A tour through the transcriptional landscape of platelets

Abstract The RNA code found within a platelet and alterations of that code continue to shed light onto the mechanistic underpinnings of platelet function and dysfunction. It is now known that features of messenger RNA (mRNA) in platelets mirror those of nucleated cells. This review serves as a tour guide for readers interested in developing a greater understanding of platelet mRNA. The tour provides an in-depth and interactive examination of platelet mRNA, especially in the context of next-generation RNA sequencing. At the end of the expedition, the reader will have a better grasp of the topography of platelet mRNA and how it impacts platelet function in health and disease.

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CBX2-dependent transcriptional landscape: implications for human sex development and its defects

Scientific Reports ◽

10.1038/s41598-019-53006-7 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Patrick Sproll ◽

Wassim Eid ◽

Anna Biason-Lauber

Keyword(s):

Next Generation Sequencing ◽

Rna Sequencing ◽

Current Knowledge ◽

Next Generation ◽

Steroidogenic Factor 1 ◽

Sex Development ◽

New Genes ◽

Differences Of Sex Development ◽

Generation Sequencing ◽

Transcriptional Landscape

Abstract Sex development, a complex and indispensable process in all vertebrates, has still not been completely elucidated, although new genes involved in sex development are constantly being discovered and characterized. Chromobox Homolog 2 (CBX2) is one of these new additions and has been identified through a 46,XY girl with double heterozygous variants on CBX2.1, causing Differences of Sex Development (DSD). The mutated CBX2.1 failed to adequately regulate downstream targets important for sex development in humans, specifically steroidogenic factor 1 (NR5A1/SF1). To better place CBX2.1 in the human sex developmental cascade, we performed siRNA and CBX2.1 overexpression experiments and created a complete CRISPR/Cas9-CBX2 knockout in Sertoli-like cells. Furthermore, we deployed Next Generation Sequencing techniques, RNA-Sequencing and DamID-Sequencing, to identify new potential CBX2.1 downstream genes. The combination of these two next generation techniques enabled us to identify genes that are both bound and regulated by CBX2.1. This allowed us not only to expand our current knowledge about the influence of CBX2.1 in human sex development, but also to advance our insight in the mechanisms governing one of the most important decisions during embryonal development, the commitment to either female or male gonads.

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Faculty Opinions recommendation of The transcriptional landscape of the yeast genome defined by RNA sequencing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1109228.565235 ◽

2008 ◽

Author(s):

Bernd Weisshaar

Keyword(s):

Rna Sequencing ◽

Yeast Genome ◽

Transcriptional Landscape

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The STING1 network regulates autophagy and cell death

Signal Transduction and Targeted Therapy ◽

10.1038/s41392-021-00613-4 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Ruoxi Zhang ◽

Rui Kang ◽

Daolin Tang

Keyword(s):

Cell Death ◽

Mitotic Cell ◽

Therapeutic Interventions ◽

Type I Interferons ◽

Microbial Pathogens ◽

Type I ◽

Autophagic Degradation ◽

Health And Disease ◽

Shed Light ◽

Pro Inflammatory Cytokines

AbstractCell death and immune response are at the core of life. In past decades, the endoplasmic reticulum (ER) protein STING1 (also known as STING or TMEM173) was found to play a fundamental role in the production of type I interferons (IFNs) and pro-inflammatory cytokines in response to DNA derived from invading microbial pathogens or damaged hosts by activating multiple transcription factors. In addition to this well-known function in infection, inflammation, and immunity, emerging evidence suggests that the STING1-dependent signaling network is implicated in health and disease by regulating autophagic degradation or various cell death modalities (e.g., apoptosis, necroptosis, pyroptosis, ferroptosis, mitotic cell death, and immunogenic cell death [ICD]). Here, we outline the latest advances in our understanding of the regulating mechanisms and signaling pathways of STING1 in autophagy and cell death, which may shed light on new targets for therapeutic interventions.

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Suitability of Bronchoscopic Biopsy Tissue Samples for Next-Generation Sequencing

Diagnostics ◽

10.3390/diagnostics11030391 ◽

2021 ◽

Vol 11 (3) ◽

pp. 391

Author(s):

Shuji Murakami ◽

Tomoyuki Yokose ◽

Daiji Nemoto ◽

Masaki Suzuki ◽

Ryou Usui ◽

...

Keyword(s):

Next Generation Sequencing ◽

Success Rate ◽

Rna Sequencing ◽

Surface Area ◽

Endobronchial Ultrasound ◽

Next Generation ◽

Endobronchial Ultrasonography ◽

Tissue Surface ◽

The Impact ◽

Generation Sequencing

A sufficiently large tissue sample is required to perform next-generation sequencing (NGS) with a high success rate, but the majority of patients with advanced non-small-cell lung cancer (NSCLC) are diagnosed with small biopsy specimens. Biopsy samples were collected from 184 patients with bronchoscopically diagnosed NSCLC. The tissue surface area, tumor cell count, and tumor content rate of each biopsy sample were evaluated. The impact of the cut-off criteria for the tissue surface area (≥1 mm2) and tumor content rate (≥30%) on the success rate of the Oncomine Dx Target Test (ODxTT) was evaluated. The mean tissue surface area of the transbronchial biopsies was 1.23 ± 0.85 mm2 when small endobronchial ultrasonography with a guide sheath (EBUS-GS) was used, 2.16 ± 1.49 mm2 with large EBUS-GS, and 1.81 ± 0.75 mm2 with endobronchial biopsy (EBB). The proportion of samples with a tissue surface area of ≥1 mm2 was 48.8% for small EBUS-GS, 79.2% for large EBUS-GS, and 78.6% for EBB. Sixty-nine patients underwent ODxTT. The success rate of DNA sequencing was 84.1% and that of RNA sequencing was 92.7% over all patients. The success rate of DNA (RNA) sequencing was 57.1% (71.4%) for small EBUS-GS (n = 14), 93.4% (96.9%) for large EBUS-GS (n = 32), 62.5% (100%) for EBB (n = 8), and 100% (100%) for endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) (n = 15). Regardless of the device used, a tissue surface area of ≥ 1 mm2 is adequate for samples to be tested with NGS.

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Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses

Apmis ◽

10.1111/apm.12477 ◽

2016 ◽

Vol 124 (1-2) ◽

pp. 127-139 ◽

Cited By ~ 8

Author(s):

Martin Sokol ◽

Karen Margrethe Jessen ◽

Finn Skou Pedersen

Keyword(s):

Rna Sequencing ◽

Endogenous Retroviruses ◽

Next Generation ◽

Human Endogenous Retroviruses

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Gestational Psittacosis Resulting in Neonatal Death Identified by Next-Generation RNA Sequencing of Postmortem, Formalin-Fixed Lung Tissue

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy172 ◽

2018 ◽

Vol 5 (8) ◽

Cited By ~ 1

Author(s):

Litty Paul ◽

Jessica Comstock ◽

Kornelia Edes ◽

Robert Schlaberg

Keyword(s):

Rna Sequencing ◽

Infant Death ◽

Neonatal Death ◽

Pathogen Detection ◽

Severe Disease ◽

Adverse Outcomes ◽

Premature Delivery ◽

Next Generation ◽

Death Studies ◽

Formalin Fixed

Abstract Psittacosis is a rare zoonosis that can cause severe disease and adverse outcomes during pregnancy. We identified a previously elusive case of psittacosis causing premature delivery and infant death by next-generation RNA sequencing of postmortem tissues. Hypothesis-free pathogen detection in postmortem specimens can increase the yield of epidemiologic and cause-of-death studies.

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The next generation of RNA vaccines: self-amplifying RNA

The Biochemist ◽

10.1042/bio_2021_142 ◽

2021 ◽

Author(s):

Anna Blakney

Keyword(s):

Side Effects ◽

Messenger Rna ◽

Rapid Development ◽

Next Generation ◽

High Efficacy ◽

Vaccine Platform ◽

The Future ◽

High Doses ◽

The Stability

The global COVID-19 pandemic has brought tremendous momentum to the field of messenger RNA (mRNA) vaccines. The advantages of this vaccine platform, such as rapid development and high efficacy, resulted in mRNA vaccines being the first approved vaccines against COVID-19. Looking forward to the development of future vaccines, how can we make RNA vaccines even better? While improvements in the stability of the formulation and cost of the vaccine are inevitable, one of the main challenges is lowering the dose of RNA in order to avoid side effects associated with high doses of RNA. One way to do this is by using self-amplifying RNA (saRNA), a type of mRNA that encodes a replicase that copies the original strand of RNA once it’s in the cell. Here, we discuss the origins of saRNA, how it works in comparison to mRNA, current challenges in the field and the future of saRNA vaccines.

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The Important Role of Breast Microbiota in Breast Cancer

10.20944/preprints202010.0437.v1 ◽

2020 ◽

Author(s):

Kar-Yan Su ◽

Wai-Leng Lee ◽

Vinod Balasubramaniam

Keyword(s):

Breast Cancer ◽

Next Generation Sequencing ◽

Racial Differences ◽

Breast Tissue ◽

Bacterial Species ◽

Cancer Therapies ◽

Next Generation ◽

Sequencing Technologies ◽

Health And Disease ◽

Generation Sequencing

One in eight women will be diagnosed with breast cancer (BC) in their lifetime, resulting in over 2 million cases annually. BC is the most common cancer among women. Unfortunately, the etiology of majority of cases remains unknown. Recently, evidence has shown that the human microbiota plays an important role in health and disease. Intriguingly, studies have revealed the presence of microorganisms in human breast tissue, which was previously presumed to be sterile. Next-generation sequencing technologies have paved way for the investigation of breast microbiota, uncovering bacterial signatures that are associated with BC. Some of the bacterial species were found to possess pro-carcinogenic and/or anti-carcinogenic properties, suggesting that the breast microbiota has potentially crucial roles in maintenance of breast health. In this review, we summarize the recent findings on breast tissue microbiota and its interplay with BC. Bacterial signatures identified via next-generation sequencing as well as their impact on breast carcinogenesis and cancer therapies are reviewed. Correlation of breast tissue microbiota and other factors, such as geographical and racial differences, in BC is discussed. Additionally, we discuss the future directions of research on breast microbiota as well as its potential role in prevention, diagnosis and treatment of BC.

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