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Dinh T, Rahm M, Wang Z, McFarland C, Khalil A. Exploring the molecular landscape of NNK-induced transformation: A comprehensive genome-wide CRISPR/Cas9 screening. Genes Dis 2024; 11:101131. [PMID: 38450101 PMCID: PMC10915513 DOI: 10.1016/j.gendis.2023.101131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 03/08/2024] Open
Affiliation(s)
- Trang Dinh
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland 44106, USA
| | - Mira Rahm
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland 44106, USA
| | - Zhenghe Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland 44106, USA
| | - Christopher McFarland
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland 44106, USA
| | - Athar Khalil
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland 44106, USA
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2
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Lazar NH, Celik S, Chen L, Fay MM, Irish JC, Jensen J, Tillinghast CA, Urbanik J, Bone WP, Gibson CC, Haque IS. High-resolution genome-wide mapping of chromosome-arm-scale truncations induced by CRISPR-Cas9 editing. Nat Genet 2024; 56:1482-1493. [PMID: 38811841 PMCID: PMC11250378 DOI: 10.1038/s41588-024-01758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/18/2024] [Indexed: 05/31/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) is a powerful tool for introducing targeted mutations in DNA, but recent studies have shown that it can have unintended effects such as structural changes. However, these studies have not yet looked genome wide or across data types. Here we performed a phenotypic CRISPR-Cas9 scan targeting 17,065 genes in primary human cells, revealing a 'proximity bias' in which CRISPR knockouts show unexpected similarities to unrelated genes on the same chromosome arm. This bias was found to be consistent across cell types, laboratories, Cas9 delivery methods and assay modalities, and the data suggest that it is caused by telomeric truncations of chromosome arms, with cell cycle and apoptotic pathways playing a mediating role. Additionally, a simple correction is demonstrated to mitigate this pervasive bias while preserving biological relationships. This previously uncharacterized effect has implications for functional genomic studies using CRISPR-Cas9, with applications in discovery biology, drug-target identification, cell therapies and genetic therapeutics.
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Affiliation(s)
| | | | - Lu Chen
- Recursion, Salt Lake City, UT, USA
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3
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Gue R, Lakhani DA. The 2021 World Health Organization Central Nervous System Tumor Classification: The Spectrum of Diffuse Gliomas. Biomedicines 2024; 12:1349. [PMID: 38927556 PMCID: PMC11202067 DOI: 10.3390/biomedicines12061349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The 2021 edition of the World Health Organization (WHO) classification of central nervous system tumors introduces significant revisions across various tumor types. These updates, encompassing changes in diagnostic techniques, genomic integration, terminology, and grading, are crucial for radiologists, who play a critical role in interpreting brain tumor imaging. Such changes impact the diagnosis and management of nearly all central nervous system tumor categories, including the reclassification, addition, and removal of specific tumor entities. Given their pivotal role in patient care, radiologists must remain conversant with these revisions to effectively contribute to multidisciplinary tumor boards and collaborate with peers in neuro-oncology, neurosurgery, radiation oncology, and neuropathology. This knowledge is essential not only for accurate diagnosis and staging, but also for understanding the molecular and genetic underpinnings of tumors, which can influence treatment decisions and prognostication. This review, therefore, focuses on the most pertinent updates concerning the classification of adult diffuse gliomas, highlighting the aspects most relevant to radiological practice. Emphasis is placed on the implications of new genetic information on tumor behavior and imaging findings, providing necessary tools to stay abreast of advancements in the field. This comprehensive overview aims to enhance the radiologist's ability to integrate new WHO classification criteria into everyday practice, ultimately improving patient outcomes through informed and precise imaging assessments.
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Affiliation(s)
- Racine Gue
- Department of Neuroradiology, West Virginia University, Morgantown, WV 26506, USA
| | - Dhairya A. Lakhani
- Department of Neuroradiology, West Virginia University, Morgantown, WV 26506, USA
- Department of Radiology and Radiological Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
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4
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Eintracht J, Owen N, Harding P, Moosajee M. Disruption of common ocular developmental pathways in patient-derived optic vesicle models of microphthalmia. Stem Cell Reports 2024; 19:839-858. [PMID: 38821055 DOI: 10.1016/j.stemcr.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 06/02/2024] Open
Abstract
Genetic perturbations influencing early eye development can result in microphthalmia, anophthalmia, and coloboma (MAC). Over 100 genes are associated with MAC, but little is known about common disease mechanisms. In this study, we generated induced pluripotent stem cell (iPSC)-derived optic vesicles (OVs) from two unrelated microphthalmia patients and healthy controls. At day 20, 35, and 50, microphthalmia patient OV diameters were significantly smaller, recapitulating the "small eye" phenotype. RNA sequencing (RNA-seq) analysis revealed upregulation of apoptosis-initiating and extracellular matrix (ECM) genes at day 20 and 35. Western blot and immunohistochemistry revealed increased expression of lumican, nidogen, and collagen type IV, suggesting ECM overproduction. Increased apoptosis was observed in microphthalmia OVs with reduced phospho-histone 3 (pH3+) cells confirming decreased cell proliferation at day 35. Pharmacological inhibition of caspase-8 activity with Z-IETD-FMK decreased apoptosis in one patient model, highlighting a potential therapeutic approach. These data reveal shared pathophysiological mechanisms contributing to a microphthalmia phenotype.
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Affiliation(s)
| | | | | | - Mariya Moosajee
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; Moorfields Eye Hospital NHS Foundation Trust, London EC1V 9EL, UK; Francis Crick Institute, London NW1 1AT, UK.
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5
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Dabrowski KR, Daws SE. Morphine-Driven m6A Epitranscriptomic Neuroadaptations in Primary Cortical Cultures. Mol Neurobiol 2024:10.1007/s12035-024-04219-z. [PMID: 38780720 DOI: 10.1007/s12035-024-04219-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Opioid overdose is the leading cause of accidental death in the United States and remains a major public health concern, despite significant resources aimed at combating opioid misuse. Neurobiological research to elucidate molecular and cellular consequences of opioid exposure is required to define avenues to explore for reversal of opioid-induced neuroadaptations. Opioids impart well-documented regulation of the transcriptome and epigenetic modifications in the brain, but opioid-induced epitranscriptomic posttranscriptional regulation of RNA is vastly understudied. N6-methyladenosine (m6A) RNA methylation is significantly enriched in the brain and involved in learning, memory, and reward. m6A modifications have not been studied in opioid use disorder, despite being the most common RNA modification. We detected significant regulation of m6A-modifying enzymes in rat primary cortical cultures following morphine treatment, including AlkB Homolog 5 (Alkbh5). The m6a demethylase ALKBH5 functions as an m6A eraser, removing m6A modifications from mRNA. We hypothesized that chronic opioid treatment regulates m6A modifications through modulation of Alkbh5 and profiled m6A modifications in primary cortical cultures following chronic morphine treatment and Alkbh5 knock-down. We observed differential regulation of m6A modifications for a common set of transcripts following morphine or Alkbh5 knock-down, and the two treatments elicited concordant m6A epitranscriptomic profiles, suggesting that a subset of morphine-driven m6A modifications may be mediated through downregulation of Alkbh5 in cortical cultures. Gene Ontology terms of commonly regulated transcripts included serotonin secretion, synapse disassembly, neuron remodeling, and immune response. Thus, we conclude that morphine can drive epitranscriptomic changes, a subset of which may occur in an Alkbh5-dependent manner.
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Affiliation(s)
- Konrad R Dabrowski
- Center for Substance Abuse Research, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Stephanie E Daws
- Center for Substance Abuse Research, Temple University, Philadelphia, PA, USA.
- Department of Neural Sciences, Temple University, Philadelphia, PA, USA.
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de Melo DG, da Cruz Rodrigues VC, de Sá Pereira GJ, de Campos TDP, Dos Santos Canciglieri R, Pauli JR, da Silva ASR, da Costa Fernandes CJ, de Moura LP. Effects of aerobic exercise on the regulation of mitochondrial carrier homolog-2 and its influence on the catabolic and anabolic activity of lipids in the mesenteric adipose tissue of obese mice. Life Sci 2024; 345:122567. [PMID: 38492919 DOI: 10.1016/j.lfs.2024.122567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
The aim was to understand the direct impact of aerobic short-term exercise on lipid metabolism, specifically in regulating the mitochondrial carrier homolog 2 (MTCH2) and how it interferes with lipid metabolism in mesenteric adipose tissue. Swiss mice were divided into three groups: control, sedentary obese, and exercised obese. The obese groups were induced into obesity for fourteen weeks of a high-fat diet, and the trained submitted to seven aerobic exercise sessions. The exercise proved the significant increase of the pPerilipin-1, a hormone-sensitive lipase gene, and modulates lipid metabolism by increasing the expression of Mtch2 and acetyl Co-A carboxylase, perhaps occurring as feedback to regulate lipid metabolism in adipose tissue. In conclusion, we demonstrate, for the first time, how aerobic physical exercise increases Mtch2 transcription in mesenteric adipose tissue. This increase was due to changes in energy demand caused by exercise, confirmed by observing the significant reduction in mesenteric adipose tissue mass in the exercised group. Also, we showed that physical exercise increased the phosphorylative capacity of PLIN1, a protein responsible for the degradation of fatty acids in the lipid droplet, providing acyl and glycerol for cellular metabolism. Although our findings demonstrate evidence of MTCH2 as a protein that regulates lipid homeostasis, scant knowledge exists concerning the signaling of the MTCH2 pathway in regulatingfatty acid metabolism. Therefore, unveiling the means of molecular signaling of MTCH2 demonstrates excellent potential for treating obesity.
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Affiliation(s)
- Diego Gomes de Melo
- Exercise Cellular Biology Laboratory, University of Campinas, Limeira, Brazil
| | | | | | | | | | - José Rodrigo Pauli
- Laboratory of Molecular Biology of Exercise, School of Applied Sciences, University of Campinas, Limeira, Brazil; Laboratory of Cell Signaling, Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, São Paulo, Brazil
| | - Adelino Sanchez Ramos da Silva
- Postgraduate Program in Rehabilitation and Functional Performance, Ribeirão Preto Medical School, School of Physical Education and Sport of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Célio Junior da Costa Fernandes
- Department of Biophysics and Pharmacology, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Leandro Pereira de Moura
- Exercise Cellular Biology Laboratory, University of Campinas, Limeira, Brazil; Laboratory of Cell Signaling, Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, São Paulo, Brazil.
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Pussila M, Laiho A, Törönen P, Björkbacka P, Nykänen S, Pylvänäinen K, Holm L, Mecklin JP, Renkonen-Sinisalo L, Lehtonen T, Lepistö A, Linden J, Mäki-Nevala S, Peltomäki P, Nyström M. Mitotic abnormalities precede microsatellite instability in lynch syndrome-associated colorectal tumourigenesis. EBioMedicine 2024; 103:105111. [PMID: 38583260 PMCID: PMC11002576 DOI: 10.1016/j.ebiom.2024.105111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Lynch syndrome (LS) is one of the most common hereditary cancer syndromes worldwide. Dominantly inherited mutation in one of four DNA mismatch repair genes combined with somatic events leads to mismatch repair deficiency and microsatellite instability (MSI) in tumours. Due to a high lifetime risk of cancer, regular surveillance plays a key role in cancer prevention; yet the observation of frequent interval cancers points to insufficient cancer prevention by colonoscopy-based methods alone. This study aimed to identify precancerous functional changes in colonic mucosa that could facilitate the monitoring and prevention of cancer development in LS. METHODS The study material comprised colon biopsy specimens (n = 71) collected during colonoscopy examinations from LS carriers (tumour-free, or diagnosed with adenoma, or diagnosed with carcinoma) and a control group, which included sporadic cases without LS or neoplasia. The majority (80%) of LS carriers had an inherited genetic MLH1 mutation. The remaining 20% included MSH2 mutation carriers (13%) and MSH6 mutation carriers (7%). The transcriptomes were first analysed with RNA-sequencing and followed up with Gorilla Ontology analysis and Reactome Knowledgebase and Ingenuity Pathway Analyses to detect functional changes that might be associated with the initiation of the neoplastic process in LS individuals. FINDINGS With pathway and gene ontology analyses combined with measurement of mitotic perimeters from colonic mucosa and tumours, we found an increased tendency to chromosomal instability (CIN), already present in macroscopically normal LS mucosa. Our results suggest that CIN is an earlier aberration than MSI and may be the initial cancer driving aberration, whereas MSI accelerates tumour formation. Furthermore, our results suggest that MLH1 deficiency plays a significant role in the development of CIN. INTERPRETATION The results validate our previous findings from mice and highlight early mitotic abnormalities as an important contributor and precancerous marker of colorectal tumourigenesis in LS. FUNDING This work was supported by grants from the Jane and Aatos Erkko Foundation, the Academy of Finland (330606 and 331284), Cancer Foundation Finland sr, and the Sigrid Jusélius Foundation. Open access is funded by Helsinki University Library.
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Affiliation(s)
- Marjaana Pussila
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
| | - Aleksi Laiho
- Organismal and Evolutionary Biology Research Program, Faculty of Biosciences, and Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Petri Törönen
- Organismal and Evolutionary Biology Research Program, Faculty of Biosciences, and Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Pauliina Björkbacka
- Department of Veterinary Biosciences, and Finnish Centre for Laboratory Animal Pathology (FCLAP), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Sonja Nykänen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kirsi Pylvänäinen
- Faculty of Sports and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Liisa Holm
- Organismal and Evolutionary Biology Research Program, Faculty of Biosciences, and Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Well Being Services County of Central Finland, Department of Science, Jyväskylä, Finland; Faculty of Sports and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Helsinki University Hospital, Helsinki, Finland; Applied Tumour Genomics, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Taru Lehtonen
- Department of Surgery, Helsinki University Hospital, Helsinki, Finland
| | - Anna Lepistö
- Department of Surgery, Helsinki University Hospital, Helsinki, Finland; Applied Tumour Genomics, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Jere Linden
- Department of Veterinary Biosciences, and Finnish Centre for Laboratory Animal Pathology (FCLAP), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Satu Mäki-Nevala
- Department of Medical and Clinical Genetics, University of Helsinki, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Finland; HUSLAB Laboratory of Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Minna Nyström
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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8
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Ma W, Long J, Dong L, Zhang J, Wang A, Zhang Y, Yan D. Uncovering the key pharmacodynamic material basis and possible molecular mechanism of Xiaoke formulation improve insulin resistant through a comprehensive investigation. JOURNAL OF ETHNOPHARMACOLOGY 2024; 323:117752. [PMID: 38216099 DOI: 10.1016/j.jep.2024.117752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/25/2023] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Xiaoke formulation (XKF) has been utilized in clinical practice for decades in China as a treatment option for mild to moderate type 2 diabetes. However, there is still a need for systematic research to uncover the key pharmacodynamic material basis and mechanism of XKF. AIM OF THE STUDY Aim of to investigate the distribution and metabolism of XKF in normal and insulin resistant (IR) mice were different, and elucidate its key pharmacodynamic material basis and mechanism of action. MATERIALS AND METHODS Ultra performance liquid chromatography/time of flight mass spectrometry technology was employed to investigate the differences in XKF absorption, distribution, and metabolism between normal and IR mice across blood, liver, feces, and urine samples. Further, network pharmacology was used to predict target proteins and their associated signaling pathways. Then, molecular docking was utilized to validate the activity of key pharmacodynamic components and targets. Finally, IR HepG2 cells were used to detect the glucose consumption under the action of key pharmacodynamic material basis. In addition, the expression of phosphatidylinositol 3-kinase (PI3K), protein kinase B (AKT) and phospho-protein kinase B (p-AKT) was determined using western blotting. RESULTS The study demonstrates significant distinctions in plasma and liver number and abundance of alkaloids, organic acids, flavonoids, iridoids and saponins between normal and IR mice when XKF was administered. Further analysis has shown that the representative components of XKF, including berberine, chlorogenic acid, calycosin, swertiamarin and astragaloside IV have significantly different metabolic pathways in plasma and liver. Prototypes and metabolites of these components were rarely detected in the urine and feces of mice. According to the network pharmacological analysis, these differential components are predicted to improve IR by targeting key factors such as SRC, JUN, HRAS, NOS3, FGF2, etc. Additionally, the signaling pathways involved in this process include PI3K-AKT pathway, GnRH signaling pathway, and T cell receptor signaling pathway. In addition, in vitro experiments indicate that berberine and its metabolites (berberine and demethyleneberine), chlorogenic acid and its metabolites (3-O-ferulic quinic acid and 5-O-ferulic quinic acid), calycosin and swertiamarin could improve IR in IR-HepG2 cells by elevating the expression of PI3K and AKT, leading to an increase in glucose consumption. CONCLUSION The key pharmacodynamic material basis of XKF, such as berberine and its metabolites (berberrubine and demethyleneberberine), chlorogenic acid and its metabolites (3-O-feruloylquinic acid and 5-O-feruloylquinic acid), calycosin and swertiamarin influence the glucose metabolism disorder of IR-HepG2 cells by regulating the PI3K/AKT signalling pathway, leading to an improvement in IR.
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Affiliation(s)
- Wenjuan Ma
- Beijing Institute of Clinical Pharmacy, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Benxi, Liaoning, 110016, China
| | - Jianglan Long
- Beijing Institute of Clinical Pharmacy, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Linjie Dong
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Benxi, Liaoning, 110016, China
| | - Jian Zhang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Aiting Wang
- Beijing Institute of Clinical Pharmacy, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Yu Zhang
- Beijing Institute of Clinical Pharmacy, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
| | - Dan Yan
- Beijing Institute of Clinical Pharmacy, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
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Csergeová L, Krbušek D, Janoštiak R. CIP/KIP and INK4 families as hostages of oncogenic signaling. Cell Div 2024; 19:11. [PMID: 38561743 PMCID: PMC10985988 DOI: 10.1186/s13008-024-00115-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
CIP/KIP and INK4 families of Cyclin-dependent kinase inhibitors (CKIs) are well-established cell cycle regulatory proteins whose canonical function is binding to Cyclin-CDK complexes and altering their function. Initial experiments showed that these proteins negatively regulate cell cycle progression and thus are tumor suppressors in the context of molecular oncology. However, expanded research into the functions of these proteins showed that most of them have non-canonical functions, both cell cycle-dependent and independent, and can even act as tumor enhancers depending on their posttranslational modifications, subcellular localization, and cell state context. This review aims to provide an overview of canonical as well as non-canonical functions of CIP/KIP and INK4 families of CKIs, discuss the potential avenues to promote their tumor suppressor functions instead of tumor enhancing ones, and how they could be utilized to design improved treatment regimens for cancer patients.
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Affiliation(s)
- Lucia Csergeová
- BIOCEV-First Faculty of Medicine, Charles University, Prague, Czechia
| | - David Krbušek
- BIOCEV-First Faculty of Medicine, Charles University, Prague, Czechia
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Che WQ, Wang YJ, Yang L, Wang HQ, Wang XY, Lyu J. Single-cell transcriptome analysis upon ECM-remodeling meningioma cells. Neurosurg Rev 2024; 47:118. [PMID: 38491247 DOI: 10.1007/s10143-024-02349-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/25/2023] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Meningiomas are the most common tumours that primarily arise in the central nervous system, but their intratumoural heterogeneity has not yet been thoroughly studied. We aimed to investigate the transcriptome characteristics and biological properties of ECM-remodeling meningioma cells. Single-cell RNA sequencing (ScRNA-seq) data from meningioma samples were acquired and used for analyses. We conducted comprehensive bioinformatics analyses, including screening for differentially expressed genes (DEGs), Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway and Gene Ontology (GO) term enrichment analyses, Gene Set Enrichment Analysis (GSEA), protein-protein interaction (PPI) analysis, and copy number variation (CNV) analysis on single-cell sequencing data from meningiomas. Eighteen cell types, including six meningioma subtypes, were identified in the data. ECM-remodeling meningioma cells (MGCs) were mainly distributed in brain-tumour interface tissues. KEGG and GO enrichment analyses revealed that 908 DEGs were mainly related to cell adhesion, extracellular matrix organization, and ECM-receptor interaction. GSEA analysis demonstrated that homophilic cell adhesion via plasma membrane adhesion molecules was significantly enriched (NES = 2.375, P < 0.001). CNV analysis suggested that ECM-remodeling MGCs showed considerably lower average CNV scores. ECM-remodeling MGCs predominantly localized at the brain-tumour interface area and adhere stably to the basement membrane with a lower degree of malignancy. This study provides novel insights into the malignancy of meningiomas.
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Affiliation(s)
- Wen-Qiang Che
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yu-Jiao Wang
- Department of Pathology, Shanxi Provincial People's Hospital, Taiyuan, 030012, China
| | - Liu Yang
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Hong-Qin Wang
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China.
| | - Xiang-Yu Wang
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Jun Lyu
- Department of Clinical Research, the First Affiliated Hospital of Jinan University, Guangzhou, 510632, China.
- Guangdong Provincial Key Laboratory of Traditional Chinese Medicine Informatization, Guangzhou, 510632, China.
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11
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Zheng C, Wei Y, Zhang P, Lin K, He D, Teng H, Manyam G, Zhang Z, Liu W, Lee HRL, Tang X, He W, Islam N, Jain A, Chiu Y, Cao S, Diao Y, Meyer-Gauen S, Höök M, Malovannaya A, Li W, Hu M, Wang W, Xu H, Kopetz S, Chen Y. CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames. Nat Struct Mol Biol 2023; 30:1878-1892. [PMID: 37932451 PMCID: PMC10716047 DOI: 10.1038/s41594-023-01117-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 09/06/2023] [Indexed: 11/08/2023]
Abstract
Emerging evidence suggests that cryptic translation beyond the annotated translatome produces proteins with developmental or physiological functions. However, functions of cryptic non-canonical open reading frames (ORFs) in cancer remain largely unknown. To fill this gap and systematically identify colorectal cancer (CRC) dependency on non-canonical ORFs, we apply an integrative multiomic strategy, combining ribosome profiling and a CRISPR-Cas9 knockout screen with large-scale analysis of molecular and clinical data. Many such ORFs are upregulated in CRC compared to normal tissues and are associated with clinically relevant molecular subtypes. We confirm the in vivo tumor-promoting function of the microprotein SMIMP, encoded by a primate-specific, long noncoding RNA, the expression of which is associated with poor prognosis in CRC, is low in normal tissues and is specifically elevated in CRC and several other cancer types. Mechanistically, SMIMP interacts with the ATPase-forming domains of SMC1A, the core subunit of the cohesin complex, and facilitates SMC1A binding to cis-regulatory elements to promote epigenetic repression of the tumor-suppressive cell cycle regulators encoded by CDKN1A and CDKN2B. Thus, our study reveals a cryptic microprotein as an important component of cohesin-mediated gene regulation and suggests that the 'dark' proteome, encoded by cryptic non-canonical ORFs, may contain potential therapeutic or diagnostic targets.
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Affiliation(s)
- Caishang Zheng
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Zhang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kangyu Lin
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dandan He
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Sema4, Inc., Stamford, CT, USA
| | - Hongqi Teng
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ganiraju Manyam
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, USA
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wen Liu
- Center for Infectious and Inflammatory Diseases, Texas A&M Health Science Center, Institute of Biosciences of Technology, Houston, TX, USA
| | - Hye Rin Lindsay Lee
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei He
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nelufa Islam
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX, USA
| | - Antrix Jain
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX, USA
| | - Yulun Chiu
- Department of Melanoma Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaolong Cao
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
- Department of Orthopedic Surgery, Duke University Medical Center, Durham, NC, USA
| | - Sherita Meyer-Gauen
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Magnus Höök
- Center for Infectious and Inflammatory Diseases, Texas A&M Health Science Center, Institute of Biosciences of Technology, Houston, TX, USA
| | - Anna Malovannaya
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, USA
- Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Han Xu
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Genetics and Epigenetics Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Quantitative Sciences Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
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12
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Wang C, He Z. Integrating bulk and single-cell RNA sequencing data reveals epithelial-mesenchymal transition molecular subtype and signature to predict prognosis, immunotherapy efficacy, and drug candidates in low-grade gliomas. Front Pharmacol 2023; 14:1276466. [PMID: 38053842 PMCID: PMC10694300 DOI: 10.3389/fphar.2023.1276466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
Objective: Epithelial-mesenchymal transition (EMT) is a tightly regulated and dynamic process occurring in both embryonic development and tumor progression. Our study aimed to comprehensively explore the molecular subtypes, immune landscape, and prognostic signature based on EMT-related genes in low-grade gliomas (LGG) in order to facilitate treatment decision-making and drug discovery. Methods: We curated EMT-related genes and performed molecular subtyping with consensus clustering algorithm to determine EMT expression patterns in LGG. The infiltration level of diverse immune cell subsets was evaluated by implementing the single-sample gene set enrichment analysis (ssGSEA) and ESTIMATE algorithms. The distinctions in clinical characteristics, mutation landscape, and immune tumor microenvironment (TME) among the subtypes were subjected to further investigation. Gene Set Variation Analysis (GSVA) was performed to explore the biological pathways that were involved in subtypes. The chemo drug sensitivity and immunotherapy of subtypes were estimated through GDSC database and NTP algorithm. To detect EMT subtype-related prognostic gene modules, the analysis of weighted gene co-expression network (WGCNA) was performed. The LASSO algorithm was utilized to construct a prognostic risk model, and its efficacy was verified through an independent CGGA dataset. Finally, the expression of the hub genes from the prognostic model was evaluated through the single-cell dataset and in-vitro experiment. Results: The TCGA-LGG dataset revealed the creation of two molecular subtypes that presented different prognoses, clinical implications, TME, mutation landscapes, chemotherapy, and immunotherapy. A three-gene signature (SLC39A1, CTSA and CLIC1) based on EMT expression pattern were established through WGCNA analysis. Low-risk patients showed a positive outlook, increased immune cell presence, and higher expression of immune checkpoint proteins. In addition, several promising drugs, including birinapant, fluvastatin, clofarabine, dasatinib, tanespimycin, TAK-733, GDC-0152, AZD8330, trametinib and ingenol-mebutate had great potential to the treatment of high risk patients. Finally, CTSA and CLIC1 were highly expressed in monocyte cell through single-cell RNA sequencing analysis. Conclusion: Our research revealed non-negligible role of EMT in the TME diversity and complexity of LGG. A prognostic signature may contribute to the personalized treatment and prognostic determination.
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Affiliation(s)
- Chengcheng Wang
- Department of Pharmacy, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, China
| | - Zheng He
- Department of Neurosurgery, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, China
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13
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Cordani N, Mologni L, Piazza R, Tettamanti P, Cogliati V, Mauri M, Villa M, Malighetti F, Di Bella C, Jaconi M, Cerrito MG, Cavaletti G, Lavitrano M, Cazzaniga ME. TWIST1 Upregulation Is a Potential Target for Reversing Resistance to the CDK4/6 Inhibitor in Metastatic Luminal Breast Cancer Cells. Int J Mol Sci 2023; 24:16294. [PMID: 38003483 PMCID: PMC10671583 DOI: 10.3390/ijms242216294] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Cyclin-dependent kinase (CDK) 4/6 inhibitors have significantly improved progression-free survival in hormone-receptor-positive (HR+), human-epidermal-growth-factor-receptor-type-2-negative (HER2-) metastatic luminal breast cancer (mLBC). Several studies have shown that in patients with endocrine-sensitive or endocrine-resistant LBC, the addition of CDK4/6 inhibitors to endocrine therapy significantly prolongs progression-free survival. However, the percentage of patients who are unresponsive or refractory to these therapies is as high as 40%, and no reliable and reproducible biomarkers have been validated to select a priori responders or refractory patients. The selection of mutant clones in the target oncoprotein is the main cause of resistance. Other mechanisms such as oncogene amplification/overexpression or mutations in other pathways have been described in several models. In this study, we focused on palbociclib, a selective CDK4/6 inhibitor. We generated a human MCF-7 luminal breast cancer cell line that was able to survive and proliferate at different concentrations of palbociclib and also showed cross-resistance to abemaciclib. The resistant cell line was characterized via RNA sequencing and was found to strongly activate the epithelial-to-mesenchymal transition. Among the top deregulated genes, we found a dramatic downregulation of the CDK4 inhibitor CDKN2B and an upregulation of the TWIST1 transcription factor. TWIST1 was further validated as a target for the reversal of palbociclib resistance. This study provides new relevant information about the mechanisms of resistance to CDK4/6 inhibitors and suggests potential new markers for patients' follow-up care during treatment.
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Affiliation(s)
- Nicoletta Cordani
- School of Medicine and Surgery, Milano-Bicocca University, 20900 Monza, Italy; (L.M.); (R.P.); (P.T.); (M.M.); (M.V.); (F.M.); (M.G.C.); (G.C.); (M.L.); (M.E.C.)
| | - Luca Mologni
- School of Medicine and Surgery, Milano-Bicocca University, 20900 Monza, Italy; (L.M.); (R.P.); (P.T.); (M.M.); (M.V.); (F.M.); (M.G.C.); (G.C.); (M.L.); (M.E.C.)
| | - Rocco Piazza
- School of Medicine and Surgery, Milano-Bicocca University, 20900 Monza, Italy; (L.M.); (R.P.); (P.T.); (M.M.); (M.V.); (F.M.); (M.G.C.); (G.C.); (M.L.); (M.E.C.)
| | - Pietro Tettamanti
- School of Medicine and Surgery, Milano-Bicocca University, 20900 Monza, Italy; (L.M.); (R.P.); (P.T.); (M.M.); (M.V.); (F.M.); (M.G.C.); (G.C.); (M.L.); (M.E.C.)
| | - Viola Cogliati
- Phase 1 Research Centre, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy (C.D.B.); (M.J.)
| | - Mario Mauri
- School of Medicine and Surgery, Milano-Bicocca University, 20900 Monza, Italy; (L.M.); (R.P.); (P.T.); (M.M.); (M.V.); (F.M.); (M.G.C.); (G.C.); (M.L.); (M.E.C.)
| | - Matteo Villa
- School of Medicine and Surgery, Milano-Bicocca University, 20900 Monza, Italy; (L.M.); (R.P.); (P.T.); (M.M.); (M.V.); (F.M.); (M.G.C.); (G.C.); (M.L.); (M.E.C.)
| | - Federica Malighetti
- School of Medicine and Surgery, Milano-Bicocca University, 20900 Monza, Italy; (L.M.); (R.P.); (P.T.); (M.M.); (M.V.); (F.M.); (M.G.C.); (G.C.); (M.L.); (M.E.C.)
| | - Camillo Di Bella
- Phase 1 Research Centre, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy (C.D.B.); (M.J.)
| | - Marta Jaconi
- Phase 1 Research Centre, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy (C.D.B.); (M.J.)
| | - Maria Grazia Cerrito
- School of Medicine and Surgery, Milano-Bicocca University, 20900 Monza, Italy; (L.M.); (R.P.); (P.T.); (M.M.); (M.V.); (F.M.); (M.G.C.); (G.C.); (M.L.); (M.E.C.)
| | - Guido Cavaletti
- School of Medicine and Surgery, Milano-Bicocca University, 20900 Monza, Italy; (L.M.); (R.P.); (P.T.); (M.M.); (M.V.); (F.M.); (M.G.C.); (G.C.); (M.L.); (M.E.C.)
| | - Marialuisa Lavitrano
- School of Medicine and Surgery, Milano-Bicocca University, 20900 Monza, Italy; (L.M.); (R.P.); (P.T.); (M.M.); (M.V.); (F.M.); (M.G.C.); (G.C.); (M.L.); (M.E.C.)
| | - Marina Elena Cazzaniga
- School of Medicine and Surgery, Milano-Bicocca University, 20900 Monza, Italy; (L.M.); (R.P.); (P.T.); (M.M.); (M.V.); (F.M.); (M.G.C.); (G.C.); (M.L.); (M.E.C.)
- Phase 1 Research Centre, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy (C.D.B.); (M.J.)
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14
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Andersen MS, Kofoed MS, Paludan-Müller AS, Pedersen CB, Mathiesen T, Mawrin C, Wirenfeldt M, Kristensen BW, Olsen BB, Halle B, Poulsen FR. Meningioma animal models: a systematic review and meta-analysis. J Transl Med 2023; 21:764. [PMID: 37898750 PMCID: PMC10612271 DOI: 10.1186/s12967-023-04620-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Animal models are widely used to study pathological processes and drug (side) effects in a controlled environment. There is a wide variety of methods available for establishing animal models depending on the research question. Commonly used methods in tumor research include xenografting cells (established/commercially available or primary patient-derived) or whole tumor pieces either orthotopically or heterotopically and the more recent genetically engineered models-each type with their own advantages and disadvantages. The current systematic review aimed to investigate the meningioma model types used, perform a meta-analysis on tumor take rate (TTR), and perform critical appraisal of the included studies. The study also aimed to assess reproducibility, reliability, means of validation and verification of models, alongside pros and cons and uses of the model types. METHODS We searched Medline, Embase, and Web of Science for all in vivo meningioma models. The primary outcome was tumor take rate. Meta-analysis was performed on tumor take rate followed by subgroup analyses on the number of cells and duration of incubation. The validity of the tumor models was assessed qualitatively. We performed critical appraisal of the methodological quality and quality of reporting for all included studies. RESULTS We included 114 unique records (78 using established cell line models (ECLM), 21 using primary patient-derived tumor models (PTM), 10 using genetically engineered models (GEM), and 11 using uncategorized models). TTRs for ECLM were 94% (95% CI 92-96) for orthotopic and 95% (93-96) for heterotopic. PTM showed lower TTRs [orthotopic 53% (33-72) and heterotopic 82% (73-89)] and finally GEM revealed a TTR of 34% (26-43). CONCLUSION This systematic review shows high consistent TTRs in established cell line models and varying TTRs in primary patient-derived models and genetically engineered models. However, we identified several issues regarding the quality of reporting and the methodological approach that reduce the validity, transparency, and reproducibility of studies and suggest a high risk of publication bias. Finally, each tumor model type has specific roles in research based on their advantages (and disadvantages). SYSTEMATIC REVIEW REGISTRATION PROSPERO-ID CRD42022308833.
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Affiliation(s)
- Mikkel Schou Andersen
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark.
- BRIDGE (Brain Research - Inter Disciplinary Guided Excellence), University of Southern Denmark, Odense, Denmark.
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| | - Mikkel Seremet Kofoed
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark
- BRIDGE (Brain Research - Inter Disciplinary Guided Excellence), University of Southern Denmark, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Asger Sand Paludan-Müller
- Nordic Cochrane Centre, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
- Centre for Evidence-Based Medicine Odense (CEBMO) and NHTA: Market Access & Health Economics Consultancy, Copenhagen, Denmark
| | - Christian Bonde Pedersen
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark
- BRIDGE (Brain Research - Inter Disciplinary Guided Excellence), University of Southern Denmark, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Tiit Mathiesen
- Department of Neurosurgery, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Christian Mawrin
- Department of Neuropathology, Otto-Von-Guericke University, Magdeburg, Germany
| | - Martin Wirenfeldt
- Department of Pathology and Molecular Biology, Hospital South West Jutland, Esbjerg, Denmark
- Department of Regional Health Research, University of Southern, Odense, Denmark
| | | | - Birgitte Brinkmann Olsen
- Clinical Physiology and Nuclear Medicine, Odense University Hospital, Odense, Denmark
- Department of Surgical Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Bo Halle
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark
- BRIDGE (Brain Research - Inter Disciplinary Guided Excellence), University of Southern Denmark, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Frantz Rom Poulsen
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark
- BRIDGE (Brain Research - Inter Disciplinary Guided Excellence), University of Southern Denmark, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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15
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Rezaei A, Shayan N, Shirazinia S, Mollazadeh S, Ghiyasi-Moghaddam N. The Prognostic Significance of P16 Immunohistochemical Expression Pattern in Women with Invasive Ductal Breast Carcinoma. Rep Biochem Mol Biol 2023; 12:83-91. [PMID: 37724141 PMCID: PMC10505467 DOI: 10.52547/rbmb.12.1.83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/08/2023] [Indexed: 09/20/2023]
Abstract
Background Breast cancer is the most common malignancy in women worldwide. The p16 protein is a cell cycle regulator and tumor suppressor implicated in several types of cancers. However, its relationship to breast cancer is still unknown. The present study aimed to assess the association of p16 protein expression with clinicopathological features in breast cancer.This study aimed to investigate the anti-cancer effects of different gum extracts on metabolic changes and their impact on gene expression in HT-29 cell. Methods The study enrolled 100 patients with invasive ductal carcinoma. The samples were collected before any adjuvant chemotherapy, and p16 protein expression was determined using immunohistochemistry. Clinicopathological features were obtained from the patient's medical records. Results Our findings demonstrated that p16 protein expression increased in estrogen receptor-positive tumor tissues (P< 0.01). However, no significant correlation was found between the p16 protein expression and the other clinicopathological features. Conclusions Our study demonstrated that p16 protein expression increased in ER-positive tumor tissue from patients with invasive ductal breast carcinoma. However, no correlation was found between the p16 protein expression and the other clinicopathological features.
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Affiliation(s)
- Alireza Rezaei
- Department of Pathology, Faculty of Medicine, Islamic Azad University, Mashhad Branch, Mashhad, Iran.
| | - Navidreza Shayan
- Department of Pathology, Faculty of Medicine, Islamic Azad University, Mashhad Branch, Mashhad, Iran.
| | - Saman Shirazinia
- Department of Pathology, Faculty of Medicine, Islamic Azad University, Mashhad Branch, Mashhad, Iran.
| | - Sara Mollazadeh
- Department of Pathology, Faculty of Medicine, Islamic Azad University, Mashhad Branch, Mashhad, Iran.
| | - Negin Ghiyasi-Moghaddam
- Department of Pathology, Faculty of Medicine, Islamic Azad University, Mashhad Branch, Mashhad, Iran.
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16
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Zhou Y, Fu R, Yang M, Liu W, Tong Z. Lycopene suppresses gastric cancer cell growth without affecting normal gastric epithelial cells. J Nutr Biochem 2023; 116:109313. [PMID: 36871837 DOI: 10.1016/j.jnutbio.2023.109313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023]
Abstract
Gastric cancer is one of the leading causes of cancer-related death worldwide. Lycopene, a natural carotenoid, has potent antioxidant activity and anti-cancer effects against several types of cancers. However, the mechanism for the anti-gastric cancer effects of lycopene remains to be fully clarified. Normal gastric epithelial cell line GES-1 and gastric cancer cell line AGS, SGC-7901, Hs746T cells were treated with different concentrations of lycopene and the effects of lycopene were compared. Lycopene specifically suppressed cell growth monitored by Real-Time Cell Analyzer, induced cell cycle arrest and cell apoptosis detected by flow cytometry, and lowered mitochondrial membrane potentials assessed by JC-1 staining of AGS and SGC-7901 cells, while did not affect those of GES-1 cells. Lycopene did not affect the cell growth of Hs746T cells harboring TP53 mutation. Further bioinformatics analysis predicted 57 genes with up-regulated expression levels in gastric cancer and decreased function in cells after lycopene treatment. Quantitative PCR and Western Blot were used to check the critical factors in the cell cycle and apoptosis signaling pathway. Lycopene decreased the high expression levels of CCNE1 and increased the levels of TP53 in AGS and SGC-7901 cells without affecting those in GES-1 cells. In summary, lycopene could effectively suppress gastric cancer cells with CCNE1-amplification, which could be a promising target therapy reagent for gastric cancer.
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Affiliation(s)
- Ying Zhou
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Wuhan, China
| | - Rishun Fu
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Wuhan, China
| | - Mei Yang
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Wuhan, China
| | - Weihuang Liu
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Wuhan, China
| | - Zan Tong
- TaiKang Medical School (School of Basic Medicine Sciences), Wuhan University, Wuhan, China.
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17
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Liu Z, Song L, Xie J, Wu XR, Gin GE, Wang B, Uchio E, Zi X. Kavalactone Kawain Impedes Urothelial Tumorigenesis in UPII-Mutant Ha-Ras Mice via Inhibition of mTOR Signaling and Alteration of Cancer Metabolism. Molecules 2023; 28:1666. [PMID: 36838656 PMCID: PMC9966944 DOI: 10.3390/molecules28041666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
UPII-mutant Ha-ras transgenic mice develop urothelial hyperplasia and low-grade papillary carcinoma, which mimics human non-muscle invasive bladder cancer (NMIBC). We investigated the effects and mechanisms of kawain, a main kavalactone in the kava plant, on oncogenic Ha-ras-driven urothelial carcinoma in these mice. The mice were fed at six weeks of age with vehicle control or kawain (6 g/kg) formulated food for approximately five months. Seventy-eight percent of the mice or more fed with kawain food survived more than six months of age, whereas only 32% control food-fed male mice survived, (p = 0.0082). The mean wet bladder weights (a surrogate for tumor burden) of UPII-mutant Ha-ras transgenic mice with kawain diet was decreased by approximately 56% compared to those fed with the control diet (p = 0.035). The kawain diet also significantly reduced the occurrence of hydronephrosis and hematuria in UPII-mutant Ha-ras transgenic mice. Histological examination and immunohistochemistry analysis revealed that vehicle control-treated mice displayed more urothelial carcinoma and Ki67-positive cells in the bladder compared to kawain treated mice. Global metabolic profiling of bladder tumor samples from mice fed with kawain food showed significantly more enrichment of serotonin and less abundance of xylulose, prostaglandin A2, D2 and E2 compared to those from control diet-fed mice, suggesting decreased shunting of glucose to the pentose phosphate pathway (PPP) and reduced inflammation. In addition, kawain selectively inhibited the growth of human bladder cancer cell lines with a significant suppression of 4E-BP1 expression and rpS6 phosphorylation. These observations indicate a potential impact of kawain consumption on bladder cancer prevention by rewiring the metabolic programs of the tumor cells.
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Affiliation(s)
- Zhongbo Liu
- Department of Urology, University of California Irvine, Orange, CA 92868, USA
| | - Liankun Song
- Department of Urology, University of California Irvine, Orange, CA 92868, USA
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Jun Xie
- Department of Urology, University of California Irvine, Orange, CA 92868, USA
| | - Xue-Ru Wu
- Department of Urology, NYU School of Medicine, New York, NY 10016, USA
- Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA
| | - Greg E. Gin
- Department of Urology, University of California Irvine, Orange, CA 92868, USA
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA
| | - Beverly Wang
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Orange, CA 92868, USA
| | - Edward Uchio
- Department of Urology, University of California Irvine, Orange, CA 92868, USA
- Chao Family Comprehensive Cancer Center, University of California Irvine, Orange, CA 92868, USA
| | - Xiaolin Zi
- Department of Urology, University of California Irvine, Orange, CA 92868, USA
- Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822, USA
- Chao Family Comprehensive Cancer Center, University of California Irvine, Orange, CA 92868, USA
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18
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Basin MF, Bratslavsky G, Nahhas N, Basnet A, Goldberg H, Necchi A, Sokol ES, Ramkissoon SH, Huang RSP, Ross JS, Jacob JM. Novel synthetic lethality drug target in urothelial bladder cancer based on MTAP genomic loss. Urol Oncol 2023; 41:109.e15-109.e22. [PMID: 36443178 DOI: 10.1016/j.urolonc.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/19/2022] [Accepted: 10/03/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND When urothelial carcinoma of the bladder (UCB) presents or progresses to chemo-refractory metastatic disease, the search for new therapeutic targets is paramount. Targeting protein arginine methyltransferase 5 accumulation in tumors with methylthioadenosine phosphorylase (MTAP) genomic loss has been proposed as a new anti-tumor strategy. We evaluated the incidence of patients with MTAP loss and correlate to treatment-guiding targets and biomarkers. METHODS Two thousand six hundred eighty-three cases of advanced UCB underwent hybrid-capture based comprehensive genomic profiling using the FDA-approved F1CDx assay to evaluate all classes of genomic alterations (GA) among 324 genes. Tumor mutational burden was determined on at least 0.8 Mbp of sequenced DNA and microsatellite instability was determined on at least 95 loci. RESULTS 650 (24%) of UCB featured MTAP loss mutations (MTAP-). The gene and age distributions were similar in MTAP intact (MTAP+) and MTAP- UCB. MTAP- UCB contained higher GA/tumor frequency than MTAP+ UCB likely reflecting the frequent co-deletions of cyclin-dependent kinase inhibitor 2A/B. Of potential therapeutic targets, fibroblast growth factor receptor 3, and phosphatase and tensin homolog GA were more frequent in MTAP- UCB. In contrast, biomarkers of immunotherapy response, including higher frequencies of high tumor mutational burden and high programmed death-ligand 1 IHC staining, were observed in the MTAP+ UCB. CONCLUSIONS When compared with MTAP+ UCB, MTAP- UCB differs in genomic signatures including an increase in potentially targetable alterations but a lower frequency of immunotherapy drug biomarkers. Thus, the genomic landscape in MTAP- UCB may play a role in the design of clinical trials incorporating combination treatment strategies when targeting protein arginine methyltransferase 5 in MTAP- tumors.
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Affiliation(s)
- Michael F Basin
- Upstate Medical University Department of Urology, Syracuse, NY
| | | | - Nathan Nahhas
- Upstate Medical University Department of Urology, Syracuse, NY
| | - Alina Basnet
- Upstate Medical University Department of Medicine, Syracuse, NY
| | - Hanan Goldberg
- Upstate Medical University Department of Urology, Syracuse, NY
| | - Andrea Necchi
- Vita-Salute San Raffaele University, Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | | | | | - Jeffrey S Ross
- Upstate Medical University Department of Urology, Syracuse, NY; Upstate Medical University Department of Medicine, Syracuse, NY; Vita-Salute San Raffaele University, Department of Medical Oncology, IRCCS Ospedale San Raffaele, Milan, Italy; Foundation Medicine, Inc, Cambridge, MA
| | - Joseph M Jacob
- Upstate Medical University Department of Urology, Syracuse, NY.
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Park SS, Lee YK, Park SH, Lim SB, Choi YW, Shin JS, Kim YH, Kim JH, Park TJ. p15 INK4B is an alternative marker of senescent tumor cells in colorectal cancer. Heliyon 2023; 9:e13170. [PMID: 36785830 PMCID: PMC9918768 DOI: 10.1016/j.heliyon.2023.e13170] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Senescent tumor cells are nonproliferating tumor cells which are closely related to cancer progression by secreting senescence-related molecules, called senescence-associated secreting phenotypes. Therefore, the presence of senescent tumor cells is considered a prognostic factor in various cancer types. Although senescence-associated β-galactosidase staining is considered the best marker for detection of senescent tumor cells, it can only be performed in fresh-frozen tissues. p16INK4A, a cyclin-dependent inhibitor, has been used as an alternative marker to detect senescent tumor cells in formalin-fixed paraffin-embedded tissues. However, other reliable markers to detect senescent tumor cells is still lacking. In the present study, using public single-cell RNA-sequencing data, we found that p15INK4B, a cyclin-dependent kinase inhibitor, is a novel marker for detection of senescent tumor cells. Moreover, p15INK4B expression was positively correlated with that of p16INK4A in colorectal cancer tissues. In in vitro studies, mRNA expression of p15INK4B was increased together with that of p16INK4A in H2O2- and therapy-induced cancer senescence models. However, the mRNA level of p15INK4B did not increase in the oncogene-induced senescence model in primary colonic epithelial cells. In conclusion, p15INK4B is a potential alternative marker for detection of senescent tumor cells together with conventional markers in advanced stages of colorectal cancer.
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Key Words
- CDK, cyclin dependent kinase
- CRC, colorectal cancer
- Cellular senescence
- Colorectal cancer
- FBS, fetal bovine serum
- FFPE, formalin-fixed paraffin-embedded
- GSEA, gene set enrichent analysis
- H3K9me3, histone H3 lysine 9 trimethylation
- IHC, immunohistochemistry
- SA-β-Gal, senescence-associated β-galactosidase
- STC, senescent tumor cell
- Senescence marker
- Senescent tumor cells
- p15INK4B
- p16INK4A
- scRNA-seq, single cell RNA sequencing
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Affiliation(s)
- Soon Sang Park
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, South Korea,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, South Korea,Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon, 16499, South Korea
| | - Young-Kyoung Lee
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, South Korea,Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon, 16499, South Korea
| | - So Hyun Park
- Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon, 16499, South Korea,Department of Pathology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Su Bin Lim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, South Korea,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, South Korea,Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon, 16499, South Korea
| | - Yong Won Choi
- Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon, 16499, South Korea,Department of Hematology and Oncology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Jun Sang Shin
- Department of Surgery, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Young Hwa Kim
- Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon, 16499, South Korea
| | - Jang-Hee Kim
- Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon, 16499, South Korea,Department of Pathology, Ajou University School of Medicine, Suwon, 16499, South Korea,Corresponding author. Department of Pathology, Ajou University School of Medicine, Suwon, 16499 South Korea.
| | - Tae Jun Park
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, South Korea,Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, South Korea,Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon, 16499, South Korea,Corresponding author. Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499 South Korea.
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20
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D'costa M, Bothe A, Das S, Udhaya Kumar S, Gnanasambandan R, George Priya Doss C. CDK regulators—Cell cycle progression or apoptosis—Scenarios in normal cells and cancerous cells. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:125-177. [PMID: 37061330 DOI: 10.1016/bs.apcsb.2022.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Serine/threonine kinases called cyclin-dependent kinases (CDKs) interact with cyclins and CDK inhibitors (CKIs) to control the catalytic activity. CDKs are essential controllers of RNA transcription and cell cycle advancement. The ubiquitous overactivity of the cell cycle CDKs is caused by a number of genetic and epigenetic processes in human cancer, and their suppression can result in both cell cycle arrest and apoptosis. This review focused on CDKs, describing their kinase activity, their role in phosphorylation inhibition, and CDK inhibitory proteins (CIP/KIP, INK 4, RPIC). We next compared the role of different CDKs, mainly p21, p27, p57, p16, p15, p18, and p19, in the cell cycle and apoptosis in cancer cells with respect to normal cells. The current work also draws attention to the use of CDKIs as therapeutics, overcoming the pharmacokinetic barriers of pan-CDK inhibitors, analyze new chemical classes that are effective at attacking the CDKs that control the cell cycle (cdk4/6 or cdk2). It also discusses CDKI's drawbacks and its combination therapy against cancer patients. These findings collectively demonstrate the complexity of cancer cell cycles and the need for targeted therapeutic intervention. In order to slow the progression of the disease or enhance clinical outcomes, new medicines may be discovered by researching the relationship between cell death and cell proliferation.
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Affiliation(s)
- Maria D'costa
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Anusha Bothe
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Soumik Das
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - R Gnanasambandan
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India.
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21
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Cancer stem/progenitor signatures refine the classification of clear cell renal cell carcinoma with stratified prognosis and decreased immunotherapy efficacy. Mol Ther Oncolytics 2022; 27:167-181. [DOI: 10.1016/j.omto.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
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22
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Mahdavi S, Jenkins DJ, El-Sohemy A. Genetic variation in 9p21, dietary patterns, and insulin sensitivity. Front Genet 2022; 13:988873. [PMID: 36313440 PMCID: PMC9616109 DOI: 10.3389/fgene.2022.988873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/14/2022] [Indexed: 11/15/2022] Open
Abstract
Background: Single nucleotide polymorphisms in the 9p21 region have been associated with cardiovascular disease and to a lesser extent insulin sensitivity. Previous studies have focused on older populations, and few have examined the impact of gene-diet interactions. The objective of this study was to determine the interaction between dietary patterns and 9p21 genotypes on insulin sensitivity in young adults from different ethnic groups. Methods: Subjects were 1,333 participants aged 20–29 years from the Toronto Nutrigenomics and Health Study (405 men and 928 women; 776 Caucasians and 557 East Asians). Fasting blood was collected to measure glucose, insulin, c-reactive protein and serum lipids, as well as to isolate DNA for genotyping subjects for five SNPs in 9p21 (rs10757274, rs10757278, rs1333049, rs2383206, and rs4977574). Insulin resistance (HOMA-IR) and beta-cell dysfunction (HOMA-Beta) were calculated from fasting insulin and glucose concentrations. The Toronto-modified Harvard 196-item semi-quantitative food frequency questionnaire was used to measure dietary intake over 1 month and principal components analysis was used to identify three dietary patterns (Prudent, Western and Eastern). ANOVA and ANCOVA were used to examine gene-diet interactions on markers of insulin sensitivity. Results: Significant gene-diet interactions on insulin sensitivity using HOMA-IR were observed with all five SNPs, which remained significant after adjusting for covariates (p < 0.05). Among those who were homozygous for the 9p21 risk allele (rs1333049), fasting insulin was 40% higher in those who were consuming a low-prudent diet compared to those consuming a high-prudent diet (p < 0.05). No differences were observed between those following a low versus high-prudent diet among those who did not carry a 9p21 risk allele. Similar findings were observed with HOMA-Beta, however, the association was only significant for rs10757274 (p = 0.04). Conclusion: Our findings suggest that a prudent dietary pattern may protect against the effects of 9p21 risk genotypes on insulin sensitivity.
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Affiliation(s)
- Sara Mahdavi
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute, Risk Factor Modification Centre and Division of Endocrinology and Metabolism, St. Michael’s Hospital, St. Michael’s Health Centre, Toronto, ON, Canada
| | - David J.A. Jenkins
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute, Risk Factor Modification Centre and Division of Endocrinology and Metabolism, St. Michael’s Hospital, St. Michael’s Health Centre, Toronto, ON, Canada
| | - Ahmed El-Sohemy
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- *Correspondence: Ahmed El-Sohemy,
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23
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Cui Y, Feng H, Liu J, Wu J, Zhu R, Huang R, Yan J. Identification of hexosamine biosynthesis pathway as a novel prognostic signature and its correlation with immune infiltration in bladder cancer. Front Mol Biosci 2022; 9:1009168. [PMID: 36158580 PMCID: PMC9493074 DOI: 10.3389/fmolb.2022.1009168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Urinary bladder cancer (UBC) is one of the common urological malignancies, lacking reliable biomarkers to predict clinical outcomes in UBC patients. Thus, it is needed to identify the novel diagnostic/prognostic biomarkers to stratify the high-risk UBC patients. As a shunt pathway of glycolysis, the hexosamine biosynthesis pathway (HBP) has been implicated in carcinogenesis. However, its prognostic value in UBC remains unclear. Methods: The RNA sequencing and mRNA microarray datasets were downloaded from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus databases. The expression levels of five HBP genes were analyzed in normal and UBC samples, and their associations with stage, grade and survival were plotted. The performance of HBP risk group was evaluated by receiver-operating characteristics (ROC) curve. The HBP signature was generated by Gene Set Variation Analysis (GSVA) and its association with clinicopathological parameters and survival were analyzed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out to examine the potential biological functions of HBP using DAVID online tool. The infiltration estimation fraction of immune cells was performed using CIBERSORT-ABS algorithm. Gene set enrichment analysis (GSEA) was used to explore the potential function of HBP in tumor immunoregulation. Results: Four HBP genes were upregulated in UBCs compared to normal tissues in TCGA-BLCA dataset. The upregulation of all five HBP genes was significantly associated with tumor grade and stage of UBC in three independent UBC datasets. The expression of HBP genes predicted poor clinical outcomes in UBC patients in both TCGA-BLCA and GSE13507 datasets. The high-risk group based on HBP genes showed a poor prognosis. Furthermore, HBP signature was positively associated with tumor grade and stage in TCGA-BLCA dataset and with tumor grade, stage, distal metastasis and poor survival in GSE13507 dataset. Interestingly, high-HBP signature group exhibited a high infiltration of immune cells, particularly the macrophage population. Conclusion: We identified that HBP was a promising prognostic biomarker in UBC patients and strongly associated with immune infiltration.
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Affiliation(s)
- Yangyan Cui
- Model Animal Research Center, Nanjing University, Nanjing, China
| | - Hanyi Feng
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jiakuan Liu
- Department of Laboratory Animal Science, Fudan University, Shanghai, China
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Jiajun Wu
- Department of Laboratory Animal Science, Fudan University, Shanghai, China
| | - Rujian Zhu
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
- *Correspondence: Rujian Zhu, ; Ruimin Huang, ; Jun Yan,
| | - Ruimin Huang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Rujian Zhu, ; Ruimin Huang, ; Jun Yan,
| | - Jun Yan
- Department of Laboratory Animal Science, Fudan University, Shanghai, China
- Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
- MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
- *Correspondence: Rujian Zhu, ; Ruimin Huang, ; Jun Yan,
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24
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Xu J, Yang R, Li J, Wang L, Cohen M, Simeone DM, Costa M, Wu XR. DNMT3A/ miR-129-2-5p/Rac1 Is an Effector Pathway for SNHG1 to Drive Stem-Cell-like and Invasive Behaviors of Advanced Bladder Cancer Cells. Cancers (Basel) 2022; 14:4159. [PMID: 36077697 PMCID: PMC9454896 DOI: 10.3390/cancers14174159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
The stem-cell-like behavior of cancer cells plays a central role in tumor heterogeneity and invasion and correlates closely with drug resistance and unfavorable clinical outcomes. However, the molecular underpinnings of cancer cell stemness remain incompletely defined. Here, we show that SNHG1, a long non-coding RNA that is over-expressed in ~95% of human muscle-invasive bladder cancers (MIBCs), induces stem-cell-like sphere formation and the invasion of cultured bladder cancer cells by upregulating Rho GTPase, Rac1. We further show that SNHG1 binds to DNA methylation transferase 3A protein (DNMT3A), and tethers DNMT3A to the promoter of miR-129-2, thus hyper-methylating and repressing miR-129-2-5p transcription. The reduced binding of miR-129-2 to the 3'-UTR of Rac1 mRNA leads to the stabilization of Rac1 mRNA and increased levels of Rac1 protein, which then stimulates MIBC cell sphere formation and invasion. Analysis of the Human Protein Atlas shows that a high expression of Rac1 is strongly associated with poor survival in patients with MIBC. Our data strongly suggest that the SNHG1/DNMT3A/miR-129-2-5p/Rac1 effector pathway drives stem-cell-like and invasive behaviors in MIBC, a deadly form of bladder cancer. Targeting this pathway, alone or in combination with platinum-based therapy, may reduce chemoresistance and improve longer-term outcomes in MIBC patients.
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Affiliation(s)
- Jiheng Xu
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Rui Yang
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Jingxia Li
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Lidong Wang
- Department of Surgery, New York University School of Medicine, New York, NY 10016, USA
| | - Mitchell Cohen
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Diane M. Simeone
- Department of Surgery, New York University School of Medicine, New York, NY 10016, USA
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Max Costa
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Xue-Ru Wu
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
- Department of Urology, New York University School of Medicine, New York, NY 10016, USA
- Veterans Affairs New York Harbor Healthcare System, Manhattan Campus, New York, NY 10010, USA
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25
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Wu Q, He Y, Liu X, Luo F, Jiang Y, Xiang M, Zhao R. Cancer stem cell-like cells-derived exosomal CDKN2B-AS1 stabilizes CDKN2B to promote the growth and metastasis of thyroid cancer via TGF-β1/Smad2/3 signaling. Exp Cell Res 2022; 419:113268. [PMID: 35750242 DOI: 10.1016/j.yexcr.2022.113268] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/14/2022] [Accepted: 06/19/2022] [Indexed: 11/30/2022]
Abstract
As CDKN2B-AS1 is demonstrated to exert promotive effects on thyroid cancer (TC), this research aims to investigate the role of cancer stem cell-like cells (CSCs)-derived exosomal CDKN2B-AS1 in TC and the underlying regulatory mechanism. Specifically, CDKN2B expression and the correlation of CDKN2B with CDKN2B-AS1 in TC were determined via bioinformatics analysis and further verified by qRT-PCR. After transfection or co-culture with CSCs-derived exosomes, viability, migration, and invasion of TPC-1 and SW579 cells were evaluated by CCK-8, wound healing, and transwell assays, respectively. The uptake of exosomes by TC cells was detected by PKH67 labeling. In vivo tumor formation and metastasis models were established. Tumor volume and weight were calculated. Metastasis loci in lung tissues were observed by hematoxylin-eosin staining. The expression levels of CDKN2B-AS1, CDKN2B, and epithelial-mesenchymal transition- and TGF-β1/Smad2/3 signaling-related factors were detected by qRT-PCR or Western blot. Concretely, CDKN2B and CDKN2B-AS1 were highly expressed in TC, and there was a positive correlation between the two. In addition, CDKN2B-AS1 promoted the translation and stability of CDKN2B. Furthermore, CDKN2B-AS1 was highly expressed in CSCs and CSCs-derived exosomes which could be absorbed by TC cells. CDKN2B silencing inhibited viability, migration, invasion, protein levels of CDKN2B, N-cadherin and Vimentin, and TGF-β1/Smad2/3 signaling, while promoting E-cadherin expression in TC cells. CSCs-derived exosomal CDKN2B-AS1 did oppositely and reversed the effects of CDKN2B silencing on TC cells. CDKN2B silencing impeded tumor growth and metastasis in TC mice, while TGF-β1 performed inversely and impaired the effects of CDKN2B silencing. Collectively, CSCs-derived exosomal CDKN2B-AS1 stabilizes CDKN2B to promote growth and metastasis of TC via TGF-β1/Smad2/3 signaling.
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Affiliation(s)
- Qinghua Wu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, China.
| | - Yonggang He
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, China
| | - Xin Liu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, China
| | - Fangxiu Luo
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, China
| | - Yimei Jiang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, China
| | - Ming Xiang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, China
| | - Ren Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, China
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26
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Machado CB, da Cunha LS, Maués JHDS, Pessoa FMCDP, de Oliveira MB, Ribeiro RM, Lopes GS, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira-Nunes CA. Role of miRNAs in Human T Cell Leukemia Virus Type 1 Induced T Cell Leukemia: A Literature Review and Bioinformatics Approach. Int J Mol Sci 2022; 23:ijms23105486. [PMID: 35628297 PMCID: PMC9141946 DOI: 10.3390/ijms23105486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
Human T cell leukemia virus type 1 (HTLV-1) was identified as the first pathogenic human retrovirus and is estimated to infect 5 to 10 million individuals worldwide. Unlike other retroviruses, there is no effective therapy to prevent the onset of the most alarming diseases caused by HTLV-1, and the more severe cases manifest as the malignant phenotype of adult T cell leukemia (ATL). MicroRNA (miRNA) dysfunction is a common feature of leukemogenesis, and it is no different in ATL cases. Therefore, we sought to analyze studies that reported deregulated miRNA expression in HTLV-1 infected cells and patients’ samples to understand how this deregulation could induce malignancy. Through in silico analysis, we identified 12 miRNAs that stood out in the prediction of targets, and we performed functional annotation of the genes linked to these 12 miRNAs that appeared to have a major biological interaction. A total of 90 genes were enriched in 14 KEGG pathways with significant values, including TP53, WNT, MAPK, TGF-β, and Ras signaling pathways. These miRNAs and gene interactions are discussed in further detail for elucidation of how they may act as probable drivers for ATL onset, and while our data provide solid starting points for comprehension of miRNAs’ roles in HTLV-1 infection, continuous effort in oncologic research is still needed to improve our understanding of HTLV-1 induced leukemia.
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Affiliation(s)
- Caio Bezerra Machado
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | | | | | - Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.B.d.O.); (A.S.K.)
| | | | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.B.d.O.); (A.S.K.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil;
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (M.B.d.O.); (A.S.K.)
- Department of Health Sciences, Northeast Biotechnology Network (RENORBIO), Itaperi Campus, Ceará State University, Fortaleza 60740-903, CE, Brazil
- Correspondence:
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RNA-binding protein MEX3A controls G1/S transition via regulating the RB/E2F pathway in clear cell renal cell carcinoma. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 27:241-255. [PMID: 34976441 PMCID: PMC8703191 DOI: 10.1016/j.omtn.2021.11.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/29/2021] [Indexed: 11/24/2022]
Abstract
MEX3A is an RNA-binding protein that mediates mRNA decay through binding to 3′ untranslated regions. However, its role and mechanism in clear cell renal cell carcinoma remain unknown. In this study, we found that MEX3A expression was transcriptionally activated by ETS1 and upregulated in clear cell renal cell carcinoma. Silencing MEX3A markedly reduced clear cell renal cell carcinoma cell proliferation in vitro and in vivo. Inhibiting MEX3A induced G1/S cell-cycle arrest. Gene set enrichment analysis revealed that E2F targets are the central downstream pathways of MEX3A. To identify MEX3A targets, systematic screening using enhanced cross-linking and immunoprecipitation sequencing, and RNA-immunoprecipitation sequencing assays were performed. A network of 4,000 genes was identified as potential targets of MEX3A. Gene ontology analysis of upregulated genes bound by MEX3A indicated that negative regulation of the cell proliferation pathway was highly enriched. Further assays indicated that MEX3A bound to the CDKN2B 3′ untranslated region, promoting its mRNA degradation. This leads to decreased levels of CDKN2B and an uncontrolled cell cycle in clear cell renal cell carcinoma, which was confirmed by rescue experiments. Our findings revealed that MEX3A acts as a post-transcriptional regulator of abnormal cell-cycle progression in clear cell renal cell carcinoma.
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28
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Lin E, Zhu P, Ye C, Huang M, Liu X, Tian K, Tang Y, Zeng J, Cheng S, Liu J, Liu Y, Yu Y. Integrative Analysis of the Genomic and Immune Microenvironment Characteristics Associated With Clear Cell Renal Cell Carcinoma Progression: Implications for Prognosis and Immunotherapy. Front Immunol 2022; 13:830220. [PMID: 35677048 PMCID: PMC9168804 DOI: 10.3389/fimmu.2022.830220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/28/2022] [Indexed: 02/05/2023] Open
Abstract
Unlike early clear cell renal cell carcinoma (ccRCC), locally advanced and metastatic ccRCC present poor treatment outcomes and prognosis. As immune checkpoint inhibitors have achieved favorable results in the adjuvant treatment of metastatic ccRCC, we aimed to investigate the immunogenomic landscape during ccRCC progression and its potential impact on immunotherapy and prognosis. Using multi-omics and immunotherapy ccRCC datasets, an integrated analysis was performed to identify genomic alterations, immune microenvironment features, and related biological processes during ccRCC progression and evaluate their relevance to immunotherapy response and prognosis. We found that aggressive and metastatic ccRCC had higher proportions of genomic alterations, including SETD2 mutations, Del(14q), Del(9p), and higher immunosuppressive cellular and molecular infiltration levels. Of these, the Del(14q) might mediate immune escape in ccRCC via the VEGFA-VEGFR2 signaling pathway. Furthermore, immune-related pathways associated with ccRCC progression did not affect the immunotherapeutic response to ccRCC. Conversely, cell cycle pathways not only affected ccRCC progression and prognosis, but also were related to ccRCC immunotherapeutic response resistance. Overall, we described the immunogenomic characteristics of ccRCC progression and their correlations with immunotherapeutic response and prognosis, providing new insights into their prediction and the development of novel therapeutic strategies.
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Affiliation(s)
- Enyu Lin
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Ping Zhu
- Department of Immunology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Chujin Ye
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - ManLi Huang
- Department of Operating Room, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Xuechao Liu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Kaiwen Tian
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yanlin Tang
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Jiayi Zeng
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Shouyu Cheng
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jiumin Liu
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yanjun Liu
- Department of Immunology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Yuming Yu
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
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29
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Uzuner D, Akkoç Y, Peker N, Pir P, Gözüaçık D, Çakır T. Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer. Sci Rep 2021; 11:15806. [PMID: 34349126 PMCID: PMC8339123 DOI: 10.1038/s41598-021-94005-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022] Open
Abstract
Primary cancer cells exert unique capacity to disseminate and nestle in distant organs. Once seeded in secondary sites, cancer cells may enter a dormant state, becoming resistant to current treatment approaches, and they remain silent until they reactivate and cause overt metastases. To illuminate the complex mechanisms of cancer dormancy, 10 transcriptomic datasets from the literature enabling 21 dormancy–cancer comparisons were mapped on protein–protein interaction networks and gene-regulatory networks to extract subnetworks that are enriched in significantly deregulated genes. The genes appearing in the subnetworks and significantly upregulated in dormancy with respect to proliferative state were scored and filtered across all comparisons, leading to a dormancy–interaction network for the first time in the literature, which includes 139 genes and 1974 interactions. The dormancy interaction network will contribute to the elucidation of cellular mechanisms orchestrating cancer dormancy, paving the way for improvements in the diagnosis and treatment of metastatic cancer.
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Affiliation(s)
- Dilara Uzuner
- Department of Bioengineering, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Yunus Akkoç
- Koç University Research Center for Translational Medicine (KUTTAM), Zeytinburnu, 34010, Istanbul, Turkey
| | - Nesibe Peker
- Koç University Research Center for Translational Medicine (KUTTAM), Zeytinburnu, 34010, Istanbul, Turkey
| | - Pınar Pir
- Department of Bioengineering, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Devrim Gözüaçık
- Koç University Research Center for Translational Medicine (KUTTAM), Zeytinburnu, 34010, Istanbul, Turkey.,Koç University School of Medicine, Sarıyer , 34450, Istanbul, Turkey.,SUNUM Nanotechnology Research and Application Center, Tuzla, 34956, Istanbul, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, 41400, Kocaeli, Turkey.
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