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  1. Article ; Online: Deciphering the immune landscape of head and neck squamous cell carcinoma: A single-cell transcriptomic analysis of regulatory T cell responses to PD-1 blockade therapy.

    Miraki Feriz, Adib / Bahraini, Fatemeh / Khosrojerdi, Arezou / Azarkar, Setareh / Sajjadi, Seyed Mehdi / HosseiniGol, Edris / Honardoost, Mohammad Amin / Saghafi, Samira / Silvestris, Nicola / Leone, Patrizia / Safarpour, Hossein / Racanelli, Vito

    PloS one

    2023  Volume 18, Issue 12, Page(s) e0295863

    Abstract: Immunotherapy is changing the Head and Neck Squamous Cell Carcinoma (HNSCC) landscape and improving outcomes for patients with recurrent or metastatic HNSCC. A deeper understanding of the tumor microenvironment (TME) is required in light of the ... ...

    Abstract Immunotherapy is changing the Head and Neck Squamous Cell Carcinoma (HNSCC) landscape and improving outcomes for patients with recurrent or metastatic HNSCC. A deeper understanding of the tumor microenvironment (TME) is required in light of the limitations of patients' responses to immunotherapy. Here, we aimed to examine how Nivolumab affects infiltrating Tregs in the HNSCC TME. We used single-cell RNA sequencing data from eight tissues isolated from four HNSCC donors before and after Nivolumab treatment. Interestingly, the study found that Treg counts and suppressive activity increased following Nivolumab therapy. We also discovered that changes in the CD44-SSP1 axis, NKG2C/D-HLA-E axis, and KRAS signaling may have contributed to the increase in Treg numbers. Furthermore, our study suggests that decreasing the activity of the KRAS and Notch signaling pathways, and increasing FOXP3, CTLA-4, LAG-3, and GZMA expression, may be mechanisms that enhance the killing and suppressive capacity of Tregs. Additionally, the result of pseudo-temporal analysis of the HNSCC TME indicated that after Nivolumab therapy, the expression of certain inhibitory immune checkpoints including TIGIT, ENTPD1, and CD276 and LY9, were decreased in Tregs, while LAG-3 showed an increased expression level. The study also found that Tregs had a dense communication network with cluster two, and that certain ligand-receptor pairs, including SPP1/CD44, HLA-E/KLRC2, HLA-E/KLRK1, ANXA1/FPR3, and CXCL9/FCGR2A, had notable changes after the therapy. These changes in gene expression and cell interactions may have implications for the role of Tregs in the TME and in response to Nivolumab therapy.
    MeSH term(s) Humans ; Squamous Cell Carcinoma of Head and Neck/drug therapy ; Squamous Cell Carcinoma of Head and Neck/genetics ; Squamous Cell Carcinoma of Head and Neck/metabolism ; T-Lymphocytes, Regulatory ; Programmed Cell Death 1 Receptor/metabolism ; Nivolumab/pharmacology ; Nivolumab/therapeutic use ; Head and Neck Neoplasms/drug therapy ; Head and Neck Neoplasms/genetics ; Head and Neck Neoplasms/metabolism ; Proto-Oncogene Proteins p21(ras)/metabolism ; Gene Expression Profiling ; Tumor Microenvironment ; B7 Antigens ; NK Cell Lectin-Like Receptor Subfamily C/metabolism
    Chemical Substances Programmed Cell Death 1 Receptor ; Nivolumab (31YO63LBSN) ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2) ; CD276 protein, human ; B7 Antigens ; KLRC2 protein, human ; NK Cell Lectin-Like Receptor Subfamily C
    Language English
    Publishing date 2023-12-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0295863
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data.

    Ranjan, Bobby / Schmidt, Florian / Sun, Wenjie / Park, Jinyu / Honardoost, Mohammad Amin / Tan, Joanna / Arul Rayan, Nirmala / Prabhakar, Shyam

    BMC bioinformatics

    2021  Volume 22, Issue 1, Page(s) 186

    Abstract: Background: Clustering is a crucial step in the analysis of single-cell data. Clusters identified in an unsupervised manner are typically annotated to cell types based on differentially expressed genes. In contrast, supervised methods use a reference ... ...

    Abstract Background: Clustering is a crucial step in the analysis of single-cell data. Clusters identified in an unsupervised manner are typically annotated to cell types based on differentially expressed genes. In contrast, supervised methods use a reference panel of labelled transcriptomes to guide both clustering and cell type identification. Supervised and unsupervised clustering approaches have their distinct advantages and limitations. Therefore, they can lead to different but often complementary clustering results. Hence, a consensus approach leveraging the merits of both clustering paradigms could result in a more accurate clustering and a more precise cell type annotation.
    Results: We present SCCONSENSUS, an [Formula: see text] framework for generating a consensus clustering by (1) integrating results from both unsupervised and supervised approaches and (2) refining the consensus clusters using differentially expressed genes. The value of our approach is demonstrated on several existing single-cell RNA sequencing datasets, including data from sorted PBMC sub-populations.
    Conclusions: SCCONSENSUS combines the merits of unsupervised and supervised approaches to partition cells with better cluster separation and homogeneity, thereby increasing our confidence in detecting distinct cell types. SCCONSENSUS is implemented in [Formula: see text] and is freely available on GitHub at https://github.com/prabhakarlab/scConsensus .
    MeSH term(s) Cluster Analysis ; Gene Expression Profiling ; Leukocytes, Mononuclear ; RNA ; Sequence Analysis, RNA ; Single-Cell Analysis
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2021-04-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-021-04028-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Highly expressed TLX1NB and NPSR1-AS1 lncRNAs could serve as diagnostic tools in colorectal cancer.

    Dastjerdi, Shaghayegh / Valizadeh, Mehdi / Nemati, Rasoul / Honardoost, Mohammad Amin / Dolatabadi, Nasrin Fattahi / Zamani, Atefeh / Tabatabaeian, Hossein

    Human cell

    2021  Volume 34, Issue 6, Page(s) 1765–1774

    Abstract: Colorectal cancer is the main cause of human death due to cancer. This fact could be due to the insufficiency of early diagnosis or poor therapeutic strategies. Various molecular tools have been utilized in studies to assess their potentials as ... ...

    Abstract Colorectal cancer is the main cause of human death due to cancer. This fact could be due to the insufficiency of early diagnosis or poor therapeutic strategies. Various molecular tools have been utilized in studies to assess their potentials as diagnostic biomarkers or determining factors in precision medicine. Among these molecules, long non-coding RNAs (lncRNA) have been emerging as accurate and potent transcripts to improve the detection of cancer. The overexpressed lncRNAs could also be deeply studied as the molecules for the targeted therapy in different malignancies, in particular colorectal cancer. Thus, we utilized an unbiased approach to select the up-regulated lncRNAs in colon adenocarcinoma via analyzing the TCGA dataset. Then, we validated the overexpression of two first-ranked lncRNAs, i.e., NPSR1-AS1 and TLX1NB, in our in-house colorectal cancer samples as compared to the paired adjacent normal tissues. The analyses revealed that these lncRNAs could significantly distinguish the tumor against the normal samples. The results may have implications in the early diagnosis and targeted therapy of colorectal cancer.
    MeSH term(s) Adenocarcinoma/diagnosis ; Adenocarcinoma/genetics ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Colorectal Neoplasms/diagnosis ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/therapy ; Datasets as Topic ; Early Detection of Cancer ; Gene Expression/genetics ; Homeodomain Proteins/genetics ; Homeodomain Proteins/metabolism ; Humans ; Molecular Targeted Therapy ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/metabolism
    Chemical Substances Biomarkers, Tumor ; Homeodomain Proteins ; NPSR1 protein, human ; Proto-Oncogene Proteins ; RNA, Long Noncoding ; Receptors, G-Protein-Coupled ; TLX1 protein, human (143275-75-6)
    Language English
    Publishing date 2021-08-18
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 1149134-6
    ISSN 1749-0774 ; 0914-7470
    ISSN (online) 1749-0774
    ISSN 0914-7470
    DOI 10.1007/s13577-021-00597-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Systematic immune cell dysregulation and molecular subtypes revealed by single-cell RNA-seq of subjects with type 1 diabetes.

    Honardoost, Mohammad Amin / Adinatha, Andreas / Schmidt, Florian / Ranjan, Bobby / Ghaeidamini, Maryam / Arul Rayan, Nirmala / Gek Liang Lim, Michelle / Joanito, Ignasius / Xiao Xuan Lin, Quy / Rajagopalan, Deepa / Qi Mok, Shi / Hwang, You Yi / Larbi, Anis / Khor, Chiea Chuen / Foo, Roger / Boehm, Bernhard Otto / Prabhakar, Shyam

    Genome medicine

    2024  Volume 16, Issue 1, Page(s) 45

    Abstract: Background: Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting : Methods: In this cross-sectional analysis, we generated a single-cell ... ...

    Abstract Background: Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting
    Methods: In this cross-sectional analysis, we generated a single-cell transcriptomic dataset of peripheral blood mononuclear cells (PBMCs) from 46 manifest T1DM (stage 3) cases and 31 matched controls.
    Results: We surprisingly detected profound alterations in circulatory immune cells (1784 dysregulated genes in 13 immune cell types), far exceeding the count in the comparator systemic autoimmune disease SLE. Genes upregulated in T1DM were involved in WNT signaling, interferon signaling and migration of T/NK cells, antigen presentation by B cells, and monocyte activation. A significant fraction of these differentially expressed genes were also altered in T1DM pancreatic islets. We used the single-cell data to construct a T1DM metagene z-score (TMZ score) that distinguished cases and controls and classified patients into molecular subtypes. This score correlated with known prognostic immune markers of T1DM, as well as with drug response in clinical trials.
    Conclusions: Our study reveals a surprisingly strong systemic dimension at the level of immune cell network in T1DM, defines disease-relevant molecular subtypes, and has the potential to guide non-invasive test development and patient stratification.
    MeSH term(s) Humans ; Diabetes Mellitus, Type 1/genetics ; Leukocytes, Mononuclear/metabolism ; Cross-Sectional Studies ; Single-Cell Gene Expression Analysis ; Autoimmune Diseases
    Language English
    Publishing date 2024-03-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2484394-5
    ISSN 1756-994X ; 1756-994X
    ISSN (online) 1756-994X
    ISSN 1756-994X
    DOI 10.1186/s13073-024-01300-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Fluctuating expression of miR-584 in primary and high-grade gastric cancer.

    Ebrahimi Ghahnavieh, Laleh / Tabatabaeian, Hossein / Ebrahimi Ghahnavieh, Zhaleh / Honardoost, Mohammad Amin / Azadeh, Mansoureh / Moazeni Bistgani, Mohamad / Ghaedi, Kamran

    BMC cancer

    2020  Volume 20, Issue 1, Page(s) 621

    Abstract: Background: Gastric cancer is the fifth most common cancer worldwide. Along with environmental factors, such as Helicobacter pylori (H. pylori) infection, genetic changes play important roles in gastric tumor formations. miR-584 is a less well- ... ...

    Abstract Background: Gastric cancer is the fifth most common cancer worldwide. Along with environmental factors, such as Helicobacter pylori (H. pylori) infection, genetic changes play important roles in gastric tumor formations. miR-584 is a less well-characterized microRNA (miRNA), with apparent activity in human cancers. However, miR-584 expression pattern in gastric cancer development has remained unclear. This study aims to analyze the expression of miR-584 in gastric cancer samples and investigates the associations between this miRNA and H. pylori infection and clinical characteristics.
    Methods: The expression level of miR-584 was studied in primary gastric cancers versus healthy control gastric mucosa samples using the RT-qPCR method. The clinical data were analyzed statistically in terms of miR-584 expression. In silico studies were employed to study miR-584 more broadly in order to assess its expression and find new potential target genes.
    Results: Both experimental and in silico studies showed up-regulation of miR-584 in patients with gastric cancer. This up-regulation seems to be induced by H. pylori infection since the infected samples showed increased levels of miR-584 expression. Deeper analyses revealed that miR-584 undergoes a dramatic down-regulation in late stages, invasive and lymph node-metastatic gastric tumors. Bioinformatics studies demonstrated that miR-584 has a substantial role in cancer pathways and has the potential to target STAT1 transcripts. Consistent with the inverse correlation between TCGA RNA-seq data of miR-584 and STAT1 transcripts, the qPCR analysis showed a significant negative correlation between these two RNAs in a set of clinical samples.
    Conclusion: miR-584 undergoes up-regulation in the stage of primary tumor formation; however, becomes down-regulated upon the progression of gastric cancer. These findings suggest the potential of miR-584 as a diagnostic or prognostic biomarker in gastric cancer.
    MeSH term(s) Adult ; Aged ; Biomarkers, Tumor/metabolism ; Case-Control Studies ; Computational Biology ; Down-Regulation ; Female ; Gastric Mucosa/microbiology ; Gastric Mucosa/pathology ; Gene Expression Regulation, Neoplastic ; Helicobacter Infections/diagnosis ; Helicobacter Infections/genetics ; Helicobacter Infections/microbiology ; Helicobacter Infections/pathology ; Helicobacter pylori/isolation & purification ; Host-Pathogen Interactions/genetics ; Humans ; Kaplan-Meier Estimate ; Male ; MicroRNAs/metabolism ; Middle Aged ; Neoplasm Grading ; Prognosis ; RNA-Seq ; STAT1 Transcription Factor/genetics ; Stomach Neoplasms/diagnosis ; Stomach Neoplasms/genetics ; Stomach Neoplasms/microbiology ; Stomach Neoplasms/mortality ; Survival Rate ; Up-Regulation
    Chemical Substances Biomarkers, Tumor ; MIRN584 microRNA, human ; MicroRNAs ; STAT1 Transcription Factor ; STAT1 protein, human
    Language English
    Publishing date 2020-07-02
    Publishing country England
    Document type Journal Article
    ISSN 1471-2407
    ISSN (online) 1471-2407
    DOI 10.1186/s12885-020-07116-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Tetra-Primer ARMS PCR Optimization for Detection of IVS-II-I (G-A) and FSC 8/9 InsG Mutations in β-Thalassemia Major Patients in Isfahan Population.

    Hajihoseini, Samaneh / Motovali-Bashi, Majid / Honardoost, Mohammad Amin / Alerasool, Nader

    Iranian journal of public health

    2015  Volume 44, Issue 3, Page(s) 380–387

    Abstract: Background: β-thalassemia, a monogenic autosomal recessive disorder, is prevalent in Middle East, particularly in Iran. In Iran, near to 20 mutations in the β-globin gene are introduced as common mutations with varying incidence frequencies in each city. ...

    Abstract Background: β-thalassemia, a monogenic autosomal recessive disorder, is prevalent in Middle East, particularly in Iran. In Iran, near to 20 mutations in the β-globin gene are introduced as common mutations with varying incidence frequencies in each city. Therefore, detection and screening for couples at high risk can help to solve the problems of this disease. In this study, optimized genotyping of two common mutations in Isfahan Province, IVSII-I (G-A) and FSC-8/9 insG, was performed using the T-ARMS method.
    Methods: In this case-control study, 10 healthy individuals and 30 patients affected by β-thalassemia major with a mean 24.76 ± 4.5 years were selected from Omid Hospital in Isfahan Province. After designing tetra primers for two prevalent mutations IVSII-I (G-A) and FSC-8/9 insG, samples were genotyped using tetra-primers ARMS PCR technique.
    Results: We have developed a sensitive single tube tetra-primers PCR assay to detect both IVSII-1 (G-A) and FS8-9 insG mutations. Moreover, we have distinguished homozygous and heterozygous forms of these mutations successfully. The frequency of IVSII-1 (G-A) mutation from 30 patients in Isfahan was 86.6% (33.3% heterozygote, and 53.3% mutant homozygote) and for FS8-9 insG mutation was 16.6% (13.3% heterozygote, and 3.3% mutant homozygote).
    Conclusion: Tetra-primers ARMS PCR could be a reliable, accurate and simple technique for genotyping SNP and different mutations. So far, no study was done on optimization methods for genotyping mutations in β-thalassemia by T-ARMS. Here, we successfully adjusted and enhanced this method for recognizing two common mutations (FSC-8/9 insG and IVSII-I (G-A)) of β-thalassemia in Isfahan population.
    Language English
    Publishing date 2015-04-23
    Publishing country Iran
    Document type Journal Article
    ISSN 2251-6085 ; 0304-4556
    ISSN 2251-6085 ; 0304-4556
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: ESRG, LINC00518 and PWRN1 are newly-identified deregulated lncRNAs in colorectal cancer.

    Jafari, Nasrin / Nasiran Najafabadi, Arezo / Hamzei, Behnaz / Ataee, Nioosha / Ghasemi, Zahra / Sadeghian-Rizi, Tahereh / Honardoost, Mohammad Amin / Zamani, Atefeh / Dolatabadi, Nasrin Fattahi / Tabatabaeian, Hossein

    Experimental and molecular pathology

    2021  Volume 124, Page(s) 104732

    Abstract: Colorectal cancer is the 2nd leading cause of death in humans because of cancer. This rank of death could be due to the high rate of incidence from one hand, and the lack of sufficient diagnostic and therapeutic approaches from the other hand. Thus, ... ...

    Abstract Colorectal cancer is the 2nd leading cause of death in humans because of cancer. This rank of death could be due to the high rate of incidence from one hand, and the lack of sufficient diagnostic and therapeutic approaches from the other hand. Thus, molecular tools have been emerging as the potential biomarker to improve the early diagnosis and therapeutic management that subsequently could lead to the heightened survival rate of colorectal cancer patients. Long non-coding RNA (lncRNAs) have shown promising capabilities to be used in clinics. The profiling methods could identify novel aberrantly expressed lncRNAs in colorectal cancer. We, thus, performed a comprehensive and unbiased approach to shortlist the dysregulated lncRNAs based on the colon adenocarcinoma TCGA data. An unbiased in silico method was used to rank the yet to profiled lncRNAs in colorectal cancer. qPCR was used to measure the expression level of selected lncRNAs. Our results nominated ESRG, LINC00518, PWRN1, and TTTY14 lncRNAs as the top-hit novel lncRNAs with aberrant expression in colon cancer. The qPCR method was used to profile these lncRNAs that showed the up-regulation of ESRG and LINC00518, and down-regulation of TTTY14 in thirty paired colorectal cancer specimens. The statistical analyses demonstrated that ESRG, LINC00518 and PWRN1 could distinguish the tumor from normal samples. Moreover, ESRG showed a negative correlation with the overall survival of patients. These diagnostic and prognostic results suggest that profiling ESRG, LINC00518 and PWRN1 s may have implications in clinics.
    MeSH term(s) Aged ; Biomarkers, Tumor ; Colorectal Neoplasms/diagnosis ; Colorectal Neoplasms/pathology ; Colorectal Neoplasms/therapy ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Medical Informatics ; Middle Aged ; Prognosis ; RNA, Long Noncoding/metabolism
    Chemical Substances Biomarkers, Tumor ; ESRG lncRNA, human ; RNA, Long Noncoding ; long non-coding RNA LINC00518, human
    Language English
    Publishing date 2021-12-09
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 207655-x
    ISSN 1096-0945 ; 0014-4800
    ISSN (online) 1096-0945
    ISSN 0014-4800
    DOI 10.1016/j.yexmp.2021.104732
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data.

    Schmidt, Florian / Ranjan, Bobby / Lin, Quy Xiao Xuan / Krishnan, Vaidehi / Joanito, Ignasius / Honardoost, Mohammad Amin / Nawaz, Zahid / Venkatesh, Prasanna Nori / Tan, Joanna / Rayan, Nirmala Arul / Ong, Sin Tiong / Prabhakar, Shyam

    Nucleic acids research

    2021  Volume 49, Issue 15, Page(s) 8505–8519

    Abstract: The transcriptomic diversity of cell types in the human body can be analysed in unprecedented detail using single cell (SC) technologies. Unsupervised clustering of SC transcriptomes, which is the default technique for defining cell types, is prone to ... ...

    Abstract The transcriptomic diversity of cell types in the human body can be analysed in unprecedented detail using single cell (SC) technologies. Unsupervised clustering of SC transcriptomes, which is the default technique for defining cell types, is prone to group cells by technical, rather than biological, variation. Compared to de-novo (unsupervised) clustering, we demonstrate using multiple benchmarks that supervised clustering, which uses reference transcriptomes as a guide, is robust to batch effects and data quality artifacts. Here, we present RCA2, the first algorithm to combine reference projection (batch effect robustness) with graph-based clustering (scalability). In addition, RCA2 provides a user-friendly framework incorporating multiple commonly used downstream analysis modules. RCA2 also provides new reference panels for human and mouse and supports generation of custom panels. Furthermore, RCA2 facilitates cell type-specific QC, which is essential for accurate clustering of data from heterogeneous tissues. We demonstrate the advantages of RCA2 on SC data from human bone marrow, healthy PBMCs and PBMCs from COVID-19 patients. Scalable supervised clustering methods such as RCA2 will facilitate unified analysis of cohort-scale SC datasets.
    MeSH term(s) Algorithms ; Animals ; Arthritis, Rheumatoid/genetics ; Bone Marrow Cells/metabolism ; COVID-19/blood ; COVID-19/pathology ; Cluster Analysis ; Cohort Studies ; Datasets as Topic ; Humans ; Leukocytes, Mononuclear/metabolism ; Leukocytes, Mononuclear/pathology ; Mice ; Organ Specificity ; Quality Control ; RNA, Small Cytoplasmic/genetics ; RNA-Seq/methods ; RNA-Seq/standards ; Single-Cell Analysis/methods ; Single-Cell Analysis/standards ; Transcriptome
    Chemical Substances RNA, Small Cytoplasmic
    Language English
    Publishing date 2021-07-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab632
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Bioinformatics prediction and experimental validation of a novel microRNA: hsa-miR-B43 within human CDH4 gene with a potential metastasis-related function in breast cancer.

    Rahimi, Azadeh / Sedighi, Rina / Emadi-Baygi, Modjtaba / Honardoost, Mohammad-Amin / Mowla, Seyed-Javad / Khanahmad, Hossein / Nikpour, Parvaneh

    Journal of cellular biochemistry

    2019  Volume 121, Issue 2, Page(s) 1307–1316

    Abstract: As a class of short noncoding RNAs, microRNAs (miRNAs) play a key role in the modulation of gene expression. Although, the regulatory roles of currently identified miRNAs in various cancer types including breast cancer have been well documented, there ... ...

    Abstract As a class of short noncoding RNAs, microRNAs (miRNAs) play a key role in the modulation of gene expression. Although, the regulatory roles of currently identified miRNAs in various cancer types including breast cancer have been well documented, there are many as yet undiscovered miRNAs. The aim of the current study was to bioinformatically reanalyze a list of 189 potentially new miRNAs introduced in a previously published paper (PMID: 21346806) and experimentally explore the existence and function of a candidate one: hsa-miR-B43 in breast cancer cells. The sequences of 189 potential miRNAs were re-checked in the miRbase database. Genomic location and conservation of them were assessed with the University of California Santa Cruz (UCSC) genome browser. SSC profiler, RNAfold, miRNAFold, MiPred, and FOMmiR bioinformatics tools were furthermore utilized to explore potential hairpin structures and differentiate real miRNA precursors from pseudo ones. hsa-miR-B43 was finally selected as one of the best candidates for laboratory verification. The expression and function of hsa-miR-B43 were examined by real-time polymerase chain reaction, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, and wound-healing assays. DIANA-microT, RNAhybrid and Enrichr tools were used to predict the miRNA target genes and for further enrichment analysis. We could detect the exogenous and endogenous expression of hsa-miR-B43, as a real novel miRNA, in cancer cell lines. Gene Ontology enrichment, pathway analysis and wound-healing assay results furthermore confirmed that a metastasis-related function may be assigned to hsa-miR-B43. Our results introduced hsa-miR-B43, as a novel functional miRNA, which might play a role in the metastatic process. Further studies will be necessary to completely survey the existence and function of hsa-miR-B43 in other cancer types.
    MeSH term(s) Apoptosis ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Breast Neoplasms/secondary ; Cadherins/genetics ; Cadherins/metabolism ; Cell Proliferation ; Computational Biology/methods ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Humans ; MicroRNAs/genetics ; Software ; Tumor Cells, Cultured ; Wound Healing
    Chemical Substances Biomarkers, Tumor ; Cadherins ; MicroRNAs ; R-cadherin
    Language English
    Publishing date 2019-09-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 392402-6
    ISSN 1097-4644 ; 0730-2312
    ISSN (online) 1097-4644
    ISSN 0730-2312
    DOI 10.1002/jcb.29367
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Investigation of sensitivity, specificity and accuracy of Tetra primer ARMS PCR method in comparison with conventional ARMS PCR, based on sequencing technique outcomes in IVS-II-I genotyping of beta thalassemia patients.

    Honardoost, Mohammad Amin / Tabatabaeian, Hosein / Akbari, Mojtaba / Salehi, Mansoor

    Gene

    2014  Volume 549, Issue 1, Page(s) 1–6

    Abstract: Purpose: Beta thalassemia is one of the most important hematic diseases all around the world and solving the problems caused by this abnormality is strongly dependent on precise detection and reliable screening of high-risk couples. The aim of our study ...

    Abstract Purpose: Beta thalassemia is one of the most important hematic diseases all around the world and solving the problems caused by this abnormality is strongly dependent on precise detection and reliable screening of high-risk couples. The aim of our study was the investigation of sensitivity, specificity and accuracy of Tetra primer ARMS PCR method comparing with conventional ARMS PCR, based on sequencing technique outcomes for genotyping of IVS-II-I mutation in beta thalassemia patients.
    Methods: Fifty seven samples including two homozygote, 49 heterozygote and 6 normal specimens were analyzed by Tetra primer ARMS PCR and conventional ARMS PCR methods. DNA was extracted by the standard method of salting out for leukocyte genomic DNA extraction of blood specimens and a high pure PCR template preparation kit was used for DNA purification of CVS samples. The results obtained by Tetra primer ARMS PCR and conventional ARMS PCR methods were compared with gold standard technique, i.e. sequencing.
    Results: All three parameters including specificity, sensitivity and accuracy were 100% for Tetra primer ARMS PCR method, while they were 100%, 92.45% and 92.7% for conventional ARMS PCR technique respectively. Comparing with Tetra primer ARMS PCR which represented 100% agreement with sequencing method, conventional ARMS PCR technique only showed 47.1% agreement, because of 4 discordant results.
    Conclusion: Tetra primer ARMS PCR method is an almost reliable, sensitive and accurate technique and it is suggested that it can be used as a complementary method for diagnostic cases instead of conventional ARMS PCR method. This suggestion originated with perfect rate of agreement between outcomes of sequencing method, as a gold standard method of detecting the mutations, and Tetra primer ARMS PCR technique comparing with conventional ARMS PCR method.
    MeSH term(s) Chorionic Villi Sampling ; DNA Primers ; Female ; Genotype ; Heterozygote ; Homozygote ; Humans ; Male ; Point Mutation ; Polymerase Chain Reaction/methods ; Pregnancy ; Sensitivity and Specificity ; Sequence Analysis, DNA ; beta-Globins/genetics ; beta-Thalassemia/diagnosis ; beta-Thalassemia/genetics
    Chemical Substances DNA Primers ; beta-Globins
    Language English
    Publishing date 2014-10-01
    Publishing country Netherlands
    Document type Comparative Study ; Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2014.05.071
    Database MEDical Literature Analysis and Retrieval System OnLINE

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