filament genes in FLNC-knockout (FLNCKO) hiPSC-CMs compared to isogenic hiPSC-CMs. Furthermore, our findings suggest that the complete loss of FLNC in cardiomyocytes led to cytoskeletal defects and the activation of focal adhesion kinase. Pharmacological inhibition of PDGFRA signaling using crenolanib (an FDA-approved drug) reduced focal adhesion kinase activation and partially normalized the focal adhesion signaling pathway. The findings from this study suggest the opportunity in repurposing FDA-approved drug as a therapeutic strategy to treat FLNC cardiomyopathy.

Network Propagation-based Identification of Oligometastatic Biomarkers in Metastatic Colorectal Cancer

Background: The oligometastatic disease has been proposed as an intermediate state between primary tumor and systemically metastatic disease, which has great potential curable with locoregional therapies. However, since no biomarker for the identification of patients with true oligometastatic disease is clinically available, the diagnosis of oligometastatic disease remains controversial. Objective: We aim to identify potential biomarkers of colorectal cancer patients with true oligometastatic states, who will benefit most from local therapy. Methods: This study retrospectively analyzed the transcriptome profiles and clinical parameters of 307 metastatic colorectal cancer patients. A novel network propagation method and network-based strategy were combined to identify oligometastatic biomarkers to predict the prognoses of metastatic colorectal cancer patients. Results: We defined two metastatic risk groups according to twelve oligometastatic biomarkers, which exhibit distinct prognoses, clinicopathological features, immunological characteristics, and biological mechanisms. The metastatic risk assessment model exhibited a more powerful capacity for survival prediction compared to traditional clinicopathological features. The low-MRS group was most consistent with an oligometastatic state, while the high-MRS might be a potential polymetastatic state, which leads to the divergence of their prognostic outcomes and response to treatments. We also identified 22 significant immune check genes between the high-MRS and low- MRS groups. The difference in molecular mechanism between the two metastatic risk groups was associated with focal adhesion, nucleocytoplasmic transport, Hippo, PI3K-Akt, TGF-β, and EMCreceptor interaction signaling pathways. Conclusion: Our study provided a molecular definition of the oligometastatic state in colorectal cancer, which contributes to precise treatment decision-making for advanced patients.

Phospho-eIF4E stimulation regulates coronavirus entry by selective expression of cell membrane-residential factors.

The eukaryotic translation initiation factor eIF4E can regulate cellular translation via phosphorylation on serine 209. In a recent study, by two rounds of TMT relative quantitative proteomics, we found that phosphorylated eIF4E (p-eIF4E) favors the translation of selected mRNAs, and the encoded proteins are mainly involved in ECM-receptor, focal adhesion, and PI3K-Akt signaling. The current paper is focused on the relationship between p-eIF4E and the downstream host cell proteins, and their presumed effect on efficient entry of PEDV. We found that the depletion of membrane-residential factor TSPAN3, CD63, and ITGB2 significantly inhibited viral invasion of PEDV, and reduced the entry of pseudotyped particles PEDV-pp, SARS-CoV-pp, and SARS-CoV-2-pp. The specific antibodies of TSPAN3, CD63, and ITGB2 blocked the adsorption of PEDV into host cells. Moreover, we detected that eIF4E phosphorylation was increased at 1 h after PEDV infection, in accordance with the expression of TSPAN3, CD63, and ITGB2. Similar trends appeared in the intestines of piglets in the early stage of PEDV challenge. Compared with Vero cells, S209A-Vero cells in which eIF4E cannot be phosphorylated showed a decrease of invading PEDV virions. MNK kinase inhibitor blocked PEDV invasion, as well as reduced the accumulation of TSPAN3, CD63, and ITGB2. Further study showed that the ERK-MNK pathway was responsible for the regulation of PEDV-induced early phosphorylation of eIF4E. This paper demonstrates for the first time the connections among p-eIF4E stimulation and membrane-residential host factors. Our findings also enrich the understanding of the biological function of phosphorylated eIF4E during the viral life cycle.IMPORTANCEThe eukaryotic translation initiation factor eIF4E can regulate cellular translation via phosphorylation. In our previous study, several host factors susceptible to a high level of p-eIF4E were found to be conducive to viral infection by coronavirus PEDV. The current paper is focused on cell membrane-residential factors, which are involved in signal pathways that are sensitive to phosphorylated eIF4E. We found that the ERK-MNK pathway was activated, which resulted in the stimulation of phosphorylation of eIF4E in early PEDV infection. Phospho-eIF4E promoted the viral invasion of PEDV by upregulating the expression of host factors TSPAN3, CD63, and ITGB2 at the translation level rather than at the transcription level. Moreover, TSPAN3, CD63, or ITGB2 facilitates the efficient entry of coronavirus SARS-CoV, SARS-CoV-2, and HCoV-OC43. Our findings broaden our insights into the dynamic phosphorylation of eIF4E during the viral life cycle, and provide further evidence that phosphorylated eIF4E regulates selective translation of host mRNA.

Studying Antifatigue Mechanism of Tyr-Pro-Leu-Pro in Exercise Mice Using Label-Free Proteomics.

In our previous study, yeast-derived peptide Tyr-Pro-Leu-Pro (YPLP) was found to prolong treadmill time and relieve muscle fatigue in ICR mice. The present study aimed to further investigate the antifatigue mechanism of YPLP. Three doses of YPLP (10, 25, and 50 mg/kg·d) were given to exercise mice for 4 weeks. Results showed that YPLP reduced the oxidative response via the nuclear factor erythroid-2-related factor 2 (Nrf2) pathway and promoted energy metabolism through the AMP-activated protein kinase (AMPK) pathway. Label-free proteomics results showed that 81 differential abundance proteins (DAPs) were regulated by high-dose YPLP. These DAPs belonged to proteasome, mitochondrial, and muscle proteins. YPLP was mainly involved in proteasome, aminoacyl-tRNA biosynthesis, focal adhesion, and MAPK signal pathways to enhance muscle endurance. Furthermore, real-time quantitative PCR and Western blotting results proved that YPLP upregulated Psmd14 expression and downregulated p38 MAPK expression. Overall, this study revealed the mechanism behind YPLP to alleviate exercise fatigue.

The integration of multi-omics analysis and machine learning for the identification of prognostic assessment and immunotherapy efficacy through aging-associated genes in lung cancer.

Recent years revealed key molecules in lung cancer research, yet their exact roles in disease onset and progression remain uncertain. Lung cancer's heterogeneity complicates prognosis prediction. This study integrates pivotal molecules to evaluate patient prognosis and immunotherapy efficacy. The WGCNA algorithm identified module genes linked to immunity. The Lasso-Cox method built a prognostic model for outcome prediction. GO and KEGG analyses explored gene pathways. ssGSEA quantified immune cell types and functions. The riskScore predicts the effectiveness of immunotherapy based on its correlation with DNA repair and immune checkpoint genes. Single-cell sequencing examined key gene expression across cell types. Using WGCNA, we identified the MEbrown module related to immunity. Lasso-Cox selected "BLK," "ITGB4," "PRKCH," and "SNAI1" for the prognostic model. MF analysis revealed enriched functions including antigen binding, GTPase regulator activity. In terms of BP, processes like immune signaling and mitotic division were enriched. CC enrichment included immunoglobulin complexes and chromosomal regions. Enriched pathways encompassed Cell cycle, Focal adhesion, Cellular senescence, and p53 signaling. ssGSEA evaluated immune cell abundance. RiskScore correlated with CTLA4 and PD1 through MMR and immune checkpoint analysis. Single-cell analysis indicated gene expression across cell types for BLK, ITGB4, PRKCH, and SNAI1. In summary, our developed prognostic model utilizing age-related genes effectively predicts lung cancer prognosis and the efficacy of immune therapy.

Drug resistance mechanisms in dopamine agonist-resistant prolactin pituitary neuroendocrine tumors and exploration for new drugs

BackgroundThe treatment of dopamine agonists (DA) resistant prolactinomas remains a formidable challenge, as the mechanism of resistance is still unclear, and there are currently no viable alternative drug therapies available. This study seeks to investigate the mechanism of DA resistance in prolactinomas and identify new potentially effective drugs. MethodsTo explore the mechanism of DA resistance in prolactinomas, this study conducted transcriptome sequencing analysis on 27 cases of DA-resistant prolactinomas and 10 cases of sensitive prolactinomas. In addition, single-cell sequencing analysis was performed on 3 cases of DA-resistant prolactinomas and 3 cases of sensitive prolactinomas. Furthermore, to screen for potential therapeutic drugs, the study successfully established an organoids model for DA-resistant prolactinomas and screened 180 small molecule compounds using 8 organoids. The efficacy of the identified drugs was verified through various assays, including CCK-8, colony formation, CTG, and flow cytometry, and their mechanisms of action were confirmed through WB and IHC. The effectiveness of the identified drugs was evaluated both in vitro and in vivo. ResultsThe results of transcriptome sequencing and single-cell sequencing analyses showed that DA resistance in prolactinomas is associated with the upregulation of the Focal Adhesion (FA) signaling pathway. Additionally, immunohistochemical validation revealed that FAK and Paxillin were significantly upregulated in DA-resistant prolactinomas. Screening of 180 small molecule compounds using 8 organoids identified Genistein as a potentially effective drug for DA-resistant prolactinomas. Experimental validation demonstrated that Genistein inhibited the proliferation of pituitary tumor cell lines and organoids and promoted apoptosis in pituitary tumor cells. Moreover, both the cell sequencing results and WB validation results of the drug-treated cells indicated that Genistein exerts its anti-tumor effect by inhibiting the FA pathway. In vivo, experiments also showed that Genistein can inhibit subcutaneous tumor formation. ConclusionDA resistance in prolactinomas is associated with upregulation of the Focal Adhesion (FA) signaling pathway, and Genistein can exert its anti-tumor effect by inhibiting the expression of the FA pathway.

PH-responsive, self-sculptured Mg/PLGA composite microfibers for accelerated revascularization and soft tissue regeneration

Biodegradable Mg/polymer composite fibers offer a promising therapeutic option for tissue injury because of bioactive Mg2+ and biomimetic microstructure. However, current studies are limited to the contribution of Mg2+ and the single microstructure. In this study, we designed Mg/poly (lactic-co-glycolic acid) (Mg/PLGA) composite microfibers that significantly enhanced angiogenesis and tissue regeneration synergistically by Mg2+ and self-sculptured microstructure, due to spontaneous in situ microphase separation in response to the weakly alkaline microenvironment. Our composite microfiber patch exhibited superior performance in the adhesion, spreading, and angiogenesis functions of human umbilical vein endothelial cells (HUVECs) due to the joint contribution of the hierarchically porous microstructure and Mg2+. Genomics and proteomics analyses revealed that the Mg/PLGA composite microfibers activated the cell focal adhesion and angiogenesis-related signaling pathways. Furthermore, the repair of typical soft tissue defects, including refractory urethral wounds and easily healed skin wounds, validated that our Mg/PLGA composite microfiber patch could provide favorable surface topography and ions microenvironment for tissue infiltration and accelerated revascularization. It could cause rapid urethral tissue regeneration and recovery of rabbit urethral function within 6 weeks and accelerate rat skin wound closure within 16 days. This work provides new insight into soft tissue regeneration through the bioactive alkaline substance/block copolymer composites interactions.

Analysis and Identification of Methylation‐Modifying Genes Associated with Hypoxia and Immunity in Keloids

Background. Keloids are benign fibroproliferative tumors that are unique to humans. However, the exact mechanism of keloid formation remains unclear. The inflammatory cytokines released by immune cells can activate fibroblasts, connective tissue cell proliferation, and angiogenesis. Hypoxia is common in the process of fibrosis in many diseases. This study aimed to investigate the relationship between immune response, hypoxia, and keloid formation. Methods. Gene methylation and expression data were downloaded from the GEO database. Thereafter, differentially methylated genes associated with immunity and hypoxia were identified. Machine learning was performed to identify potential diagnostic/immunity/hypoxia‐related differentially methylated/expressed genes, followed by analysis of functional enrichment, transcription factors, protein‐protein interactions, and expression validation by reverse transcription quantitative polymerase chain reaction and immunohistochemistry. Results. In total, 16 immunity/hypoxia‐related hypermethylated low‐expression genes and 18 immunity/hypoxia‐related hypomethylated high‐expression genes were identified in keloids. Based on machine learning, nine differentially methylated and expressed genes were selected as potential diagnostic markers for keloids, including two hypoxia‐related genes (CDKN1A and PGAM2) and seven immunity‐related genes (DCD, PTGDS, WFIKKN1, SEMA5A, IL1R1, ITGAL, and SOS1). Some significantly enriched signaling pathways were identified, including the FoxO, PI3K‐Akt, focal adhesion, and ErbB signaling pathways. SOS1 is involved in disease regulation with 65 transcription factors and has a higher interaction score with other molecules. Conclusions. Two hypoxia‐related genes (CDKN1A and PGAM2) and seven immunity‐related genes (DCD, PTGDS, WFIKKN1, SEMA5A, IL1R1, ITGAL, and SOS1) could be considered potential diagnostic markers for keloids, and may be helpful in understanding the importance of oxygen balance and immune regulation in keloids.

Labeled-free quantitative proteomic analysis of cervical squamous cell carcinoma identifies potential protein biomarkers.

Cervical cancer remains a prevalent cancer among women, and reliance on surgical and radio-chemical therapies can irreversibly affect patients' life span and quality of life. Thus, early diagnosis and further exploration into the pathogenesis of cervical cancer are crucial. Mass spectrometry technology is widely applied in clinical practice and can be used to further investigate the protein alterations during the onset of cervical cancer. Employing labeled-free quantitative proteomics technology and bioinformatics tools, we analyzed and compared the differential protein expression profiles between normal cervical squamous cell tissues and cervical squamous cell cancer tissues. GEPIA is an online website for analyzing the RNA sequencing expression data of tumor and normal tissue data from the TCGA and the GTEx databases. This approach aided in identifying qualitative and quantitative changes in key proteins related to the progression of cervical cancer. Compared to normal samples, a total of 562 differentially expressed proteins were identified in cervical cancer samples, including 340 up-regulated and 222 down-regulated proteins. Gene ontology functional annotation, and KEGG pathway, and enrichment analysis revealed that the differentially expressed proteins mainly participated in metabolic pathways, spliceosomes, regulation of the actin cytoskeleton, and focal adhesion signaling pathways. Specifically, desmoplakin (DSP), protein phosphatase 1, regulatory (inhibitor) subunit 13 like (PPP1R13L) and ANXA8 may be involved in cervical tumorigenesis by inhibiting apoptotic signal transmission. Moreover, we used GEPIA database to validate the expression of DSP, PPP1R13L and ANXA8 in human cancers and normal cervix. In this study, we identified 562 differentially expressed proteins, and there were three proteins expressed higher in the cervical cancer tissues. The functions and signaling pathways of these differentially expressed proteins lay a theoretical foundation for elucidating the molecular mechanisms of cervical cancer.

Comprehensive Multiomics Analysis of Monozygotic Twin Discordant for Double Outlet Right Ventricle

AbstractThe objective of this study was to understand and measure epigenetic changes associated with the occurrence of CHDs by utilizing the discordant monozygotic twin model. A unique set of monozygotic twins discordant for double-outlet right ventricles (DORVs) was used for this multiomics study. The cardiac and muscle tissue samples from the twins were subjected to whole genome sequencing, whole genome bisulfite sequencing, RNA-sequencing and liquid chromatography-tandem mass spectrometry analysis. Sporadic DORV cases and control fetuses were used for validation. Global hypomethylation status was observed in heart tissue samples from the affected twins. Among 36,228 differentially methylated regions (DMRs), 1097 DMRs involving 1039 genes were located in promoter regions. A total of 419 genes, and lncRNA–mRNA pairs involved 30 genes, and 62 proteins were significantly differentially expressed. Multiple omics integrative analysis revealed that five genes, including BGN, COL1A1, COL3A1, FBLN5, and FLAN, and three pathways, including ECM-receptor interaction, focal adhesion and TGF-β signaling pathway, exhibited differences at all three levels. This study demonstrates a multiomics profile of discordant twins and explores the possible mechanism of DORV development. Global hypomethylation might be associated with the risk of CHDs. Specific genes and specific pathways, particularly those involving ECM–receptor interaction, focal adhesion and TGF–β signaling, might be involved in the occurrence of CHDs.

Super‐Stable Homogeneously Sustained‐Release System Mediates Transcatheter Arterial Ionic‐Embolization Strategy for Hepatocellular Carcinoma Therapy

AbstractThe clinical effectiveness of locoregional therapies in treating hepatocellular carcinoma (HCC) is frequently constrained by multi‐drug resistance and/or tumor metastasis. To surmount these challenges, a promising approach, transcatheter arterial ionic‐embolization (TAIE) is proposed, which can specifically and continuously disrupt the intracellular ionic balance to significantly inhibit tumor activity and invasion. The hydrophilic micro‐nanoscale sodium chloride particles (SCPs) are ingeniously intermixed with hydrophobic lipiodol to create a super‐stable homogeneous embolic formulation (lipiodol‐sodium chloride, LSC). After interventional administration, the LSC selectively deposits in HCC lesions, where lipiodol stably delivers SCPs to disrupt the cell's ionic balance, causing cell death without drug resistance. Notably, it is demonstrated that LSC can significantly hinder tumor cell migration and invasion. The mechanism is through SCP disruption of the ionic balance, which induces cell swelling and subsequent vimentin hydrolysis‐mediated cytoskeletal remodeling. In addition, it is found that LSC treatment notably downregulates the expression of MYLK, TLN, and THBS2 genes in the focal adhesion (FA) signaling pathway of HepG2 cells. LSC formulation integrated tumor‐specific deposition, intratumoral sustained release, efficient tumoricidal activity, significant metastasis inhibition, and excellent biological safety, thereby demonstrating superior in vivo tumor therapeutic effects via TAIE strategy, and showing a promising cancer therapeutic approach for clinical application.

Dual targeting of MAPK and PI3K pathways unlocks redifferentiation of Braf-mutated thyroid cancer organoids.

Thyroid cancer is the most common endocrine malignancy and several genetic events have been described to promote the development of thyroid carcinogenesis. Besides the effects of specific mutations on thyroid cancer development, the molecular mechanisms controlling tumorigenesis, tumor behavior, and drug resistance are still largely unknown. Cancer organoids have been proposed as a powerful tool to study aspects related to tumor development and progression and appear promising to test individual responses to therapies. Here, using mESC-derived thyroid organoids, we developed a BrafV637E-inducible model able to recapitulate the features of papillary thyroid cancer in vitro. Overexpression of the murine BrafV637E mutation, equivalent to BrafV600E in humans, rapidly triggers to MAPK activation, cell dedifferentiation, and disruption of follicular organization. BrafV637E-expressing organoids show a transcriptomic signature for p53, focal adhesion, ECM-receptor interactions, EMT, and inflammatory signaling pathways. Finally, PTC-like thyroid organoids were used for drug screening assays. The combination of MAPK and PI3K inhibitors reversed BrafV637E oncogene-promoted cell dedifferentiation while restoring thyroid follicle organization and function in vitro. Our results demonstrate that pluripotent stem cells-derived thyroid cancer organoids can mimic tumor development and features while providing an efficient tool for testing novel targeted therapies.

TMIC-28. TARGETING TUMOR-ASSOCIATED SMOOTH MUSCLE ACTIN (ACTA2) EXPRESSION IN MOUSE PRE-CLINICAL GLIOMA MODELS REDUCES TUMOR PROGRESSION AND EXTENDS SURVIVAL

Abstract The ACTA2 gene, which encodes α-smooth-muscle actin, is known to be involved in contractility and oncogenic transformation. However, the specific role of tumor-associated ACTA2 mesenchymal cells in gliomas is unknown. Using genetically engineered mouse models (GEMM) of glioma, we discovered that ACTA2 expression was increased within oncostreams, which are malignant multicellular structures found in high-grade gliomas. Furthermore, we observed reduced expression of ACAT2 mRNA in IDH-Mut mouse gliomas vs WT tumors. Analyzing human glioma TCGA and CCGA databases revealed a negative correlation between tumor ACTA2 expression and overall survival in glioma patients. ACTA2 mRNA expression was also higher in grade IV and recurrent tumors. To investigate the role of ACTA2 in glioma cells, we created ACTA2 knockdown GEMM of glioma. These mice showed very large increases (~300%) in median survival (NPDS: 253 days, NPAS: 329 days) in comparison to their respective control groups (NPD: 89 days, NPA: 97 days). Glioma neurospheres derived from knockdown tumors confirmed downregulation of ACTA2, and showed reduced cell proliferation compared to controls. Moreover, orthotopic models revealed a decreased potential for tumor development in vivo. To explore the mechanism mediating the effects of ACTA2 downregulation, we conducted RNA-Seq analysis of ACTA2 knockdown neurospheres. This analysis identified approximately 5000 differentially expressed genes, with gene ontology analysis highlighting significant enrichment in biological processes such as cell adhesion, cell communication, and regulation of locomotion. Pathway analysis identified cytokine-receptor interactions, focal adhesion, and NFK-B signaling as the most significant signaling pathways affected by ACTA2 downregulation. Finally, we evaluated the release of cytokines into the cell-conditioned media and found significantly decreased levels of GSCF and GMSCF cytokines in ACTA2 knockdown compared to controls. These findings indicate that ACTA2 expression is a pro-tumoral gene involved in glioma progression and plays an essential role in altering the TME.

Integrative proteomic and phosphoproteomic analysis in the female goat hypothalamus to study the onset of puberty

BackgroundPuberty marks the end of childhood and achieve sexual maturation and fertility. The role of hypothalamic proteins in regulating puberty onset is unclear. We performed a comprehensive differential proteomics and phosphoproteomics analysis in prepubertal and pubertal goats to determine the roles of hypothalamic proteins and phosphoproteins during the onset of puberty.ResultsWe used peptide and posttranslational modifications peptide quantification and statistical analyses, and identified 69 differentially expressed proteins from 5,057 proteins and 576 differentially expressed phosphopeptides from 1574 phosphorylated proteins. Combined proteomic and phosphoproteomics, 759 correlated proteins were identified, of which 5 were differentially expressed only at the protein level, and 201 were only differentially expressed at the phosphoprotein level. Pathway enrichment analyses revealed that the majority of correlated proteins were associated with glycolysis/gluconeogenesis, Fc gamma R-mediated phagocytosis, focal adhesion, GABAergic synapse, and Rap1 signaling pathway. These pathways are related to cell proliferation, neurocyte migration, and promoting the release of gonadotropin-releasing hormone in the hypothalamus. CTNNB1 occupied important locations in the protein-protein interaction network and is involved in focal adhesion.ConclusionThe results demonstrate that the proteins differentially expression only at the protein level or only differentially expressed at the phosphoprotein level and their related signalling pathways are crucial in regulating puberty in goats. These differentially expressed proteins and phosphorylated proteins may constitute the proteomic backgrounds between the two different stages.

Differential network analysis of ROS1 inhibitors reveals lorlatinib polypharmacology through co-targeting PYK2

Multiple tyrosine kinase inhibitors (TKIs) are often developed for the same indication. However, their relative overall efficacy is frequently incompletely understood and they may harbor unrecognized targets that cooperate with the intended target. We compared several ROS1 TKIs for inhibition of ROS1-fusion-positive lung cancer cell viability, ROS1 autophosphorylation and kinase activity, which indicated disproportionately higher cellular potency of one TKI, lorlatinib. Quantitative chemical and phosphoproteomics across four ROS1 TKIs and differential network analysis revealed that lorlatinib uniquely impacted focal adhesion signaling. Functional validation using pharmacological probes, RNA interference, and CRISPR-Cas9 knockout uncovered a polypharmacology mechanism of lorlatinib by dual targeting ROS1 and PYK2, which form a multiprotein complex with SRC. Rational multi-targeting of this complex by combining lorlatinib with SRC inhibitors exhibited pronounced synergy. Taken together, we show that systems pharmacology-based differential network analysis can dissect mixed canonical/non-canonical polypharmacology mechanisms across multiple TKIs enabling the design of rational drug combinations.