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Science (New York, N.Y.) Aug 2019How cellular and organismal complexity emerges from combinatorial expression of genes is a central question in biology. High-content phenotyping approaches such as...
How cellular and organismal complexity emerges from combinatorial expression of genes is a central question in biology. High-content phenotyping approaches such as Perturb-seq (single-cell RNA-sequencing pooled CRISPR screens) present an opportunity for exploring such genetic interactions (GIs) at scale. Here, we present an analytical framework for interpreting high-dimensional landscapes of cell states (manifolds) constructed from transcriptional phenotypes. We applied this approach to Perturb-seq profiling of strong GIs mined from a growth-based, gain-of-function GI map. Exploration of this manifold enabled ordering of regulatory pathways, principled classification of GIs (e.g., identifying suppressors), and mechanistic elucidation of synergistic interactions, including an unexpected synergy between and driving erythroid differentiation. Finally, we applied recommender system machine learning to predict interactions, facilitating exploration of vastly larger GI manifolds.
Topics: Apoptosis; CRISPR-Cas Systems; Calcium-Binding Proteins; Cell Cycle Checkpoints; Cell Line, Tumor; Epistasis, Genetic; Erythroid Cells; Erythropoiesis; Female; Gene Expression Profiling; Granulocytes; Humans; Microfilament Proteins; Proto-Oncogene Proteins c-cbl; Sequence Analysis, RNA; Single-Cell Analysis; Calponins
PubMed: 31395745
DOI: 10.1126/science.aax4438 -
Frontiers in Cell and Developmental... 2023Calponin and transgelin (originally named SM22) are homologous cytoskeleton proteins that regulate actin-activated myosin motor functions in smooth muscle contraction... (Review)
Review
Calponin and transgelin (originally named SM22) are homologous cytoskeleton proteins that regulate actin-activated myosin motor functions in smooth muscle contraction and non-muscle cell motility during adhesion, migration, proliferation, phagocytosis, wound healing, and inflammatory responses. They are abundant cytoskeleton proteins present in multiple cell types whereas their physiological functions remain to be fully established. This focused review summarizes the evolution of genes encoding calponin and transgelin and their isoforms and discusses the structural similarity and divergence in vertebrate and invertebrate species in the context of functions in regulating cell motility. As the first literature review focusing on the evolution of the calponin-transgelin family of proteins in relevance to their structure-function relationship, the goal is to outline a foundation of current knowledge for continued investigations to understand the biological functions of calponin and transgelin in various cell types during physiological and pathological processes.
PubMed: 37363722
DOI: 10.3389/fcell.2023.1206147 -
Matrix Biology : Journal of the... Jan 2023The mechanical microenvironment regulated by cancer-associated fibroblasts (CAFs) influence tumor progression. Chemotherapeutic interventions including 5-Fluorouracil...
The mechanical microenvironment regulated by cancer-associated fibroblasts (CAFs) influence tumor progression. Chemotherapeutic interventions including 5-Fluorouracil (5-Fu) are commonly used for primary treatment of patients with advanced gastric cancer (GC), and the development of acquired resistance to 5-Fu limits the clinical efficacy of these chemotherapies. However, if and how the interplay between CAFs and the mechanical microenvironment regulates GC response to 5-Fu is poorly understood. In this study, we demonstrate that high-level expression of calponin 1(CNN1) in gastric CAFs predicts poor clinical outcomes of GC patients, especially for those treated with 5-Fu. CNN1 knockdown in CAFs improves the effectiveness of 5-Fu in reducing tumor growth in a mouse GC model and confers increased sensitivity to 5-Fu in a 3D culture system. Furthermore, CNN1 knockdown impairs CAF contraction and reduces matrix stiffness without affecting the expression of matrix proteins. Mechanistically, CNN1 interacts with PDZ and LIM Domain 7 (PDLIM7) and prevents its degradation by the E3 ubiquitin ligase NEDD4-1, which leads to activation of the ROCK1/MLC pathway. The increased matrix stiffness, in turn, contributes to 5-Fu resistance in GC cells by activating YAP. Taken together, our data reveal a critical role of the mechanical microenvironment in 5-Fu resistance, which is modulated by CNN1 CAFs-mediated matrix stiffening, indicating that targeting CAFs may provide a novel option for overcoming drug resistance in GC.
Topics: Animals; Mice; Stomach Neoplasms; Drug Resistance, Neoplasm; Cancer-Associated Fibroblasts; Cell Line, Tumor; Fluorouracil; Tumor Microenvironment; Calponins
PubMed: 36423735
DOI: 10.1016/j.matbio.2022.11.005 -
Gene Jul 2016Calponin is an actin filament-associated regulatory protein expressed in smooth muscle and many types of non-muscle cells. Three homologous genes, CNN1, CNN2 and CNN3,... (Review)
Review
Calponin is an actin filament-associated regulatory protein expressed in smooth muscle and many types of non-muscle cells. Three homologous genes, CNN1, CNN2 and CNN3, encoding calponin isoforms 1, 2, and 3, respectively, are present in vertebrate species. All three calponin isoforms are actin-binding proteins with functions in inhibiting actin-activated myosin ATPase and stabilizing the actin cytoskeleton, while each isoform executes different physiological roles based on their cell type-specific expressions. Calponin 1 is specifically expressed in smooth muscle cells and plays a role in fine-tuning smooth muscle contractility. Calponin 2 is expressed in both smooth muscle and non-muscle cells and regulates multiple actin cytoskeleton-based functions. Calponin 3 participates in actin cytoskeleton-based activities in embryonic development and myogenesis. Phosphorylation has been extensively studied for the regulation of calponin functions. Cytoskeleton tension regulates the transcription of CNN2 gene and the degradation of calponin 2 protein. This review summarizes our knowledge learned from studies over the past three decades, focusing on the evolutionary lineage of calponin isoform genes, their tissue- and cell type-specific expressions, structure-function relationships, and mechanoregulation.
Topics: Actin Cytoskeleton; Calcium-Binding Proteins; Cell Movement; Humans; Mechanoreceptors; Microfilament Proteins; Muscle Contraction; Myocytes, Smooth Muscle; Myosins; Organ Specificity; Protein Isoforms; Structure-Activity Relationship; Calponins
PubMed: 26970176
DOI: 10.1016/j.gene.2016.02.040 -
FEBS Letters Jul 1998A sequence motif of about 100 amino acids, termed the 'calponin homology domain' has been suggested to confer actin binding to a variety of cytoskeletal and signalling... (Review)
Review
A sequence motif of about 100 amino acids, termed the 'calponin homology domain' has been suggested to confer actin binding to a variety of cytoskeletal and signalling molecules. Here we analyse and compare the sequences of all calponin homology domain-containing proteins identified to date. We propose that single calponin homology domains do not confer actin-binding per se and that the actin-binding motifs of cross-linking proteins, which comprise two disparate calponin homology domains, represent a unique protein module.
Topics: Actins; Amino Acid Sequence; Animals; Calcium-Binding Proteins; Databases, Factual; Humans; Microfilament Proteins; Molecular Sequence Data; Phylogeny; Protein Conformation; Sequence Homology, Amino Acid; Calponins
PubMed: 9708889
DOI: 10.1016/s0014-5793(98)00751-0 -
Cytoskeleton (Hoboken, N.J.) May 2021The calponin family proteins in vertebrates, including calponin and transgelin (also known as SM22 or NP25), regulate actin-myosin interaction and actin filament...
The calponin family proteins in vertebrates, including calponin and transgelin (also known as SM22 or NP25), regulate actin-myosin interaction and actin filament stability and are involved in regulation of muscle contractility and cell migration. Related proteins are also present in invertebrates and fungi. Animals have multiple genes encoding calponin family proteins with variable molecular features, which are often expressed in the same tissues or cells. However, functional studies of this class of proteins have been reported only in limited species. Through database searches, I found that the calponin family proteins were diversified in animals by gene amplification and repeat expansion of calponin-like (CLIK) motifs, which function as actin-binding sequences. Transgelin-like proteins with a single CLIK motif are the most primitive type and present in fungi and animals. In many animals, additional calponin family proteins containing multiple CLIK motifs, as represented by vertebrate calponins with three CLIK motifs, are present. Interestingly, in several invertebrate species, there are uncharacterized calponin-related proteins with highly expanded repeats of CLIK motifs (up to 23 repeats in mollusks). These variable molecular features of the calponin family proteins may be results of evolutionary adaptation to a broad range of cell biological events.
Topics: Actin Cytoskeleton; Actins; Animals; Calcium-Binding Proteins; Gene Amplification; Microfilament Proteins; Calponins
PubMed: 34333878
DOI: 10.1002/cm.21683 -
Molecular Metabolism May 2023In the fibrotic kidneys, the extent of a formed deleterious microenvironment is determined by cellular mechanical forces. This process requires metabolism for energy....
OBJECTIVE
In the fibrotic kidneys, the extent of a formed deleterious microenvironment is determined by cellular mechanical forces. This process requires metabolism for energy. However, how cellular mechanics and metabolism are connected remains unclear.
METHODS
A multi-disciplinary approach was employed: the fibrotic kidney disease models were induced by renal ischemia-reperfusion injury and unilateral ureteral obstruction in Calponin 2 (CNN2) knockdown mice. Proteomics, bioinformatics, and in vivo and in vitro molecular experimental pathology studies were performed.
RESULT
Our proteomics revealed that actin filament binding and cell metabolism are the two most dysregulated events in the fibrotic kidneys. As a prominent actin stabilizer, CNN2 was predominantly expressed in fibroblasts and pericytes. In CKD patients, CNN2 levels was markedly induced in blood. In mice, CNN2 knockdown preserves kidney function and alleviates fibrosis. Global proteomics profiled that CNN2 knockdown enhanced the activities of the key rate-limiting enzymes and regulators of fatty acid oxidation (FAO) in the diseased kidneys. Inhibiting carnitine palmitoyltransferase 1α in the FAO pathway resulted in lipid accumulation and extracellular matrix deposition in the fibrotic kidneys, which were restored after CNN2 knockdown. Bioinformatics and chromatin immunoprecipitation showed that CNN2 interactor, estrogen receptor 2 (ESR2), binds peroxisome proliferator-activated receptor-α (PPARα) to transcriptionally regulate FAO downstream target genes expression amid kidney fibrosis. In vitro, ESR2 knockdown repressed the mRNA levels of PPARα and the key genes in the FAO pathway. Conversely, activation of PPARα reduced CNN2-induced matrix inductions.
CONCLUSIONS
Our results suggest that balancing cell mechanics and metabolism is crucial to develop therapeutic strategies to halt kidney fibrosis.
Topics: Animals; Mice; Fibrosis; Kidney; Kidney Diseases; PPAR alpha; Calmodulin-Binding Proteins; Calponins
PubMed: 36963615
DOI: 10.1016/j.molmet.2023.101712 -
Frontiers in Pharmacology 2023Emerging evidence has suggested a pro-oncogenic role of calponin 1 (CNN1) in the initiation of a variety of cancers. Despite this, CNN1 remains unknown in terms of its...
Emerging evidence has suggested a pro-oncogenic role of calponin 1 (CNN1) in the initiation of a variety of cancers. Despite this, CNN1 remains unknown in terms of its effects and mechanisms on angiogenesis, prognosis, and immunology in cancer. The expression of CNN1 was extracted and analyzed using the TIMER, UALCAN, and GEPIA databases. Meanwhile, we analyzed the diagnostic value of CNN1 by using PrognoScan and Kaplan-Meier plots. To elucidate the value of CNN1 in immunotherapy, we used the TIMER 2.0 database, TISIDB database, and Sangerbox database. Gene set enrichment analysis (GSEA) was used to analyze the expression pattern and bio-progression of CNN1 and the vascular endothelium growth factor (VEGF) in cancer. The expressions of CNN1 and VEGF in gastric cancer were confirmed using immunohistochemistry. We used Cox regression analysis to investigate the association between pathological characteristics, clinical prognosis, and CNN1 and VEGF expressions in patients with gastric cancer. CNN1 expression was higher in normal tissues than it was in tumor tissues of most types of cancers. However, the expression level rebounds during the development of tumors. High levels of CNN1 indicate a poor prognosis for 11 tumors, which include stomach adenocarcinoma (STAD). There is a relationship between CNN1 and tumor-infiltrating lymphocytes (TILs), and the marker genes NRP1 and TNFRSF14 of TILs are significantly related to CNN1 expression in gastric cancers. The GSEA results confirmed the lower expression of CNN1 in tumors when compared to normal tissues. However, CNN1 again showed an increasing trend during tumor development. In addition, the results also suggest that CNN1 is involved in angiogenesis. The immunohistochemistry results validated the GSEA result (take gastric cancer as an example). Cox analysis suggested that high CNN1 expression and high VEGF expression are closely associated with poor clinical prognosis. Our study has shown that CNN1 expression is aberrantly elevated in various cancers and positively correlates with angiogenesis and the immune checkpoint, contributing to cancer progression and poor prognosis. These results suggest that CNN1 could serve as a promising candidate for pan-cancer immunotherapy.
PubMed: 37153789
DOI: 10.3389/fphar.2023.1184250 -
International Journal of Surgical... 2016Extrarenal retroperitoneal angiomyolipomas are rare. (Review)
Review
BACKGROUND
Extrarenal retroperitoneal angiomyolipomas are rare.
AIM
To review the literature.
RESULTS
Angiomyolipomas, previously classified as hamartomas, are now classified as benign tumours. Thirty cases of primary retroperitoneal angiomyolipomas have been reported. Diagnosis of the disease upon is based radiological and pathological findings of triphasic features of (a) fat and (b) blood vessels and myoid tissue. Immunohistochemistry tends to be positive for HMB45, MART1, HHF35, calponin, NKI-C3, and CD117. The lesion is common in women. Treatment options have included the following: (a) radical surgical excision of the lesion with renal sparing surgery or radical nephrectomy in cases where malignant tumours could not be excluded and (b) selective embolization of the lesion alone or prior to surgical excision. One case of retroperitoneal angiomyolipoma was reported in a patient 15 years after undergoing radical nephrectomy for angiomyolipoma of kidney and two cases of distant metastases of angiomyolipoma have been reported following radical resection of the tumour.
CONCLUSIONS
With the report of two cases of metastases ensuing surgical resection of the primary lesions there is need for academic pathologists to debate and review angiomyolipomas to decide whether to reclassify angiomyolipomas as slow-growing malignant tumours or whether the reported cases of metastases were de novo tumours or metastatic lesions.
Topics: Actins; Adult; Aged; Aged, 80 and over; Angiomyolipoma; Biomarkers, Tumor; Calcium-Binding Proteins; Diagnosis, Differential; Embolization, Therapeutic; Female; Humans; Immunohistochemistry; Kidney Neoplasms; MART-1 Antigen; Male; Melanoma-Specific Antigens; Microfilament Proteins; Middle Aged; Nephrectomy; Rare Diseases; Retroperitoneal Neoplasms; Sex Factors; Treatment Outcome; gp100 Melanoma Antigen; Calponins
PubMed: 26989509
DOI: 10.1155/2016/6347136 -
American Journal of Physiology. Cell... Aug 2021Calponin 2 is an actin cytoskeleton-associated protein and plays a role in regulating cell motility-related functions such as phagocytosis, migration, and division. We...
Calponin 2 is an actin cytoskeleton-associated protein and plays a role in regulating cell motility-related functions such as phagocytosis, migration, and division. We previously reported that overexpression of calponin 2 inhibits the rate of cell proliferation. To investigate the underlying mechanism, our present study found that the levels of endogenous calponin 2 in NIH3T3 and HEK293 cells rapidly decreased before cell division characterized by an absence at the actin contractile ring. In cells lacking endogenous calponin 2, transfective expression of GFP-fusion calponin 2 inhibited cell proliferation similar to that of nonfusion calponin 2. Fluorescent imaging studies of mitotic cells indicated that a proper level of calponin 2 expression and effective degradation during cytokinesis are necessary for normal cell division. Computer-assisted dynamic image analysis of dividing cells revealed that overexpression of calponin 2 significantly affects motility and shape behaviors of cells only on the interval from the start of anaphase to the start of cytokinesis, i.e., the pre-cytokinesis phase, but not on the interval from the start of cytokinesis to 50% completion of cytokinesis. The pre-cytokinesis degradation of calponin 2 was attenuated by MG132 inhibition of the ubiquitin proteasome and inhibitor of protein kinase C (PKC), suggesting that PKC phosphorylation-triggered degradation of calponin 2 could determine the rate of cytokinesis. The novel role of calponin 2 in regulating the rate of cytokinesis may be targeted for therapeutic applications such as in an inhibition of malignant tumor growth.
Topics: Actin Cytoskeleton; Actins; Animals; Calmodulin-Binding Proteins; Cytokinesis; HEK293 Cells; Humans; Mice; Microfilament Proteins; NIH 3T3 Cells; Phosphorylation
PubMed: 34133238
DOI: 10.1152/ajpcell.00569.2020