Microtubule actin cross-linking factor 1, a novel potential target in cancer

Identification of chemoresistance targets in doxorubicin-resistant lung adenocarcinoma cells using LC-MS/MS-based proteomics

Acquired chemoresistance remains a significant challenge in the clinics as most of the treated cancers eventually emerge as hard-to-treat phenotypes. Therefore, identifying chemoresistance targets is highly warranted to manage the disease better. In this study, we employed a label-free LC-MS/MS-based quantitative proteomics analysis to identify potential targets and signaling pathways underlying acquired chemoresistance in a sub-cell line (A549DR) derived from the parental lung adenocarcinoma cells (A549) treated with gradually increasing doses of doxorubicin (DOX). Our proteomics analysis identified 146 upregulated and 129 downregulated targets in A549DR cells. The KEGG pathway and Gene ontology (GO) analysis of differentially expressed upregulated and downregulated proteins showed that most abundant upregulated pathways were related to metabolic pathways, cellular senescence, cell cycle, and p53 signaling. Meanwhile, the downregulated pathways were related to spliceosome, nucleotide metabolism, DNA replication, nucleotide excision repair, and nuclear-cytoplasmic transport. Further, STRING analysis of upregulated biological processes showed a protein-protein interaction (PPI) between CDK1, AKT2, SRC, STAT1, HDAC1, FDXR, FDX1, NPC1, ALDH2, GPx1, CDK4, and B2M, proteins. The identified proteins in this study might be the potential therapeutic targets for mitigating DOX resistance.

LRRC1 knockdown downregulates MACF1 to inhibit the malignant progression of acute myeloid leukemia by inactivating β-catenin/c-Myc signaling

Acute myeloid leukemia (AML) is a hematologic disease associated with genetic abnormalities. This study aimed to explore the role of leucine-rich repeat-containing protein 1 (LRRC1) in the malignant activities of AML and to reveal the molecular mechanism related to microtubule actin cross-linking factor 1 (MACF1). GEPIA database was used to analyze the expression of LRRC1 in bone marrow tissues of AML patients and the correlation between LRRC1 expression and survival analysis. LRRC1 was knocked down to assess the change of AML cell proliferation, cell cycle and apoptosis using CCK-8 assay and flow cytometry. Besides, the contents of extracellular acidification and oxygen consumption rates were measured to evaluate the glycolysis. Additionally, the interaction between LRRC1 and MACF1 predicted by MEM database and was verified by co-immunoprecipitation (Co-IP) assay. Then, MACF1 was overexpressed to conduct the rescue experiments. Expression of proteins in β-catenin/c-Myc signaling was detected by western blot. Finally, AML xenograft mouse model was established to observe the impacts of LRRC1 silencing on the tumor development. Notably upregulated LRRC1 expression was observed in bone marrow tissues of AML patients and AML cells, and patients with the higher LRRC1 expression displayed the lower overall survival. LRRC1 depletion promoted cell cycle arrest and apoptosis and inhibited the glycolysis. Co-IP confirmed the interaction between LRRC1 and MACF1. MACF1 upregulation relieved the impacts of LRRC1 knockdown on the malignant activities of AML cells. Moreover, LRRC1 silencing inhibited the development of xenograft tumor growth of HL-60 cells in nude mice, suppressed MACF1 expression and inactivated the β-catenin/c-Myc signaling. Collectively, LRRC1 knockdown suppressed proliferation, glycolysis and promoted apoptosis in AML cells by downregulating MACF1 expression to inactivate β-catenin/c-Myc signaling.

TBC1D1 represses glioma progression by altering the integrity of the cytoskeleton

BACKGROUND

Glioma is one of the most aggressive malignant brain tumors and is characterized by invasive growth and poor prognosis. TBC1D1, a member of the TBC family, is associated with the development of various malignancies. However, the role of TBC1D1 in glioma-genesis remains unclear.

METHODS

The effect of TBC1D1 on the prognosis of glioma patients and related influencing factors were analyzed in the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) databases. Expression of TBC1D1 in glioma cell lines was detected by western blotting. Cell viability and proliferation were measured by EdU and Colony formation assays, respectively. Transwell and wound healing assays were performed to determine the cell migration and invasion capacities. Immunofluorescence was used to observe actin morphology in the cytoskeleton.

RESULTS

We discovered that high TBC1D1 expression in gliomas led to poor prognosis. Downregulation of TBC1D1 in glioma cells significantly inhibited multiple important functions, such as proliferation, migration, and invasion. We further demonstrated that the tumor-inhibitory effect of TBC1D1 might occur through the P-LIMK/cofilin pathway, destroying the cytoskeletal structure and affecting the depolymerization of F-actin, thereby inhibiting glioma migration.

CONCLUSION

TBC1D1 affects the balance and integrity of the actin cytoskeleton via cofilin, thereby altering the morphology and aggressiveness of glioma cells. This study provides a new perspective on its role in tumorigenesis, thereby identifying a potential therapeutic target for the treatment of gliomas.

A prognostic model for bladder cancer based on cytoskeleton-related genes

BACKGROUND

A typical cancerous growth in the urinary tract, bladder cancer (BLCA) has a dismal survival rate and a poor chance of being cured. The cytoskeleton has been shown to be tightly related to tumor invasion and metastasis. Nevertheless, the expression of genes associated with the cytoskeleton and their prognostic significance in BLCA remain unknown.

METHODS

In our study, we performed differential expression analysis of cytoskeleton-related genes between BLCA versus normal bladder tissues. According to the outcomes of this analysis of differentially expressed genes, all BLCA cases doing nonnegative matrix decomposition clustering analysis be classified into different molecular subtypes and were subjected to Immune cell infiltration analysis. We then constructed a cytoskeleton-associated gene prediction model for BLCA, and performed risk score independent prognostic analysis and receiver operating characteristic curve analyses to evaluate and validate the prognostic value of the model. Furthermore, enrichment analysis, clinical correlation analysis of prognostic models, and immune cell correlation analysis were carried out.

RESULTS

We identified 546 differentially expressed genes that are linked to the cytoskeleton, including 314 up-regulated genes and 232 down-regulated genes. All BLCA cases doing nonnegative matrix decomposition clustering analysis could be classified into 2 molecular subtypes, and we observed differences (P < .05) in C1 and C2 immune scores about 9 cell types. Next, we obtained 129 significantly expressed cytoskeleton-related genes. A final optimized model was constructed consisting of 11 cytoskeleton-related genes. Survival curves and risk assessment predicted the prognostic risk in both groups of patients with BLCA. Survival curves and receiver operating characteristic curves were used to evaluate and validate the prognostic value of the model. Significant enrichment pathways for cytoskeleton-associated genes in bladder cancer samples were explored by Gene set enrichment analysis enrichment analysis. After we obtained the risk scores, a clinical correlation analysis was performed to examine which clinical traits were related to the risk scores. Finally, we demonstrated a correlation between different immune cells.

CONCLUSION

Cytoskeleton-related genes have an important predictive value for BLCA, and the prognostic model we constructed may enable personalized treatment of BLCA.

The role of MACF1 on acute myeloid leukemia cell proliferation is involved in Runx2-targeted PI3K/Akt signaling

Acute myeloid leukemia (AML) is a type of hematologic diseases, which is related to abnormal genes. The aberrant microtubule actin cross-linking factor 1 (MACF1) is associated with progression of multiple tumors by initiating cell proliferation. Nevertheless, the function and action mechanism of MACF1 in AML cell proliferation remain mostly unknown. Our study aimed to explore the influence of MACF1 on AML cell proliferation by CCK-8 and EdU staining assays. Moreover, we aimed to explore the effect of MACF1 on downstream Runx2 and the PI3K/Akt signaling. MACF1 expression in AML patients was predicted by bioinformatics analysis. Cells were transfected with si-con, si-MACF1 or Runx2 using Lipofectamine 2000. Upregulated MACF1 was found in AML patients and predicted worse overall survival. MACF1 expression was upregulated in AML cells compared with that in hematopoietic stem and progenitor cells. MACF1 silencing reduced AML cell proliferation. Runx2 level was increased in AML cells, and decreased by silencing MACF1. Runx2 upregulation rescued MACF1 silencing-mediated inhibition of proliferation. MACF1 downregulation inhibited activation of the PI3K/Akt pathway by decreasing Runx2. Activation of the PI3K/Akt pathway abrogated the suppressive role of MACF1 downregulation in AML cell proliferation. In conclusion, MACF1 knockdown decreased AML cell proliferation by reducing Runx2 and inactivating the PI3K/Akt signaling.

MACF1 overexpression in BMSCs alleviates senile osteoporosis in mice through TCF4/miR-335-5p signaling pathway

Background

The decreased osteogenic differentiation ability of mesenchymal stem cells (MSCs) is one of the important reasons for SOP. Inhibition of Wnt signaling in MSCs is closely related to SOP. Microtubule actin crosslinking factor 1 (MACF1) is an important regulator in Wnt/β-catenin signal transduction. However, whether the specific expression of MACF1 in MSC regulates SOP and its mechanism remains unclear.

Methods

We established MSC-specific Prrx1 (Prx1) promoter-driven MACF1 conditional knock-in (MACF-KI) mice, naturally aged male mice, and ovariectomized female mice models. Micro-CT, H&E staining, double calcein labeling, and the three-point bending test were used to explore the effects of MACF1 on bone formation and bone microstructure in the SOP mice model. Bioinformatics analysis, ChIP-PCR, qPCR, and ALP staining were used to explore the effects and mechanisms of MACF1 on MSCs' osteogenic differentiation.

Results

Microarray analysis revealed that the expression of MACF1 and positive regulators of the Wnt pathway (such as TCF4, β-catenin, Dvl) was decreased in human MSCs (hMSCs) isolated from aged osteoporotic than non-osteoporotic patients. The ALP activity and osteogenesis marker genes (Alp, Runx2, and Bglap) expression in mouse MSCs was downregulated during aging. Furthermore, Micro-CT analysis of the femur from 2-month-old MSC-specific Prrx1 (Prx1) promoter-driven MACF1 conditional knock-in (MACF-cKI) mice showed no significant trabecular bone changes compared to wild-type littermate controls, whereas 18- and 21-month-old MACF1 c-KI animals displayed increased bone mineral densities (BMD), improved bone microstructure, and increased maximum compression stress. In addition, the ovariectomy (OVX)-induced osteoporosis model of MACF1 c-KI mice had significantly higher trabecular volume and number, and increased bone formation rate than that in control mice. Mechanistically, ChIP-PCR showed that TCF4 could bind to the promoter region of the host gene miR-335-5p. Moreover, MACF1 could regulate the expression of miR-335-5p by TCF4 during the osteogenic differentiation of MSCs.

Conclusion

These data indicate that MACF1 positively regulates MSCs osteogenesis and bone formation through the TCF4/miR-335-5p signaling pathway in SOP, suggesting that targeting MACF1 may be a novel therapeutic approach against SOP.

The translational potential of this article

MACF1, an important switch in the Wnt signaling pathway, can alleviate SOP through the TCF4/miR-335-5p signaling pathway in mice model. It might act as a therapeutic target for the treatment of SOP to improve bone function.

Serum miR-34a as a potential biomarker for diagnosis of inflammatory bowel diseases in Egyptian patients

Background

IBD is a multifactorial disease. Although dysbiosis of commensal bacteria and breakdown of the intestinal barrier are considered as major pathological mechanisms in the development of IBD, other important factors such as genetic aberrations also contribute to its development.

Results

Our results revealed that serum miR-34a RQ values were significantly lower and serum MACF1 RQ values were significantly higher in IBD patients compared to healthy controls. In addition, serum miR-34a in relation to pathological activity and disease severity in the IBD group revealed a significant difference (p>0.05).

Conclusion

Serum miR-34a RQ and serum MACF1 RQ value-based biomarker panels can act as a potential biomarker for IBD diagnosis and prognosis.

Pan-Cancer Analysis for Immune Cell Infiltration and Mutational Signatures Using Non-Negative Canonical Correlation Analysis

Mutational signatures indicate the mutational processes and substitution patterns in cancer cell genomes. However, the functional consequences of mutational signatures remain unclear, and there have been no comprehensive systematic studies to examine the relationships between the mutational signatures and the immune cell infiltration. Here, the relationship between mutational signatures and immune cell infiltration using non-negative canonical correlation analysis based on 8927 patients across 25 tumor types was investigated. By inspecting mutational signatures with the maximal coefficients determined by the non-negative canonical correlation analysis, the study identified mutational signatures related to immune cell infiltration composed of tumor microenvironments. The analysis was validated by showing that the genes associated with the identified mutational signatures were linked to overall survival by a Kaplan–Meier curve and a log-rank test and were mainly related to immunity by gene set enrichment analysis. These results will help expand our knowledge of tumor biology and recognize the functional roles and associations of immune systems with mutational signatures.

Classification of Breast Cancer Nottingham Prognostic Index Using High-Dimensional Embedding and Residual Neural Network

The Nottingham Prognostics Index (NPI) is a prognostics measure that predicts operable primary breast cancer survival. The NPI value is calculated based on the size of the tumor, the number of lymph nodes, and the tumor grade. Next-generation sequencing advancements have led to measuring different biological indicators called multi-omics data. The availability of multi-omics data triggered the challenge of integrating and analyzing these various biological measures to understand the progression of the diseases. High-dimensional embedding techniques are incorporated to present the features in the lower dimension, i.e., in a 2-dimensional map. The dataset consists of three -omics: gene expression, copy number alteration (CNA), and mRNA from 1885 female patients. The model creates a gene similarity network (GSN) map for each omic using t-distributed stochastic neighbor embedding (t-SNE) before being merged into the residual neural network (ResNet) classification model. The aim of this work was to (i) extract multi-omics biomarkers that are associated with the prognosis and prediction of breast cancer survival; and (ii) build a prediction model for multi-class breast cancer NPI classes. We evaluated this model and compared it to different high-dimensional embedding techniques and neural network combinations. The proposed model outperformed the other methods with an accuracy of 98.48%, and the area under the curve (AUC) equals 0.9999. The findings in the literature confirm associations between some of the extracted omics and breast cancer prognosis and survival including CDCA5, IL17RB, MUC2, NOD2 and NXPH4 from the gene expression dataset; MED30, RAD21, EIF3H and EIF3E from the CNA dataset; and CENPA, MACF1, UGT2B7 and SEMA3B from the mRNA dataset.

Classification of Breast Cancer Nottingham Prognostic Index Using High-Dimensional Embedding and Residual Neural Network

Simple Summary

A deep learning model based on multi-omics data to classify Nottingham prognostic Index score levels. The model represents each omic dataset using 2-dimensional map before integrating all omics maps into the prediction model. The literature confirms the relationship between the extracted omics features with the progression and survival of breast cancer.

Abstract

The Nottingham Prognostics Index (NPI) is a prognostics measure that predicts operable primary breast cancer survival. The NPI value is calculated based on the size of the tumor, the number of lymph nodes, and the tumor grade. Next-generation sequencing advancements have led to measuring different biological indicators called multi-omics data. The availability of multi-omics data triggered the challenge of integrating and analyzing these various biological measures to understand the progression of the diseases. High-dimensional embedding techniques are incorporated to present the features in the lower dimension, i.e., in a 2-dimensional map. The dataset consists of three -omics: gene expression, copy number alteration (CNA), and mRNA from 1885 female patients. The model creates a gene similarity network (GSN) map for each omic using t-distributed stochastic neighbor embedding (t-SNE) before being merged into the residual neural network (ResNet) classification model. The aim of this work was to (i) extract multi-omics biomarkers that are associated with the prognosis and prediction of breast cancer survival; and (ii) build a prediction model for multi-class breast cancer NPI classes. We evaluated this model and compared it to different high-dimensional embedding techniques and neural network combinations. The proposed model outperformed the other methods with an accuracy of 98.48%, and the area under the curve (AUC) equals 0.9999. The findings in the literature confirm associations between some of the extracted omics and breast cancer prognosis and survival including CDCA5, IL17RB, MUC2, NOD2 and NXPH4 from the gene expression dataset; MED30, RAD21, EIF3H and EIF3E from the CNA dataset; and CENPA, MACF1, UGT2B7 and SEMA3B from the mRNA dataset.

Extracellular Nucleotides Affect the Proangiogenic Behavior of Fibroblasts, Keratinocytes, and Endothelial Cells

Chronic wound healing is currently a severe problem due to its incidence and associated complications. Intensive research is underway on substances that retain their biological activity in the wound microenvironment and stimulate the formation of new blood vessels critical for tissue regeneration. This group includes synthetic compounds with proangiogenic activity. Previously, we identified phosphorothioate analogs of nucleoside 5′-O-monophosphates as multifunctional ligands of P2Y6 and P2Y14 receptors. The effects of a series of unmodified and phosphorothioate nucleotide analogs on the secretion of VEGF from keratinocytes and fibroblasts, as well as their influence on the viability and proliferation of keratinocytes, fibroblasts, and endothelial cells were analyzed. In addition, the expression profiles of genes encoding nucleotide receptors in tested cell models were also investigated. In this study, we defined thymidine 5′-O-monophosphorothioate (TMPS) as a positive regulator of angiogenesis. Preliminary analyses confirmed the proangiogenic potency of TMPS in vivo.

Functional and behavioral effects of de novo mutations in calcium-related genes in patients with bipolar disorder

Bipolar disorder is a common mental illness occurring in approximately 1% of individuals and exhibits lifetime prevalence. Although genetic factors are known to contribute to this disorder, the genetic architecture has not yet been completely clarified. Our initial trio-based exome sequencing study of bipolar disorder showed enrichment of de novo, loss-of-function (LOF) or protein-altering mutations in a combined group with bipolar I and schizoaffective disorders, and the identified de novo mutations were enriched in calcium-related genes. These findings suggested a role for de novo mutations in bipolar disorder. The validity of these statistical associations can be demonstrated if the functional impact of the mutations on cellular function and behavior are identified. In this study, we focused on two de novo LOF mutations in calcium-related genes, EHD1 and MACF1, found in patients with bipolar disorder. We first showed that the EHD1 mutation resulted in a truncated protein with diminished effect on neurite outgrowth and inhibited endocytosis. Next, we used CRISPR/Cas9 to establish two knock-in mouse lines to model the in vivo effects of these mutations. We performed behavioral screening using IntelliCage and long-term wheel running analysis. Ehd1 mutant mice showed higher activity in the light phase. Macf1 mutant mice showed diminished attention and persistence to rewards. These behavioral alterations were similar to the phenotypes in previously proposed animal models of bipolar disorder. These findings endorse the possible role of de novo mutations as a component of the genetic architecture of bipolar disorder which was suggested by the statistical evidence.

Numerical analysis of the impact of cytoskeletal actin filament density alterations onto the diffusive vesicle-mediated cell transport

The interior of a eukaryotic cell is a highly complex composite material which consists of water, structural scaffoldings, organelles, and various biomolecular solutes. All these components serve as obstacles that impede the motion of vesicles. Hence, it is hypothesized that any alteration of the cytoskeletal network may directly impact or even disrupt the vesicle transport. A disruption of the vesicle-mediated cell transport is thought to contribute to several severe diseases and disorders, such as diabetes, Parkinson’s and Alzheimer’s disease, emphasizing the clinical relevance. To address the outlined objective, a multiscale finite element model of the diffusive vesicle transport is proposed on the basis of the concept of homogenization, owed to the complexity of the cytoskeletal network. In order to study the microscopic effects of specific nanoscopic actin filament network alterations onto the vesicle transport, a parametrized three-dimensional geometrical model of the actin filament network was generated on the basis of experimentally observed filament densities and network geometries in an adenocarcinomic human alveolar basal epithelial cell. Numerical analyzes of the obtained effective diffusion properties within two-dimensional sampling domains of the whole cell model revealed that the computed homogenized diffusion coefficients can be predicted statistically accurate by a simple two-parameter power law as soon as the inaccessible area fraction, due to the obstacle geometries and the finite size of the vesicles, is known. This relationship, in turn, leads to a massive reduction in computation time and allows to study the impact of a variety of different cytoskeletal alterations onto the vesicle transport. Hence, the numerical simulations predicted a 35% increase in transport time due to a uniformly distributed four-fold increase of the total filament amount. On the other hand, a hypothetically reduced expression of filament cross-linking proteins led to sparser filament networks and, thus, a speed up of the vesicle transport.

Many vital processes in our eukaryotic cells and organs require an astonishingly precise routing of intermediate products to various intra- and extracellular destinations using vesicles as transporters. This can be illustrated by numerous examples, such as the production and destruction of proteins, the export of neurotransmitters or insulin to the extracellular domain, etc. However, the inside of a cell is tightly packed with numerous structural scaffoldings (filaments), which serve as obstacles and impede the vesicle motion. It is thought that any disturbances of the vesicle-mediated cell transport contribute to numerous degenerative diseases and disorders, which highlights the clinical relevance for investigating this intracellular transport mechanism by developing computational models and performing experimental studies. In this study, we numerically quantified how different specific alterations of the filament density inside a human lung cell—due to changed mechanical loadings or genetic disorders of proteins being responsible for filament branching—affect the diffusion of vesicles inside the intracellular fluid. Therefore, based on the concept of homogenization, a computationally efficient numerical method was developed and utilized to simulate the diffusion of vesicles inside the whole cell, considering the detailed structural information of the filament network.

FENDRR: A pivotal, cancer-related, long non-coding RNA

Long non-coding RNAs (lncRNAs) have more than 200 nucleotides and do not encode proteins. Based on numerous studies, lncRNAs have emerged as new and crucial regulators of biological function and have been implicated in the pathogenesis of a variety of diseases, especially cancers. Specific lncRNAs have been identified as novel molecular biomarkers for cancer diagnosis, prognosis, and treatment efficacy. Fetal-lethal non-coding developmental regulatory RNA (FENDRR, also known as FOXF1-AS1) is a novel lncRNA that is located at chr3q13.31 and has four exons and 3099 nucleotides, and its genomic site is located at chr3q13.31. FENDRR is abnormally expressed in a variety of cancers and is significantly associated with different clinical characteristics. In addition, FENDRR has shown potential as a biomarker for cancer diagnosis, prognosis, and treatment. In this review, we summarize the current understanding of FENDRR and its mechanistic role in cancer progression. We also discuss recent insights into the clinical significance of FENDRR for cancer diagnosis, prognosis, and treatment.

Microtubule-associated proteins (MAPs) in microtubule cytoskeletal dynamics and spermatogenesis

The microtubule (MT) cytoskeleton in Sertoli cells, a crucial cellular structure in the seminiferous epithelium of adult mammalian testes that supports spermatogenesis, was studied morphologically decades ago. However, its biology, in particular the involving regulatory biomolecules and the underlying mechanism(s) in modulating MT dynamics, are only beginning to be revealed in recent years. This lack of studies in delineating the biology of MT cytoskeletal dynamics undermines other studies in the field, in particular the plausible therapeutic treatment and management of male infertility and fertility since studies have shown that the MT cytoskeleton is one of the prime targets of toxicants. Interestingly, much of the information regarding the function of actin-, MT- and intermediate filament-based cytoskeletons come from studies using toxicant models including some genetic models. During the past several years, there have been some advances in studying the biology of MT cytoskeleton in the testis, and many of these studies were based on the use of pharmaceutical/toxicant models. In this review, we summarize the results of these findings, illustrating the importance of toxicant/pharmaceutical models in unravelling the biology of MT dynamics, in particular the role of microtubule-associated proteins (MAPs), a family of regulatory proteins that modulate MT dynamics but also actin- and intermediate filament-based cytoskeletons. We also provide a timely hypothetical model which can serve as a guide to design functional experiments to study how the MT cytoskeleton is regulated during spermatogenesis through the use of toxicants and/or pharmaceutical agents.

New insights into the genetic basis of premature ovarian insufficiency: Novel causative variants and candidate genes revealed by genomic sequencing

Ovarian deficiency, including premature ovarian insufficiency (POI) and diminished ovarian reserve (DOR), represents one of the main causes of female infertility. POI is a genetically heterogeneous condition but current understanding of its genetic basis is far from complete, with the cause remaining unknown in the majority of patients. The genes that regulate DOR have been reported but the genetic basis of DOR has not been explored in depth. Both conditions are likely to lie along a continuum of degrees of decrease in ovarian reserve. We performed genomic analysis via whole exome sequencing (WES) followed by in silico analyses and functional experiments to investigate the genetic cause of ovarian deficiency in ten affected women. We achieved diagnoses for three of them, including the identification of novel variants in STAG3, GDF9, and FANCM. We identified potentially causative FSHR variants in another patient. This is the second report of biallelic GDF9 and FANCM variants, and, combined with functional support, validates these genes as bone fide autosomal recessive "POI genes". We also identified new candidate genes, NRIP1, XPO1, and MACF1. These genes have been linked to ovarian function in mouse, pig, and zebrafish respectively, but never in humans. In the case of NRIP1, we provide functional support for the deleterious nature of the variant via SUMOylation and luciferase/β-galactosidase reporter assays. Our study provides multiple insights into the genetic basis of POI/DOR. We have further elucidated the involvement of GDF9, FANCM, STAG3 and FSHR in POI pathogenesis, and propose new candidate genes, NRIP1, XPO1, and MACF1, which should be the focus of future studies.

Single Cell ADNP Predictive of Human Muscle Disorders: Mouse Knockdown Results in Muscle Wasting

Activity-dependent neuroprotective protein (ADNP) mutations are linked with cognitive dysfunctions characterizing the autistic-like ADNP syndrome patients, who also suffer from delayed motor maturation. We thus hypothesized that ADNP is deregulated in versatile myopathies and that local ADNP muscle deficiency results in myopathy, treatable by the ADNP fragment NAP. Here, single-cell transcriptomics identified ADNP as a major constituent of the developing human muscle. ADNP transcript concentrations further predicted multiple human muscle diseases, with concentrations negatively correlated with the ADNP target interacting protein, microtubule end protein 1 (EB1). Reverting back to modeling at the single-cell level of the male mouse transcriptome, Adnp mRNA concentrations age-dependently correlated with motor disease as well as with sexual maturation gene transcripts, while Adnp expressing limb muscle cells significantly decreased with aging. Mouse Adnp heterozygous deficiency exhibited muscle microtubule reduction and myosin light chain (Myl2) deregulation coupled with motor dysfunction. CRISPR knockdown of adult gastrocnemius muscle Adnp in a Cas9 mouse resulted in treadmill (male) and gait (female) dysfunctions that were specifically ameliorated by treatment with the ADNP snippet, microtubule interacting, Myl2-regulating, NAP (CP201). Taken together, our studies provide new hope for personalized diagnosis/therapeutics in versatile myopathies.

Overexpression of wild type or a Q311E mutant MB21D2 promotes a pro-oncogenic phenotype in HNSCC

Cadherin‐mediated cell–cell contacts regulated by intracellular binders play critical roles in tissue homeostasis and tumorigenesis. Here, we screened mutational profiles of 312 annotated genes involved in cadherin binding in human squamous cell carcinomas and found MB21D2 to carry a unique recurrent Q311E mutation. MB21D2 overexpression was also frequently found in head and neck cancer (HNSCC) and was associated with poor clinical outcomes. Cell‐based characterizations revealed pro‐oncogenic roles for MB21D2 wild‐type (WT) and its Q311E mutant (Q311E) in cell proliferation, colony formation, sphere growth, and migration/invasion by promoting epithelial–mesenchymal transition. Conversely, MB21D2 knockdown in MB21D2‐overexpressing cells resulted in cell growth arrest and apoptosis. Xenograft tumor models with Q311E‐expressing cells formed larger and more aggressive lesions, compared to models with WT‐MB21D2‐expressing cells or an empty vector. Transcriptome and protein interactome analyses revealed enrichment of KRAS signaling by MB21D2 expression. Immunoblotting confirmed RAS elevation, along with upregulation/phosphorylation of PI3K, AKT, and CREB. Blocking RAS signaling in MB21D2‐expressing cells by manumycin significantly reduced cell growth and survival. Our study thus defined RAS signaling‐dependent pro‐oncogenic roles for MB21D2 overexpression and Q311E MB21D2 expression in HNSCC development.

Construction of a 6-gene prognostic signature to assess prognosis of patients with pancreatic cancer

Pancreatic cancer (PaCa) is one of the most fatal cancers in the world. Although great efforts have made to explore the mechanisms of PaCa oncogenesis, the prognosis of PaCa patients is still unsatisfactory. Thus, it is imperative to further understand the potential carcinogenesis of PaCa and reliable prognostic models.The gene expression profile and clinical information of GSE21501 were downloaded from the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was applied to explore the potent genes associated with the overall survival (OS) events of PaCa patients. Cox regression model was applied to selecting prognostic genes and establish prognostic model. The prognostic values of six-gene signature were validated in TCGA-PAAD cohort.According to the WGCNA analysis, a total of 19 modules were identified and 115 hub genes in the mostly associated module were reserved for next analysis. According to the univariate and multivariate Cox regression analysis, we established a six-gene signature (FTSJ3, STAT1, STX2, CDX2, RASSF4, MACF1) which could effectively evaluate the overall survival (OS) of PaCa patients. In validated patients' cohorts, the six-gene signature exhibited excellent prognostic value in TCGA-PAAD cohort as well.We developed a six-gene signature to exactly predict OS of PaCa patients and provide a novel personalized strategy for evaluating prognosis. The findings may be contributed to medical customization and therapeutic decision in clinical practice.

Comprehensive analysis of protein expression levels and phosphorylation levels in host skin in response to tick (Haemaphysalis longicornis) bite

Ticks are parasitic arthropods that suck blood from the surface of most vertebrates. They can transmit a variety of pathogens. The blood sucking of ticks causes varying degrees of damage to the skin of the host. Proteins related to immune regulation, vascular repair, and wound healing in mammalian skin respond to tick bites by regulating their expression and post-translational modifications to protect the skin from injury. Phosphorylation of proteins, as the most common post-translational modification of proteins, plays an important role in the rapid regulation of cell signal transduction, gene expression and cell cycle. To systematically explore the molecular regulatory mechanisms employed by mammalian skin to resist tick bites, larval, nymphal, and adult Haemaphysalis longicornis were used to bite the skin tissues of healthy rabbits in the present study. The quantitative proteomic technology data-independent acquisition was then carried out to investigate in depth the changes in protein expression and phosphorylation in rabbit skin after tick bite. The results showed that among the 4034 proteins and 1795 phosphorylated proteins identified, a total of 202 proteins and 435 phosphorylation sites were changed after H. longicornis bite. In order to provide convenience for sucking blood, active substances in the saliva of H. longicornis injected into the rabbit's skin can cause the expression level of trichohyalin and peptidyl arginine deiminase 3 in the skin of the host downregulate, which can make the host hair loss and regeneration disorders. At the same time, the active substances in saliva of the H. longicornis led to the phosphorylation of microtubule actin cross-linking factor 1 in the host's skin and further inactivation, so as to delay the healing of the host wound. In response to tick bites, the host skin promotes coagulation through high expression of fibrinogen and fibronectin, and vascular repair through high expression of integrin linked kinase and tenascin C, as well as accelerated phosphorylation of the phosphorylated protein Nck adaptor protein 1, and wound healing through high expression of ezrin and integrin. The upregulation of proteins such as coronin, NADPH oxidase, calnexin, and calreticulin and phosphorylation level of IL-4R in the host skin after the H. longicornis bite indicated that the immune response was playing an important defensive role in response to tick bites. Meanwhile, we found that the upregulated two lectins, mannose receptor C-type 1 and DC-SIGN, may serve as molecular makers to identify and monitor whether the skin is bitten by ticks. SIGNIFICANCE: Haemaphysalis longicornis are parasitic arthropods that suck blood from the surface of most vertebrates. They can transmit a variety of pathogens and are harmful to humans and livestock. The present study is the first quantitative proteomic study on protein expression levels in the rabbit skin after infection by H. longicornis. It is also the first quantitative phosphoproteomic study in the host skin infected by ticks. In this study, we found that tick bites cause the host hair loss and regeneration disorders. For resisting tick bite, the host activates the immune response and initiates vascular repair and wound-healing systems. In addition, some phosphorylated proteins promote host immunity and vascular repair. These results can help us further understand the defence mechanism of the host against tick bites, provide a basis for the development of an anti-tick vaccine, the development of anti-tick drugs, and the diagnosis of tick-borne diseases.

Decreasing Microtubule Actin Cross-Linking Factor 1 Inhibits Melanoma Metastasis by Decreasing Epithelial to Mesenchymal Transition

Background

The microtubule actin cross-linking factor 1 (MACF1) is involved in cellular migration, adhesion, and invasion processes. Its abnormal expression initiates tumor cell proliferation and metastasis in numerous cancer types.

Methods

In this study, we utilized short hair-pin RNA interference of MACF1 to assess the inhibitory effects on the metastatic potential of B16F10 melanoma cells both in vitro and in vivo a mouse model.

Results

The MACF1 expression was increased in B16F10 cells-induced tumor tissues; while the down-regulation of MACF1 impacted the B16F10 melanoma cell metastatic behavior by decreasing the ability of colony formation and invasion in vitro as well as inhibiting B16F10 cells-induced tumor growth and lung metastasis in vivo. The results of Western blot and immunohistochemistry indicated that the expression of E-cadherin and Smad-7 was significantly increased whereas the expression of N-cadherin and TGF-β1 was significantly decreased in tumor tissue of mice challenged with the B16F10/MACF1-RNAi cells when compared with the B16F10 cells challenged mice.

Conclusion

The data presented in this study demonstrated that down-regulated MACF1 expression decreased B16F10 melanoma metastasis in mice by inhibiting the epithelial to mesenchymal transition program. Thus, MACF1 may be a novel target for melanoma therapy.

Mutations of MACF1, Encoding Microtubule-Actin Crosslinking-Factor 1, Cause Spectraplakinopathy

As a member of spectraplakin family of cytoskeletal crosslinking proteins, microtubule-actin crosslinking factor 1 (MACF1) controls cytoskeleton network dynamics. Knockout of Macf1 in mice resulted in the developmental retardation and embryonic lethality. Spectraplakinopathy type I, a novel neuromuscular condition characterized by periodic hypotonia, lax muscles, joint contracture, and diminished motor skill, was reported to be associated with heterozygous genomic duplication involving the MACF1 loci, with incomplete penetrance and highly variable clinical presentation in a single pedigree. In this study, parental-derived compound heterozygous novel missense mutations of MACF1, c.1517C>T (p.Thr506Ile) and c.11654T>C (p.Ile3885Thr), were found to co-segregate with disease status in two affected brothers presenting with progressive spastic tetraplegia, dystonia, joint contracture, feeding difficulty and developmental delay. We speculated that MACF1 mutations cause spectraplakinopathy inherited in an autosomal recessive manner. Our clinical findings expanded the phenotype of this neuromuscular disorder and provided new insights into the function of MACF1.

Interaction of melatonin and Bmal1 in the regulation of PI3K/AKT pathway components and cellular survival

The circadian rhythm is driven by a master clock within the suprachiasmatic nucleus which regulates the rhythmic secretion of melatonin. Bmal1 coordinates the rhythmic expression of transcriptome and regulates biological activities, involved in cell metabolism and aging. However, the role of Bmal1 in cellular- survival, signaling, its interaction with intracellular proteins, and how melatonin regulates its expression is largely unclear. Here we observed that melatonin increases the expression of Bmal1 and both melatonin and Bmal1 increase cellular survival after oxygen glucose deprivation (OGD) while the inhibition of Bmal1 resulted in the decreased cellular survival without affecting neuroprotective effects of melatonin. By using a planar surface immunoassay for PI3K/AKT signaling pathway components, we revealed that both melatonin and Bmal1 increased phosphorylation of AKT, ERK-1/2, PDK1, mTOR, PTEN, GSK-3αβ, and p70S6K. In contrast, inhibition of Bmal1 resulted in decreased phosphorylation of these proteins, which the effect of melatonin on these signaling molecules was not affected by the absence of Bmal1. Besides, the inhibition of PI3K/AKT decreased Bmal1 expression and the effect of melatonin on Bmal1 after both OGD in vitro and focal cerebral ischemia in vivo. Our data demonstrate that melatonin controls the expression of Bmal1 via PI3K/AKT signaling, and Bmal1 plays critical roles in cellular survival via activation of survival kinases.

Cellular Interactome Dynamics during Paclitaxel Treatment

Cell-cycle inhibitors, including paclitaxel, are among the most widely used and effective cancer therapies. However, several challenges limit the success of paclitaxel, including drug resistance and toxic side effects. Paclitaxel is thought to act primarily by stabilizing microtubules, locking cells in a mitotic state. However, the resulting cytotoxicity and tumor shrinkage rates observed cannot be fully explained by this mechanism alone. Here we apply quantitative chemical cross-linking with mass spectrometry analysis to paclitaxel-treated cells. Our results provide large-scale measurements of relative protein levels and, perhaps more importantly, changes to protein conformations and interactions that occur upon paclitaxel treatment. Drug concentration-dependent changes are revealed in known drug targets including tubulins, as well as many other proteins and protein complexes involved in apoptotic signaling and cellular homeostasis. As such, this study provides insight into systems-level changes to protein structures and interactions that occur with paclitaxel treatment.

Proteomic Analysis of miR-195 and miR-497 Replacement Reveals Potential Candidates that Increase Sensitivity to Oxaliplatin in MSI/P53wt Colorectal Cancer Cells

Most patients with advanced colorectal cancer (CRC) eventually develop resistance to systemic combination therapy. miR-195-5p and miR-497-5p are downregulated in CRC tissues and associated with drug resistance. Sensitization to 5-FU, oxaliplatin, and irinotecan by transfection with miR-195-5p and miR-497-5p mimics was studied using cell viability and clonogenic assays in cell lines HCT116, RKO, DLD-1, and SW480. In addition, proteomic analysis of transfected cells was implemented to identify potential targets. Significantly altered proteins were subjected to STRING (protein-protein interaction networks) database analysis to study the potential mechanisms of drug resistance. Cell viability analysis of transfected cells revealed increased sensitivity to oxaliplatin in microsatellite instable (MSI)/P53 wild-type HCT116 and RKO cells. HCT116 transfected cells formed significantly fewer colonies when treated with oxaliplatin. In sensitized cells, proteomic analysis showed 158 and 202 proteins with significantly altered expression after transfection with miR-195-5p and miR-497-5p mimics respectively, of which CHUK and LUZP1 proved to be coinciding downregulated proteins. Resistance mechanisms of these proteins may be associated with nuclear factor kappa-B signaling and G1 cell-cycle arrest. In conclusion, miR-195-5p and miR-497-5p replacement enhanced sensitivity to oxaliplatin in treatment naïve MSI/P53 wild-type CRC cells. Proteomic analysis revealed potential miRNA targets associated with the cell-cycle which possibly bare a relation with chemotherapy sensitivity.

Microtubule actin crosslinking factor 1 (MACF1) knockdown inhibits RANKL-induced osteoclastogenesis via Akt/GSK3β/NFATc1 signalling pathway

Osteoclasts are responsible for bone resorption and play essential roles in causing bone diseases such as osteoporosis. Microtubule actin crosslinking factor 1 (MACF1) is a large spectraplakin protein that has been implicated in regulating cytoskeletal distribution, cell migration, cell survival and cell differentiation. However, whether MACF1 regulates the differentiation of osteoclasts has not been elucidated. In this study, we found that the expression of MACF1 was increased in primary bone marrow-derived monocytes (BMMs) of osteoporotic mice and was downregulated during receptor activator of nuclear factor kappa-B ligand (RANKL)-induced osteoclastogenesis of pre-osteoclast cell lines RAW264.7 cells. RAW264.7 cells were transfected with shMACF1 using a lentiviral vector to study the role of MACF1 in osteoclastogenic differentiation. Knockdown of MACF1 in RAW264.7 cells inhibited the formation of multinucleated osteoclasts and decreased the expression of osteoclast-marker genes (Ctsk, Acp5, Mmp9 and Oscar) during RANKL-induced osteoclastogenesis. Additionally, knockdown of MACF1 disrupted actin ring formation in osteoclasts and further blocked the bone resorption activity of osteoclasts by reducing the area and depth of pits. Knockdown of MACF1 had no effect on the survival of pre-osteoclasts and mature osteoclasts. We further established that knockdown of MACF1 attenuated the phosphorylation of Akt and GSK3β and inhibited the expression of its downstream target NFATc1. Akt activator rescued the inhibition of osteoclast differentiation by MACF1 knockdown. These data demonstrate that MACF1 positively regulates osteoclast differentiation via the Akt/GSK3β/NFATc1 signalling pathway, suggesting that targeting MACF1 may be a novel therapeutic approach against osteoporosis.

Biomedical potential of mammalian spectraplakin proteins: Progress and prospect

The cytoskeleton is an essential element of a eukaryotic cell which informs both form and function and ultimately has physiological consequences for the organism. Equally as important as the major cytoskeletal networks are crosslinkers which coordinate and regulate their activities. One such category of crosslinker is the spectraplakins, a family of giant, evolutionarily conserved crosslinking proteins with the rare ability to interact with each of the three major cytoskeletal networks. In particular, a mammalian spectraplakin isotype called MACF1 (microtubule actin crosslinking factor 1), also known as ACF7 (actin crosslinking factor 7), has been of particular interest in the years since its discovery; MACF1 has come under such scrutiny due to the mounting list of biological phenomena in which it has been implicated. This review is an overview of the current knowledge on the structure and function of the known spectraplakin isotypes with an emphasis on MACF1, recent studies on MACF1, and finally, an analysis of the potential of MACF1 to advance medicine.

Impact statement

Spectraplakins are a highly conserved group of proteins which have the rare ability to bind to each of the three major cytoskeletal networks. The mammalian spectraplakin MACF1/ACF7 has proven to be instrumental in many cellular processes (e.g. signaling and cell migration) since its identification and, as such, has been the focus of various research studies. This review is a synthesis of scientific reports on the structure, confirmed functions, and implicated roles of MACF1/ACF7 as of 2019. Based on what has been revealed thus far in terms of MACF1/ACF7’s role in complex pathologies such as metastatic cancers and inflammatory bowel disease, it appears that MACF1/ACF7 and the continued study thereof hold great potential to both enhance the design of future therapies for various diseases and vastly expand scientific understanding of organismal physiology as a whole.

Emerging roles of allosteric modulators in the regulation of protein-protein interactions (PPIs): A new paradigm for PPI drug discovery

Protein-protein interactions (PPIs) are closely implicated in various types of cellular activities and are thus pivotal to health and disease states. Given their fundamental roles in a wide range of biological processes, the modulation of PPIs has enormous potential in drug discovery. However, owing to the general properties of large, flat, and featureless interfaces of PPIs, previous attempts have demonstrated that the generation of therapeutic agents targeting PPI interfaces is challenging, rendering them almost "undruggable" for decades. To date, rapid progress in chemical and structural biology techniques has promoted the exploitation of allostery as a novel approach in drug discovery. By attaching to allosteric sites that are topologically and spatially distinct from PPI interfaces, allosteric modulators can achieve improved physiochemical properties. Thus, allosteric modulators may represent an alternative strategy to target intractable PPIs and have attracted intense pharmaceutical interest. In this review, we first briefly introduce the characteristics of PPIs and then present different approaches for investigating PPIs, as well as the latest methods for modulating PPIs. Importantly, we comprehensively review the recent progress in the development of allosteric modulators to inhibit or stabilize PPIs. Finally, we conclude with future perspectives on the discovery of allosteric PPI modulators, especially the application of computational methods to aid in allosteric PPI drug discovery.

Katanin P80 expression correlates with lymph node metastasis and worse overall survival in patients with breast cancer

OBJECTIVE

The aim of this study was to investigate the correlation of katanin P80 expression with clinicopathological features and overall survival (OS) in surgical breast cancer (BC) patients.

METHODS

Four hundred and fourteen BC patients underwent surgery were analyzed in this retrospective cohort study. Katanin P80 expression was examined by immunofluorescence assay. The median follow-up duration was 118.0 months (quantiles: 99.0-140.5 months), the last follow-up date was Jul 1st 2017.

RESULTS

Eighty-five patients (20.5%) with katanin P80 positive expression and 329 patients (79.5%) with katanin P80 negative expression were observed in this research. Katanin P80 positive expression was correlated with higher N stage (p< 0.001) and TNM stage (p< 0.001). K-M curve and log-rank test revealed that katanin P80 positive patients presented with shorter OS compared with katanin P80 negative patients (p< 0.001). Multivariate Cox's regression analysis disclosed that katanin P80 positive expression (p< 0.001) and histologic grade (p< 0.001) could independently predict unfavorable OS. Furthermore, subgroups analysis was performed, which illuminated that katanin P80 positive expression was correlated with shorter OS in all subgroups divided by molecular subtyping and TNM stage (all p< 0.05) except in TNM stage I subgroup (p= 0.573).

CONCLUSION

Katanin P80 expression positively correlated with lymph node metastasis and could abe a novel biomarker for prognosis in BC patients.

Cathelicidin Suppresses Colon Cancer Metastasis via a P2RX7-Dependent Mechanism

The antimicrobial peptide cathelicidin inhibits development of colitis-associated colon cancer. However, the role of cathelicidin in colon cancer metastasis remains unknown. We hypothesized that cathelicidin is effective in inhibiting colon cancer metastasis. Human colon cancer HT-29 cells were injected intravenously into nude mice. Control HA-tagged adeno-associated virus (HA-AAV) or cathelicidin-overexpressing AAV (CAMP-HA-AAV) were injected intravenously into nude mice on the same day. Four weeks later, the nude mice were assessed for lung and liver metastases. Human colon cancer SW620 cells were used to study the effect of cathelicidin on cell migration and cytoskeleton. Incubation of SW620 cells with cathelicidin dose-dependently reduced cell migration, disrupted cytoskeletal structure, and reduced βIII-tubulin (TUBB3) mRNA expression. The addition of the P2RX7 antagonist KN62, but not the FPRL1 antagonist WRW4, prevented the LL-37-mediated inhibition of cell migration and TUBB3 mRNA expression. The CAMP-HA-AAV-overexpressing group showed significantly reduced human CK20 protein (by 60%) and TUBB3 mRNA expression (by 40%) in the lungs and liver of the HT-29-loaded nude mice, compared to the HA-AAV control group. Intraperitoneal injection of KN62 reversed the CAMP-HA-AAV-mediated inhibition of human CK20 and TUBB3 expression in the lungs and liver of HT-29-loaded nude mice. In conclusion, cathelicidin inhibits colon cancer metastasis via a P2RX7-dependent pathway.

Regression-Based Network Estimation for High-Dimensional Genetic Data

Given the continuous advancement in genome sequencing technology, large volumes of gene expression data can be easily obtained. However, the corresponding increase in genetic information necessitates adoption of a new approach for network estimation. Data dimensions increase with the progress in genome sequencing technology, thereby making it difficult to estimate gene networks by causing multicollinearity. Furthermore, such a problem also occurs when hub nodes exist, where gene networks are known to have regulator genes that can be interpreted as hub nodes. This study aims at developing methods that demonstrate good performance when handling high-dimensional data with hub nodes. We propose regression-based approaches as feasible solutions in this article. Elastic-net and adaptive elastic-net penalty regressions were applied to compensate for the disadvantages of existing regression-based approaches employing LASSO or adaptive LASSO. Experiments were performed to compare the proposed regression-based approaches with other conventional methods. We confirmed the superior performance of the regression-based approaches and applied it to actual genetic data to verify the suitability to estimate gene networks. As results, robustness of the proposed methods was demonstrated with respect to high-dimensional gene expression data.

Allosteric Modulators of Protein-Protein Interactions (PPIs)

Protein-protein interactions (PPIs) represent promising drug targets of broad-spectrum therapeutic interests due to their critical implications in both health and disease circumstances. Hence, they are widely accepted as the Holy Grail of drug development. Historically, PPIs were rendered "undruggable" for their large, flat, and pocket-less structures. Current attempts to drug these "intractable" targets include orthosteric and allosteric methodologies. Previous efforts employing orthosteric approaches like protein therapeutics and orthosteric small molecules frequently suffered from poor performance caused by the difficulties in directly targeting PPI interfaces. As structural biology progresses rapidly, allosteric modulators, which direct to the allosteric regulatory sites remote to the PPI surfaces, have gradually established as a potential solution. Allosteric pockets are topologically distal from the PPI orthosteric sites, and their ligands do not need to compete with the PPI partners, which helps to improve the physiochemical and pharmacological properties of allosteric PPI modulators. Thus, exploiting allostery to tailor PPIs is regarded as a tempting strategy in future PPI drug discovery. Here, we provide a comprehensive review of our representative achievements along the way we utilize allosteric effects to tame the difficult PPI systems into druggable targets. Importantly, we provide an in-depth mechanistic analysis of this success, which will be instructive to future related lead optimizations and drug design. Finally, we discuss the current challenges in allosteric PPI drug discovery. Their solutions as well as future perspectives are also presented.

Insights into photoreceptor ciliogenesis revealed by animal models

Photoreceptors are polarized neurons, with very specific subcellular compartmentalization and unique requirements for protein expression and trafficking. Each photoreceptor contains an outer segment, the site of photon capture that initiates vision, an inner segment that houses the biosynthetic machinery and a synaptic terminal for signal transmission to downstream neurons. Outer segments and inner segments are connected by a connecting cilium (CC), the equivalent of a transition zone (TZ) of primary cilia. The connecting cilium is part of the basal body/axoneme backbone that stabilizes the outer segment. This report will update the reader on late developments in photoreceptor ciliogenesis and transition zone formation, specifically in mouse photoreceptors, focusing on early events in photoreceptor ciliogenesis. The connecting cilium, an elongated and narrow structure through which all outer segment proteins and membrane components must traffic, functions as a gate that controls access to the outer segment. Here we will review genes and their protein products essential for basal body maturation and for CC/TZ genesis, sorted by phenotype. Emphasis is given to naturally occurring mouse mutants and gene knockouts that interfere with CC/TZ formation and ciliogenesis.

Identification of a novel biomarker in tangeretin‑induced cell death in AGS human gastric cancer cells

Proteomic analysis serves as an important biological tool for identifying biological events. Novel biomarkers of a specific disease such as cancer may be identified using these promising techniques. The aim of the present study was to investigate the effect of tangeretin and to identify potential biomarkers in AGS gastric cancer cells using a proteomics approach. The results of the present study revealed that tangeretin inhibited AGS cell viability dose‑dependently with a half‑maximal inhibitory concentration of 100 µM. Two‑dimensional gel electrophoresis was performed to determine the potential biomarker between control and tangeretin (100 µM)‑treated AGS cells. A total of 16 proteins was identified from 36 significant protein spots using matrix‑assisted laser‑desorption/ionization time‑of‑flight‑mass spectrometry using peptide fingerprinting. The bioinformatics tools Protein ANalysis THrough Evolutionary Relationships (PANTHER) and Database for Annotation, Visualization and Integrated Discovery (DAVID) were used to identify the functional properties and association of the proteins obtained. Using western blot analysis, the regulatory pattern of four selected proteins, protein kinase Cε, mitogen‑activated protein kinase 4, phosphoinositide 4‑kinase and poly(ADP‑ribose) polymerase 14, were successfully verified in replicate sample sets. These selected proteins are primarily involved in apoptosis signaling, angiogenesis, cell cycle regulation, receptor kinase binding, intracellular cytoplasmic and nuclear alterations. Therefore, aim of the present study was to identify potential diagnostic biomarkers from the functional categories of altered protein expression in tangeretin‑inhibited AGS gastric cancer cell viability.

Pan-Cancer Analysis Reveals the Functional Importance of Protein Lysine Modification in Cancer Development

Large-scale tumor genome sequencing projects have revealed a complex landscape of genomic mutations in multiple cancer types. A major goal of these projects is to characterize somatic mutations and discover cancer drivers, thereby providing important clues to uncover diagnostic or therapeutic targets for clinical treatment. However, distinguishing only a few somatic mutations from the majority of passenger mutations is still a major challenge facing the biological community. Fortunately, combining other functional features with mutations to predict cancer driver genes is an effective approach to solve the above problem. Protein lysine modifications are an important functional feature that regulates the development of cancer. Therefore, in this work, we have systematically analyzed somatic mutations on seven protein lysine modifications and identified several important drivers that are responsible for tumorigenesis. From published literature, we first collected more than 100,000 lysine modification sites for analysis. Another 1 million non-synonymous single nucleotide variants (SNVs) were then downloaded from TCGA and mapped to our collected lysine modification sites. To identify driver proteins that significantly altered lysine modifications, we further developed a hierarchical Bayesian model and applied the Markov Chain Monte Carlo (MCMC) method for testing. Strikingly, the coding sequences of 473 proteins were found to carry a higher mutation rate in lysine modification sites compared to other background regions. Hypergeometric tests also revealed that these gene products were enriched in known cancer drivers. Functional analysis suggested that mutations within the lysine modification regions possessed higher evolutionary conservation and deleteriousness. Furthermore, pathway enrichment showed that mutations on lysine modification sites mainly affected cancer related processes, such as cell cycle and RNA transport. Moreover, clinical studies also suggested that the driver proteins were significantly associated with patient survival, implying an opportunity to use lysine modifications as molecular markers in cancer diagnosis or treatment. By searching within protein-protein interaction networks using a random walk with restart (RWR) algorithm, we further identified a series of potential treatment agents and therapeutic targets for cancer related to lysine modifications. Collectively, this study reveals the functional importance of lysine modifications in cancer development and may benefit the discovery of novel mechanisms for cancer treatment.

Mammalian Plakins, Giant Cytolinkers: Versatile Biological Functions and Roles in Cancer

Cancer is a highly lethal disease that is characterized by aberrant cell proliferation, migration, and adhesion, which are closely related to the dynamic changes of cytoskeletons and cytoskeletal-adhesion. These will further result in cell invasion and metastasis. Plakins are a family of giant cytolinkers that connect cytoskeletal elements with each other and to junctional complexes. With various isoforms composed of different domain structures, mammalian plakins are broadly expressed in numerous tissues. They play critical roles in many cellular processes, including cell proliferation, migration, adhesion, and signaling transduction. As these cellular processes are key steps in cancer development, mammalian plakins have in recent years attracted more and more attention for their potential roles in cancer. Current evidence shows the importance of mammalian plakins in various human cancers and demonstrates mammalian plakins as potential biomarkers for cancer. Here, we introduce the basic characteristics of mammalian plakins, review the recent advances in understanding their biological functions, and highlight their roles in human cancers, based on studies performed by us and others. This will provide researchers with a comprehensive understanding of mammalian plakins, new insights into the development of cancer, and novel targets for cancer diagnosis and therapy.

Microtubule actin cross-linking factor 1, a novel potential target in cancer

Cancer is a polygenic disease characterized by uncontrolled growth of normal body cells, deregulation of the cell cycle as well as resistance to apoptosis. The spectraplakin protein microtubule actin cross-linking factor 1 (MACF1) plays an essential function in various cellular processes, including cell proliferation, migration, signaling transduction and embryo development. MACF1 is also involved in processes such as metastatic invasion in which cytoskeleton organization is a critical element that contributes to tumor progression in various human cancers. Aberrant expression of MACF1 initiates the tumor cell proliferation, and migration and metastasis in numerous cancers, such as breast cancer, colon cancer, lung cancer and glioblastoma. In this review, we summarized the current knowledge of MACF1 and its critical role in different human cancers. This will be helpful for researchers to investigate the novel functional role of MACF1 in human cancers and as a potential target to enhance the efficacy of therapeutic treatment modalities.