Establishing a correlation between RIN and A260/280 along with the multivariate evaluation of factors affecting the quality of RNA in cryopreserved cancer bio-specimen

Shah, Sanket; Rashid, Mudasir; Verma, Tripti; Ludbe, Madan; Khade, Bharat; Gera, Poonam; Gupta, Sanjay

doi:10.1007/s10561-019-09782-7

Cited by 17 publications

(16 citation statements)

References 22 publications

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“…In brain tissue, RNA quality of controls has been reported to be significantly higher than in disease conditions, but overall RNA quality was independent of PMD up to 36 h (White et al, 2018). In addition, RNA quality is independent of storage time (White et al, 2018;Shah et al, 2019). RNA quality differences within one dataset might mask biologically relevant information.…”

Section: Preanalytical Factors To Consider During Microglia Transcripmentioning

confidence: 99%

High-Resolution Transcriptomic and Proteomic Profiling of Heterogeneity of Brain-Derived Microglia in Multiple Sclerosis

Miedema

Wijering

Eggen

et al. 2020

Front. Mol. Neurosci.

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Microglia are important for central nervous system (CNS) homeostasis and first to respond to tissue damage and perturbations. Microglia are heterogeneous cells; in case of pathology, microglia adopt a range of phenotypes with altered functions. However, how these different microglia subtypes are implicated in CNS disease is largely unresolved. Multiple sclerosis (MS) is a chronic demyelinating disease of the CNS, characterized by inflammation and axonal degeneration, ultimately leading to neurological decline. One way microglia are implicated in MS is through stimulation of remyelination. They facilitate efficient remyelination by phagocytosis of myelin debris. In addition, microglia recruit oligodendrocyte precursor cells (OPCs) to demyelinated areas and stimulate remyelination. The development of high-resolution technologies to profile individual cells has greatly contributed to our understanding of microglia heterogeneity and function under normal and pathological conditions. Gene expression profiling technologies have evolved from whole tissue RNA sequencing toward singlecell or nucleus sequencing. Single microglia proteomic profiles are also increasingly generated, offering another layer of high-resolution data. Here, we will review recent studies that have employed these technologies in the context of MS and their respective advantages and disadvantages. Moreover, recent developments that allow for (single) cell profiling while retaining spatial information and tissue context will be discussed.

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Section: Preanalytical Factors To Consider During Microglia Transcripmentioning

confidence: 99%

High-Resolution Transcriptomic and Proteomic Profiling of Heterogeneity of Brain-Derived Microglia in Multiple Sclerosis

Miedema

Wijering

Eggen

et al. 2020

Front. Mol. Neurosci.

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“…It is made The copyright holder for this preprint this version posted March 10, 2021. ; https://doi.org/10.1101/2021.03.10.434738 doi: bioRxiv preprint ovary; infiltrating ductal carcinoma of the breast; squamous cell carcinoma of head and neck (tongue, buccal mucosa) and penis; hepatocellular carcinoma of the liver; glioblastoma of the brain; renal cell carcinoma of kidney and seminoma of testis were retrieved from EMR database of TMH (http://10.100.52.12/emrtmhact/default.asp). Histopathology analysis of tissues was confirmed earlier (Shah et al, 2019). The samples with more than 70% tumor content were processed for further studies.…”

Section: Human Normal Rnamentioning

confidence: 71%

“…The protocol was adapted from Shah et al 2019. In brief, total RNA was isolated from human normal and tumor tissues according to manufacture protocol (Agilent Cat#400800), and the quantity and quality were confirmed by NanoDrop 2000C spectrophotometer, and agarose formaldehyde denaturing gel electrophoresis.…”

Section: Methodsmentioning

confidence: 99%

Differential expression of H2A isoforms contribute to tissue and lineage specificity with HIST2H2AC as a potential cancer biomarker

Shah

Rashid

Natu

et al. 2021

Preprint

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Recent advancements in the field of histone biology imply non-redundancy in the function of histone H2A isoforms; however, the expression of H2A isoforms in various normal tissue types, the correlation among organs and tumor/tumor type-specific expression remain poorly investigated. The profiling of sixteen H2A isoforms in eleven different normal human tissue types strongly suggests their tissue-specific or predominant expression. Further, clustering analysis shows a lineage-specific correlation of H2A isoforms. In continuation, the expression analysis in twelve human tumor types shows overexpression of HIST2H2AC. Moreover, overexpression was observed exclusively in tumor samples but not with fetal samples; highlighting the cancer-specific association of HIST2H2AC. Further, in silico analysis of TCGA pan-cancer data also showed tumor-specific over-expression of the HIST2H2AC isoform. Our findings provide insights into tissue-type-specificity of histone H2A isoforms expression patterns and advance our understanding of their importance in lineage specification and cancer.

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“…The concentration, purity, and integrity of the extracted RNA greatly affect the results of gene testing. The concentration and purity of RNA are mainly affected by the impurities in BPE [21-24]. The more the impurities, the lower the concentration and purity of extracted RNA, and the better the integrity and representativeness of RNA, the closer the transcribed cDNA is to the natural state.…”

Section: Discussionmentioning

confidence: 99%

Using Disposable Membrane Cell Collector to Enrich Lung Adenocarcinoma Cells in Bloody Pleural Effusion for Anaplastic Lymphoma Kinase Fusion Gene Detection

Guo

Zhao

et al. 2021

Acta Cytologica

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Purpose: For anaplastic lymphoma kinase (ALK) gene detection, the centrifugal sedimentation method (CSM) and cell block method (CBM) are commonly used to process samples of bloody pleural effusions (BPEs). However, in practice, the impurity content in the processed samples often affects the results and even leads to the detection failure. The purpose of this study was to establish a cell enrichment method (CEM) by using a disposable membrane cell collector to remove blood and inflammatory cells and enrich lung adenocarcinoma cells in BPE for more efficient RNA extraction and ALK gene detection. Materials and Methods: CEM proposed in this study and the traditional CSM and CBM were used to treat BPE samples collected from 37 lung adenocarcinoma patients. A DeNovix DS-11 ultraviolet spectrophotometer was used to measure the concentration and purity of extracted RNA. Amplification refractory mutation systems (ARMS) and ABI 7500 fluorescence qPCR were used to detect ALK gene. Through statistical analysis, the CEM was compared with the CSM and CBM in RNA concentration, purity, and ALK gene detection results. Results: The concentration of RNA extracted by using the CEM was significantly higher than that extracted by using the CBM and CSM (p < 0.001). The purity of RNA extracted by using the CEM was significantly higher than that by the other 2 methods (p = 0.011, p = 0.005). ALK gene testing with PCR was successful in all the samples using the CEM, but 2 cases by the CSM and 1 case by the CBM failed. Conclusions: Using the disposable membrane cell collector to process BPE of lung adenocarcinoma patients for RNA extraction and ALK gene detection is more effective and successful compared with the traditional methods, and it is suggested to be further applied and popularized in clinical practice.

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Establishing a correlation between RIN and A260/280 along with the multivariate evaluation of factors affecting the quality of RNA in cryopreserved cancer bio-specimen

Cited by 17 publications

References 22 publications

High-Resolution Transcriptomic and Proteomic Profiling of Heterogeneity of Brain-Derived Microglia in Multiple Sclerosis

High-Resolution Transcriptomic and Proteomic Profiling of Heterogeneity of Brain-Derived Microglia in Multiple Sclerosis

Differential expression of H2A isoforms contribute to tissue and lineage specificity with HIST2H2AC as a potential cancer biomarker

Using Disposable Membrane Cell Collector to Enrich Lung Adenocarcinoma Cells in Bloody Pleural Effusion for Anaplastic Lymphoma Kinase Fusion Gene Detection

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