Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood

Kalikiri, Mahesh Kumar Reddy; Manjunath, Harshitha Shobha; Vempalli, Fazulur Rehaman; Mathew, Lisa S.; Liu, Li; Wang, Li; Wang, Gui-Shuang; Wang, Kun; Soloviov, Oleksandr; Lorenz, Stephan; Tomei, Sara

doi:10.1038/s41598-023-30629-5

Cited by 3 publications

(1 citation statement)

References 32 publications

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“…Improvements in sample collection methods, preservation techniques, and sample processing automation can optimize the efficiency and quality of biobanking operations. New cryopreservation technologies, such as vitrification, in which elevated cryoprotectant concentrations and rapid cooling rates quickly convert a solution into a transparent non-crystalline solid compound [ 93 , 94 ] may be employed and more automation of sample processing will lead to less technical variation [ 95 ].…”

Section: Future Directions and Emerging Technologiesmentioning

confidence: 99%

Neuro-Urology and Biobanking: An Integrated Approach for Advancing Research and Improving Patient Care

Botter,

Kessler

2023

IJMS

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Understanding the molecular mechanisms underlying neuro-urological disorders is crucial for the development of targeted therapeutic interventions. Through the establishment of comprehensive biobanks, researchers can collect and store various biological specimens, including urine, blood, tissue, and DNA samples, to study these mechanisms. In the context of neuro-urology, biobanking facilitates the identification of genetic variations, epigenetic modifications, and gene expression patterns associated with neurogenic lower urinary tract dysfunction. These conditions often present as symptoms of neurological diseases such as Alzheimer’s disease, multiple sclerosis, Parkinson’s disease, spinal cord injury, and many others. Biobanking of tissue specimens from such patients is essential to understand why these diseases cause the respective symptoms and what can be done to alleviate them. The utilization of high-throughput technologies, such as next-generation sequencing and gene expression profiling, enables researchers to explore the molecular landscape of these conditions in an unprecedented manner. The development of specific and reliable biomarkers resulting from these efforts may help in early detection, accurate diagnosis, and effective monitoring of neuro-urological conditions, leading to improved patient care and management. Furthermore, these biomarkers could potentially facilitate the monitoring of novel therapies currently under investigation in neuro-urological clinical trials. This comprehensive review explores the synergistic integration of neuro-urology and biobanking, with particular emphasis on the translation of biobanking approaches in molecular research in neuro-urology. We discuss the advantages of biobanking in neuro-urological studies, the types of specimens collected and their applications in translational research. Furthermore, we highlight the importance of standardization and quality assurance when collecting samples and discuss challenges that may compromise sample quality and impose limitations on their subsequent utilization. Finally, we give recommendations for sampling in multicenter studies, examine sustainability issues associated with biobanking, and provide future directions for this dynamic field.

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Section: Future Directions and Emerging Technologiesmentioning

confidence: 99%

Neuro-Urology and Biobanking: An Integrated Approach for Advancing Research and Improving Patient Care

Botter,

Kessler

2023

IJMS

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Metabolic reprogramming-related gene classifier distinguishes malignant from the benign pulmonary nodules

Huang,

Li,

Jiang

et al. 2024

Heliyon

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Initial TCR Signal Strength Imprints GATA3 and Tbet Expression Driving T-helper Cell Fate Decisions

Al-Aghbar,

Khan,

Guarch

et al. 2024

Preprint

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With the exception of the T-helper 2 (Th2) subset, cytokine driven pathways provide a robust mechanistic explanation for the observed outcomes of CD4+ T-cell differentiation. Using a quantitative model of activation, we studied the integration of TCR-signal-strength with cytokine signalling during Th2 differentiation. Upon the initial activation of Th-naïve cells, TCR signalling was found to set early expression levels for the master regulators of differentiation Tbet and GATA3, independent of the presence of polarizing cytokines.Subsequently cytokine stimuli modulated transcription factor (TF) expression levels to tune the outcome of differentiation. Here, weak TCR signalling was sufficient to drive the early upregulation of GATA3 and induce Th2 differentiation, in an IL-4 independent manner. Th1 differentiation was however shown to require additional cytokine signalling input, either in the form of autocrine IFNγ or exogenous IL-12. Using mathematical modelling we demonstrate that T-helper differentiation occurs along a continuum of states. Set by the relative co-expression of regulatory TFs, where effector cytokine production is controlled in a probabilistic manner determined by the relative levels GATA3 and Tbet expressed.Together, our data indicate TCR signalling inputs drive an early bifurcation in the T-helper differentiation pathway. Together, the integration of TCR signal strength with cytokine inputs act as a mechanism for the detection of immuno-evasive parasitic infections, whilst providing an additional checkpoint to prevent aberrant Th1 associated immunopathology.

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Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood

Cited by 3 publications

References 32 publications

Neuro-Urology and Biobanking: An Integrated Approach for Advancing Research and Improving Patient Care

Neuro-Urology and Biobanking: An Integrated Approach for Advancing Research and Improving Patient Care

Metabolic reprogramming-related gene classifier distinguishes malignant from the benign pulmonary nodules

Initial TCR Signal Strength Imprints GATA3 and Tbet Expression Driving T-helper Cell Fate Decisions

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