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Open AccessEditorial

An Overview of 10^th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors

by Hiroshi Miyamoto

Cells 2023, 12(1), 55; https://doi.org/10.3390/cells12010055 - 23 Dec 2022

Cited by 1 | Viewed by 1203

Abstract

The year 2021 marked the 10^th anniversary of the publication of Cells [...] Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

Research

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17 pages, 4707 KiB

Open AccessArticle

The Retinoblastoma Tumor Suppressor Is Required for the NUP98-HOXA9-Induced Aberrant Nuclear Envelope Phenotype

by Marcela Vaz and Birthe Fahrenkrog

Cells 2021, 10(11), 2851; https://doi.org/10.3390/cells10112851 - 22 Oct 2021

Cited by 3 | Viewed by 2566

Abstract

Chromosomal translocations involving the nucleoporin NUP98 gene are recurrently identified in leukemia; yet, the cellular defects accompanying NUP98 fusion proteins are poorly characterized. NUP98 fusions cause changes in nuclear and nuclear envelope (NE) organization, in particular, in the nuclear lamina and the lamina [...] Read more.

Chromosomal translocations involving the nucleoporin NUP98 gene are recurrently identified in leukemia; yet, the cellular defects accompanying NUP98 fusion proteins are poorly characterized. NUP98 fusions cause changes in nuclear and nuclear envelope (NE) organization, in particular, in the nuclear lamina and the lamina associated polypeptide 2α (LAP2α), a regulator of the tumor suppressor retinoblastoma protein (RB). We demonstrate that, for NUP98-HOXA9 (NHA9), the best-studied NUP98 fusion protein, its effect(s) on nuclear architecture largely depend(s) on RB. Morphological alterations caused by the expression of NHA9 are largely diminished in the absence of RB, both in human cells expressing the human papillomavirus 16 E7 protein and in mouse embryonic fibroblasts lacking RB. We further show that NHA9 expression associates with distinct histone modification. Moreover, the pattern of trimethylation of histone H3 lysine-27 is affected by NHA9, again in an RB-dependent manner. Our results pinpoint to an unexpected interplay between NUP98 fusion proteins and RB, which may contribute to leukemogenesis. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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25 pages, 7906 KiB

Open AccessArticle

The LEDGF/p75 Integrase Binding Domain Interactome Contributes to the Survival, Clonogenicity, and Tumorsphere Formation of Docetaxel-Resistant Prostate Cancer Cells

by Greisha L. Ortiz-Hernandez, Evelyn S. Sanchez-Hernandez, Pedro T. Ochoa, Catherine C. Elix, Hossam R. Alkashgari, James R. W. McMullen, Ubaldo Soto, Shannalee R. Martinez, Carlos J. Diaz Osterman, Michael Mahler, Sourav Roy and Carlos A. Casiano

Cells 2021, 10(10), 2723; https://doi.org/10.3390/cells10102723 - 12 Oct 2021

Cited by 9 | Viewed by 3992

Abstract

Patients with prostate cancer (PCa) receiving docetaxel chemotherapy invariably develop chemoresistance. The transcription co-activator lens epithelium-derived growth factor p75 (LEDGF/p75), also known as DFS70 and PSIP1, is upregulated in several human cancers, including PCa and promotes resistance to docetaxel and other drugs. The [...] Read more.

Patients with prostate cancer (PCa) receiving docetaxel chemotherapy invariably develop chemoresistance. The transcription co-activator lens epithelium-derived growth factor p75 (LEDGF/p75), also known as DFS70 and PSIP1, is upregulated in several human cancers, including PCa and promotes resistance to docetaxel and other drugs. The C-terminal region of LEDGF/p75 contains an integrase binding domain (IBD) that tethers nuclear proteins, including the HIV-1 integrase and transcription factors, to active chromatin to promote viral integration and transcription of cellular survival genes. Here, we investigated the contribution of the LEDGF/p75 IBD interactome to PCa chemoresistance. Quantitative immunoblotting revealed that LEDGF/p75 and its IBD-interacting partners are endogenously upregulated in docetaxel-resistant PCa cell lines compared to docetaxel-sensitive parental cells. Using specific human autoantibodies, we co-immunoprecipitated LEDGF/p75 with its endogenous IBD-interacting partners JPO2, menin, MLL, IWS1, ASK1, and PogZ, as well as transcription factors c-MYC and HRP2, in docetaxel-resistant cells, and confirmed their nuclear co-localization by confocal microscopy. Depletion of LEDGF/p75 and selected interacting partners robustly decreased the survival, clonogenicity, and tumorsphere formation capacity of docetaxel-resistant cells. These results implicate the LEDGF/p75 IBD interactome in PCa chemoresistance and could lead to novel therapeutic strategies targeting this protein complex for the treatment of docetaxel-resistant tumors. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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11 pages, 682 KiB

Open AccessArticle

Serum miRNAs Support the Indication for MRI-Ultrasound Fusion-Guided Biopsy of the Prostate in Patients with Low-PI-RADS Lesions

by Bastian Keck, Angelika Borkowetz, Julia Poellmann, Thilo Jansen, Moritz Fischer, Susanne Fuessel, Andreas Kahlmeyer, Manfred Wirth, Johannes Huber, Alexander Cavallaro, Matthias Hammon, Ivan Platzek, Arndt Hartmann, Gustavo Baretton, Frank Kunath, Danijel Sikic, Helge Taubert, Bernd Wullich, Kati Erdmann and Sven Wach

Cells 2021, 10(6), 1315; https://doi.org/10.3390/cells10061315 - 25 May 2021

Cited by 5 | Viewed by 2475

Abstract

Multiparametric MRI (mpMRI) and targeted biopsy of the prostate enhance the tumor detection rate. However, the prediction of clinically significant prostate cancer (PCa) is still limited. Our study tested the additional value of serum levels of selected miRNAs in combination with clinical and [...] Read more.

Multiparametric MRI (mpMRI) and targeted biopsy of the prostate enhance the tumor detection rate. However, the prediction of clinically significant prostate cancer (PCa) is still limited. Our study tested the additional value of serum levels of selected miRNAs in combination with clinical and mpMRI information for PCa prediction and classification. A total of 289 patients underwent targeted mpMRI-ultrasound fusion-guided prostate biopsy complemented by systematic biopsy. Serum miRNA levels of miRNAs (miR-141, miR-375, miR-21-5p, miR-320b, miR-210-3p, let-7c, and miR-486) were determined by quantitative PCR. Detection of any PCa and of significant PCa were the outcome variables. The patient age, pre-biopsy PSA level, previous biopsy procedure, PI-RADS score, and serum miRNA levels were covariates for regularized binary logistic regression models. The addition of miRNA expression of miR-486 and let-7c to the baseline model, containing only clinical parameters, increased the predictive accuracy. Particularly in patients with PI-RADS ≤3, we determined a sensitivity for detecting significant PCa (Gleason score ≥ 7a corresponding to Grade group ≥2) of 95.2%, and an NPV for absence of significant PCa of 97.1%. This accuracy could be useful to support patient counseling in selected cases. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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21 pages, 4363 KiB

Open AccessArticle

Widespread Alternative Splicing Changes in Metastatic Breast Cancer Cells

by Jagyeong Oh, Davide Pradella, Changwei Shao, Hairi Li, Namjeong Choi, Jiyeon Ha, Sonia Ruggiero, Xiang-Dong Fu, Xuexiu Zheng, Claudia Ghigna and Haihong Shen

Cells 2021, 10(4), 858; https://doi.org/10.3390/cells10040858 - 9 Apr 2021

Cited by 13 | Viewed by 4433

Abstract

Aberrant alternative splicing (AS) is a hallmark of cancer and a potential target for novel anti-cancer therapeutics. Breast cancer-associated AS events are known to be linked to disease progression, metastasis, and survival of breast cancer patients. To identify altered AS programs occurring in [...] Read more.

Aberrant alternative splicing (AS) is a hallmark of cancer and a potential target for novel anti-cancer therapeutics. Breast cancer-associated AS events are known to be linked to disease progression, metastasis, and survival of breast cancer patients. To identify altered AS programs occurring in metastatic breast cancer, we perform a global analysis of AS events by using RNA-mediated oligonucleotide annealing, selection, and ligation coupled with next-generation sequencing (RASL-seq). We demonstrate that, relative to low-metastatic, high-metastatic breast cancer cells show different AS choices in genes related to cancer progression. Supporting a global reshape of cancer-related splicing profiles in metastatic breast cancer we found an enrichment of RNA-binding motifs recognized by several splicing regulators, which have aberrant expression levels or activity during breast cancer progression, including SRSF1. Among SRSF1-regulated targets we found DCUN1D5, a gene for which skipping of exon 4 in its pre-mRNA introduces a premature termination codon (PTC), thus generating an unstable transcript degraded by nonsense-mediated mRNA decay (NMD). Significantly, distinct breast cancer subtypes show different DCUN1D5 isoform ratios with metastatic breast cancer expressing the highest level of the NMD-insensitive DCUN1D5 mRNA, thus showing high DCUN1D5 expression levels, which are ultimately associated with poor overall and relapse-free survival in breast cancer patients. Collectively, our results reveal global AS features of metastatic breast tumors, which open new possibilities for the treatment of these aggressive tumor types. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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13 pages, 2820 KiB

Open AccessArticle

Simple and Efficient Protocol for Subcellular Fractionation of Normal and Apoptotic Cells

by Viacheslav V. Senichkin, Evgeniia A. Prokhorova, Boris Zhivotovsky and Gelina S. Kopeina

Cells 2021, 10(4), 852; https://doi.org/10.3390/cells10040852 - 9 Apr 2021

Cited by 28 | Viewed by 13217

Abstract

Subcellular fractionation approaches remain an indispensable tool among a large number of biochemical methods to facilitate the study of specific intracellular events and characterization of protein functions. During apoptosis, the best-known form of programmed cell death, numerous proteins are translocated into and from [...] Read more.

Subcellular fractionation approaches remain an indispensable tool among a large number of biochemical methods to facilitate the study of specific intracellular events and characterization of protein functions. During apoptosis, the best-known form of programmed cell death, numerous proteins are translocated into and from the nucleus. Therefore, suitable biochemical techniques for the subcellular fractionation of apoptotic cells are required. However, apoptotic bodies and cell fragments might contaminate the fractions upon using the standard protocols. Here, we compared different nucleus/cytoplasm fractionation methods and selected the best-suited approach for the separation of nuclear and cytoplasmic contents. The described methodology is based on stepwise lysis of cells and washing of the resulting nuclei using non-ionic detergents, such as NP-40. Next, we validated this approach for fractionation of cells treated with various apoptotic stimuli. Finally, we demonstrated that nuclear fraction could be further subdivided into nucleosolic and insoluble subfractions, which is crucial for the isolation and functional studies of various proteins. Altogether, we developed a method for simple and efficient nucleus/cytoplasm fractionation of both normal and apoptotic cells. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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22 pages, 3766 KiB

Open AccessFeature PaperArticle

A Trans-Omics Comparison Reveals Common Gene Expression Strategies in Four Model Organisms and Exposes Similarities and Differences between Them

by Jaume Forés-Martos, Anabel Forte, José García-Martínez and José E. Pérez-Ortín

Cells 2021, 10(2), 334; https://doi.org/10.3390/cells10020334 - 5 Feb 2021

Cited by 5 | Viewed by 2924

Abstract

The ultimate goal of gene expression regulation is on the protein level. However, because the amounts of mRNAs and proteins are controlled by their synthesis and degradation rates, the cellular amount of a given protein can be attained by following different strategies. By [...] Read more.

The ultimate goal of gene expression regulation is on the protein level. However, because the amounts of mRNAs and proteins are controlled by their synthesis and degradation rates, the cellular amount of a given protein can be attained by following different strategies. By studying omics data for six expression variables (mRNA and protein amounts, plus their synthesis and decay rates), we previously demonstrated the existence of common expression strategies (CESs) for functionally related genes in the yeast Saccharomyces cerevisiae. Here we extend that study to two other eukaryotes: the yeast Schizosaccharomyces pombe and cultured human HeLa cells. We also use genomic data from the model prokaryote Escherichia coli as an external reference. We show that six-variable profiles (6VPs) can be constructed for every gene and that these 6VPs are similar for genes with similar functions in all the studied organisms. The differences in 6VPs between organisms can be used to establish their phylogenetic relationships. The analysis of the correlations among the six variables supports the hypothesis that most gene expression control occurs in actively growing organisms at the transcription rate level, and that translation plays a minor role. We propose that living organisms use CESs for the genes acting on the same physiological pathways, especially for those belonging to stable macromolecular complexes, but CESs have been modeled by evolution to adapt to the specific life circumstances of each organism. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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Review

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17 pages, 2776 KiB

Open AccessReview

Dunking into the Lipid Bilayer: How Direct Membrane Binding of Nucleoporins Can Contribute to Nuclear Pore Complex Structure and Assembly

by Mohamed Hamed and Wolfram Antonin

Cells 2021, 10(12), 3601; https://doi.org/10.3390/cells10123601 - 20 Dec 2021

Cited by 12 | Viewed by 6242

Abstract

Nuclear pore complexes (NPCs) mediate the selective and highly efficient transport between the cytoplasm and the nucleus. They are embedded in the two membrane structure of the nuclear envelope at sites where these two membranes are fused to pores. A few transmembrane proteins [...] Read more.

Nuclear pore complexes (NPCs) mediate the selective and highly efficient transport between the cytoplasm and the nucleus. They are embedded in the two membrane structure of the nuclear envelope at sites where these two membranes are fused to pores. A few transmembrane proteins are an integral part of NPCs and thought to anchor these complexes in the nuclear envelope. In addition, a number of nucleoporins without membrane spanning domains interact with the pore membrane. Here we review our current knowledge of how these proteins interact with the membrane and how this interaction can contribute to NPC assembly, stability and function as well as shaping of the pore membrane. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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42 pages, 1233 KiB

Open AccessReview

Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus

by Zaur M. Kachaev, Sergey D. Ivashchenko, Eugene N. Kozlov, Lyubov A. Lebedeva and Yulii V. Shidlovskii

Cells 2021, 10(11), 3239; https://doi.org/10.3390/cells10113239 - 19 Nov 2021

Cited by 8 | Viewed by 5836

Abstract

Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such [...] Read more.

Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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20 pages, 6160 KiB

Open AccessReview

Loop-Mediated Isothermal Amplification (LAMP): The Better Sibling of PCR?

by Marianna Soroka, Barbara Wasowicz and Anna Rymaszewska

Cells 2021, 10(8), 1931; https://doi.org/10.3390/cells10081931 - 29 Jul 2021

Cited by 201 | Viewed by 18733

Abstract

In 1998, when the PCR technique was already popular, a Japanese company called Eiken Chemical Co., Ltd. designed a method known as the loop-mediated isothermal amplification of DNA (LAMP). The method can produce up to 10⁹ copies of the amplified DNA within [...] Read more.

In 1998, when the PCR technique was already popular, a Japanese company called Eiken Chemical Co., Ltd. designed a method known as the loop-mediated isothermal amplification of DNA (LAMP). The method can produce up to 10⁹ copies of the amplified DNA within less than an hour. It is also highly specific due to the use of two to three pairs of primers (internal, external, and loop), which recognise up to eight specific locations on the DNA or RNA targets. Furthermore, the Bst DNA polymerase most used in LAMP shows a high strand displacement activity, which eliminates the DNA denaturation stage. One of the most significant advantages of LAMP is that it can be conducted at a stable temperature, for instance, in a dry block heater or an incubator. The products of LAMP can be detected much faster than in standard techniques, sometimes only requiring analysis with the naked eye. The following overview highlights the usefulness of LAMP and its effectiveness in various fields; it also considers the superiority of LAMP over PCR and presents RT-LAMP as a rapid diagnostic tool for SARS-CoV-2. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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21 pages, 878 KiB

Open AccessReview

Affecting HEK293 Cell Growth and Production Performance by Modifying the Expression of Specific Genes

by Laura Abaandou, David Quan and Joseph Shiloach

Cells 2021, 10(7), 1667; https://doi.org/10.3390/cells10071667 - 2 Jul 2021

Cited by 65 | Viewed by 22726

Abstract

The HEK293 cell line has earned its place as a producer of biotherapeutics. In addition to its ease of growth in serum-free suspension culture and its amenability to transfection, this cell line’s most important attribute is its human origin, which makes it suitable [...] Read more.

The HEK293 cell line has earned its place as a producer of biotherapeutics. In addition to its ease of growth in serum-free suspension culture and its amenability to transfection, this cell line’s most important attribute is its human origin, which makes it suitable to produce biologics intended for human use. At the present time, the growth and production properties of the HEK293 cell line are inferior to those of non-human cell lines, such as the Chinese hamster ovary (CHO) and the murine myeloma NSO cell lines. However, the modification of genes involved in cellular processes, such as cell proliferation, apoptosis, metabolism, glycosylation, secretion, and protein folding, in addition to bioprocess, media, and vector optimization, have greatly improved the performance of this cell line. This review provides a comprehensive summary of important achievements in HEK293 cell line engineering and on the global engineering approaches and functional genomic tools that have been employed to identify relevant genes for targeted engineering. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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18 pages, 538 KiB

Open AccessReview

Alzheimer and Purinergic Signaling: Just a Matter of Inflammation?

by Stefania Merighi, Tino Emanuele Poloni, Anna Terrazzan, Eva Moretti, Stefania Gessi and Davide Ferrari

Cells 2021, 10(5), 1267; https://doi.org/10.3390/cells10051267 - 20 May 2021

Cited by 19 | Viewed by 4245

Abstract

Alzheimer’s disease (AD) is a widespread neurodegenerative pathology responsible for about 70% of all cases of dementia. Adenosine is an endogenous nucleoside that affects neurodegeneration by activating four membrane G protein-coupled receptor subtypes, namely P1 receptors. One of them, the A_2A subtype, [...] Read more.

Alzheimer’s disease (AD) is a widespread neurodegenerative pathology responsible for about 70% of all cases of dementia. Adenosine is an endogenous nucleoside that affects neurodegeneration by activating four membrane G protein-coupled receptor subtypes, namely P1 receptors. One of them, the A_2A subtype, is particularly expressed in the brain at the striatal and hippocampal levels and appears as the most promising target to counteract neurological damage and adenosine-dependent neuroinflammation. Extracellular nucleotides (ATP, ADP, UTP, UDP, etc.) are also released from the cell or are synthesized extracellularly. They activate P2X and P2Y membrane receptors, eliciting a variety of physiological but also pathological responses. Among the latter, the chronic inflammation underlying AD is mainly caused by the P2X7 receptor subtype. In this review we offer an overview of the scientific evidence linking P1 and P2 mediated purinergic signaling to AD development. We will also discuss potential strategies to exploit this knowledge for drug development. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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16 pages, 2610 KiB

Open AccessReview

Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19

by Rohitash Yadav, Jitendra Kumar Chaudhary, Neeraj Jain, Pankaj Kumar Chaudhary, Supriya Khanra, Puneet Dhamija, Ambika Sharma, Ashish Kumar and Shailendra Handu

Cells 2021, 10(4), 821; https://doi.org/10.3390/cells10040821 - 6 Apr 2021

Cited by 319 | Viewed by 26402

Abstract

Coronavirus belongs to the family of Coronaviridae, comprising single-stranded, positive-sense RNA genome (+ ssRNA) of around 26 to 32 kilobases, and has been known to cause infection to a myriad of mammalian hosts, such as humans, cats, bats, civets, dogs, and camels with [...] Read more.

Coronavirus belongs to the family of Coronaviridae, comprising single-stranded, positive-sense RNA genome (+ ssRNA) of around 26 to 32 kilobases, and has been known to cause infection to a myriad of mammalian hosts, such as humans, cats, bats, civets, dogs, and camels with varied consequences in terms of death and debilitation. Strikingly, novel coronavirus (2019-nCoV), later renamed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), and found to be the causative agent of coronavirus disease-19 (COVID-19), shows 88% of sequence identity with bat-SL-CoVZC45 and bat-SL-CoVZXC21, 79% with SARS-CoV and 50% with MERS-CoV, respectively. Despite key amino acid residual variability, there is an incredible structural similarity between the receptor binding domain (RBD) of spike protein (S) of SARS-CoV-2 and SARS-CoV. During infection, spike protein of SARS-CoV-2 compared to SARS-CoV displays 10–20 times greater affinity for its cognate host cell receptor, angiotensin-converting enzyme 2 (ACE2), leading proteolytic cleavage of S protein by transmembrane protease serine 2 (TMPRSS2). Following cellular entry, the ORF-1a and ORF-1ab, located downstream to 5′ end of + ssRNA genome, undergo translation, thereby forming two large polyproteins, pp1a and pp1ab. These polyproteins, following protease-induced cleavage and molecular assembly, form functional viral RNA polymerase, also referred to as replicase. Thereafter, uninterrupted orchestrated replication-transcription molecular events lead to the synthesis of multiple nested sets of subgenomic mRNAs (sgRNAs), which are finally translated to several structural and accessory proteins participating in structure formation and various molecular functions of virus, respectively. These multiple structural proteins assemble and encapsulate genomic RNA (gRNA), resulting in numerous viral progenies, which eventually exit the host cell, and spread infection to rest of the body. In this review, we primarily focus on genomic organization, structural and non-structural protein components, and potential prospective molecular targets for development of therapeutic drugs, convalescent plasm therapy, and a myriad of potential vaccines to tackle SARS-CoV-2 infection. Full article

(This article belongs to the Special Issue 10th Anniversary of Cells—Advances in Cell Nuclei: Function, Transport and Receptors)

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