A recording of the September CFDE Workshop is available now on YouTube, link below!
For a description of the workshop please see the original post CFDE Virtual Workshop – exRNA Portal
A recording of the September CFDE Workshop is available now on YouTube, link below!
For a description of the workshop please see the original post CFDE Virtual Workshop – exRNA Portal
If you missed the September 27th webinar in the CFDE Public Webinar Series featuring Keyang Yu from the Milosavljevic lab at Baylor College of Medicine you can find the recording here: CFDE webinar 27Sep2024 (youtube.com)
08.16.24
Common Fund Data Ecosystem (CFDE) Virtual Workshop:
“Biomarker discovery from extracellular (cell-free) RNA-seq and tissue of origin from GTEx RNA-seq profiles”
Thursday September 12th 2024
1-3 pm ET / 10am-Noon PT
Requires Free Registration by September 9th (below)
Join us for an engaging hands-on workshop where Srimeenakshi (Meenu) Srinivasan of the Louise Laurent Lab at the University of California-San Diego will demonstrate how to perform integrative data analysis utilizing data from two Common Fund Data Ecosystem (CFDE) Data Coordinating Center portals followed by an interactive Q&A session.
The featured use case will illustrate biomarker discovery from extracellular cell-free RNA-seq data with tissue of origin identification through integrative analysis of GTEx tissue-derived RNA-seq data and plasma-derived small RNA-seq data from the ERCC exRNA Atlas.
To conduct workshop exercises in real time, attendees wishing to take part in the hands-on analysis will need to have the following installed prior to dialing into the workshop as there will not be time to conduct installations during the workshop.
We also strongly encourage attendees to have Jupyter Notebook installed as well as this will be the platform used during the workshop. The Jupyter Notebook/files that will be used will be sent out via email.
Attendees who are not looking to conduct the analyses during the workshop are welcome to attend and observe.
A link to the virtual meeting will be provided in a confirmation email.
If you have any questions, please feel free to contact us at info@exrna.org
We look forward to seeing you there!
To learn more about the projects & resources that will be discussed please see:
Common Fund Data Ecosystem (CFDE): https://commonfund.nih.gov/dataecosystem
Extracellular RNA Communication Consortium (ERCC): https://exrna.org/
Genotype-Tissue Expression Project (GTEx): https://www.gtexportal.org/
Registration and more information:
When: October 17 – 19, 2024
Where: Bethesda North Marriott Hotel & Conference Center
Abstracts are due August 30, 2024
Registration deadline: September 25, 2024
The ASIC Annual Meeting is an intellectual “home” and support network for new and seasoned investigators, students, and postdocs. Over three days you’ll exchange ideas on emerging questions and cutting-edge developments in non-EV research including:
Extracellular Vesicles (EVs)
Extracellular Particles (EPs)
Particulate carriers of extracellular RNA (exRNA) as biological mediators, regulators, and diagnostic analytes.
The meeting also covers a broad range of intercellular communication processes including:
EVs
EPs
exRNA in Cancer
CNS Diseases
Infections (both bacterial and viral)
WHY ATTEND?
You’ll have a valuable opportunity to network with investigators from diverse scientific and clinical fields, discuss and advance the impact of EV/EP/ExRNA in diagnostics and treatments, and better understand the biogenesis of normal vs. disease states.
Are you new to the field? You can work with colleagues and mentors so you can improve your grants and develop their skills to become successful independent researchers.
Women and those from underrepresented groups are especially encouraged to attend and connect with seasoned researchers who have years of mentoring experience.
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Thanks to Baylor College of Medicine for allowing us to share this press release here. |
An international team led by researchers at Baylor College of Medicine with the National Institutes of Health Extracellular RNA Communication Consortium and the Bogdan Mateescu laboratory at the ETH Zürich and University of Zürich has developed a powerful new resource to study extracellular RNA (exRNA), a novel form of cell-to-cell communication. The study, published in the journal Cell Genomics, lays the foundation to examine how exRNA and its carrier proteins found in bodily fluids function in a healthy as well as a diseased setting, potentially providing a means to accurately implement early detection and monitor disease processes.
| This blog is a repost of the NIH Directors’ blog from April 4th, 2023. |
With just a blood sample from a patient, a promising technology has the potential to accurately diagnose non-small cell lung cancer (NSCLC), the most-common form of the disease, more than 90 percent of the time. The same technology can even predict from the same blood sample whether a patient will respond well to a targeted immunotherapy treatment.
This work is a good example of research supported by the NIH Common Fund. Many Common Fund programs support development of new tools that catalyze research across the full spectrum of biomedical science without focusing on a single disease or organ system.
The emerging NSCLC prediction technology was developed as part of our Extracellular RNA Communication Program. The program develops technologies to understand RNA circulating in the body, known as extracellular RNA (exRNA). These molecules can be easily accessed in bodily fluids such as blood, urine, and saliva, and they have enormous potential as biomarkers to better understand cancer and other diseases.
When the body’s immune system detects a developing tumor, it activates various immune cells that work together to kill the suspicious cells. But many tumors have found a way to evade the immune system by producing a protein called PD-L1.
Displayed on the surface of a cancer cell, PD-L1 can bind to a protein found on immune cells with the similar designation of PD-1. The binding of the two proteins keeps immune cells from killing tumor cells. One type of immunotherapy interferes with this binding process and can restore the natural ability of the immune system to kill the tumor cells.
However, tumors differ from person to person, and this form of cancer immunotherapy doesn’t work for everyone. People with higher levels of PD-L1 in their tumors generally have better response rates to immunotherapy, and that’s why oncologists test for the protein before attempting the treatment.
Because cancer cells within a tumor can vary greatly, a single biopsy taken at a single site in the tumor may miss cells with PD-L1. In fact, current prediction technologies using tissue biopsies correctly predict just 20 – 40 percent of NSCLC patients who will respond well to immunotherapy. This means some people receive immunotherapy who shouldn’t, while others don’t get it who might benefit.
To improve these predictions, a research team led by Eduardo Reátegui, The Ohio State University, Columbus, engineered a new technology to measure exRNA and proteins found within and on the surface of extracellular vesicles (EVs) [1]. EVs are tiny molecular containers released by cells. They carry RNA and proteins (including PD-L1) throughout the body and are known to play a role in communication between cells.
As the illustration above shows, EVs can be shed from tumors and then circulate in the bloodstream. That means their characteristics and internal cargo, including exRNA, can provide insight into the features of a tumor. But collecting EVs, breaking them open, and pooling their contents for assessment means that molecules occurring in small quantities (like PD-L1) can get lost in the mix. It also exposes delicate exRNA molecules to potential breakdown outside the protective EV.
The new technology solves these problems. It sorts and isolates individual EVs and measures both PD-1 and PD-L1 proteins, as well as exRNA that contains their genetic codes. This provides a more comprehensive picture of PD-L1 production within the tumor compared to a single biopsy sample. But also, measuring surface proteins and the contents of individual EVs makes this technique exquisitely sensitive.
By measuring proteins and the exRNA cargo from individual EVs, Reátegui and team found that the technology correctly predicted whether a patient had NSCLC 93.2 percent of the time. It also predicted immunotherapy response with an accuracy of 72.2 percent, far exceeding the current gold standard method.
The researchers are working on scaling up the technology, which would increase precision and allow for more simultaneous measurements. They are also working with the James Comprehensive Cancer Center at The Ohio State University to expand their testing. That includes validating the technology using banked clinical samples of blood and other bodily fluids from large groups of cancer patients. With continued development, this new technology could improve NSCLC treatment while, critically, lowering its cost.
The real power of the technology, though, lies in its flexibility. Its components can be swapped out to recognize any number of marker molecules for other diseases and conditions. That includes other cancers, neurodegenerative diseases, traumatic brain injury, viral diseases, and cardiovascular diseases. This broad applicability is an example of how Common Fund investments catalyze advances across the research spectrum that will help many people now and in the future.
[1] Nyugen LTH et al. An immunogold single extracellular vesicular RNA and protein (AuSERP) biochip to predict responses to immunotherapy in non-small cell lung cancer patients J Extracell Vesicles (2023) 11: e12258. doi: 10.1002/jev2.12258 PMID: 36093740.
Extracellular RNA Communication Program (ERCC) (Common Fund)
Video: Unlocking the Mysteries of Extracellular RNA Communication
Upcoming Meeting: ERCC19 Research Meeting (May 1-2, 2023)
Dr. Lawrence Tabak, who performs the duties of the NIH Director, has asked the heads of NIH’s Institutes, Centers, and Offices to contribute occasional guest posts to the blog to highlight some of the interesting science that they support and conduct. This is the 27th in the series of NIH guest posts that will run until a new permanent NIH director is in place.
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This blog originated as a press release from the International Communications Office at Nagoya University. Thanks to them for allowing us to repost it here. |
Researchers at Nagoya University in Japan have used a new device to identify a key membrane protein in urine that indicates whether the patient has a brain tumor. Their protein could be used to detect brain cancer, avoiding the need for invasive tests, and increasing the likelihood of tumors being detected early enough for surgery. This research could also have potential implications for detecting other types of cancer. The research was published in ACS Nano.
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This blog originated as a press release from Hokkaido University. Thanks to them for allowing us to repost it here. |
Researchers from Hokkaido University and Toppan have developed a method to detect build-up of amyloid β in the brain, a characteristic of Alzheimer’s disease, from biomarkers in blood samples.
Alzheimer’s disease is a neurodegenerative disease, characterised by a gradual loss of neurons and synapses in the brain. One of the primary causes of Alzheimer’s disease is the accumulation of amyloid β (Aβ) in the brain, where it forms plaques. Alzheimer’s disease is mostly seen in individuals over 65 years of age, and cannot currently be stopped or reversed. Thus, Alzheimer’s disease is a major concern for nations with ageing populations, such as Japan.
A team of scientists from Hokkaido University and Toppan, led by Specially Appointed Associate Professor Kohei Yuyama at the Faculty of Advanced Life Science, Hokkaido University, have developed a biosensing technology that can detect Aβ-binding exosomes in the blood of mice, which increase as Aβ accumulates in the brain. Their research was published in the journal Alzheimer’s Research & Therapy.
Cells can communicate with one another to coordinate essential processes such as development, growth, and repair through the release of signaling intermediates. One class of signaling intermediates are extracellular vesicles (EVs) that contain nucleic acids and proteins that mediate cell-cell communication. In cancer, the cargo of these EVs is altered in order to promote tumor progression, improving the ability to proliferate, invade, metastasize, and develop drug resistance, among other cancer characteristics. While most EVs range in diameter from 50 nanometers to one micron, there has been an increasing interest in smaller particles that might also be released from cells and contribute to cancer. Only recently has technology evolved enough to detect these previously undiscernible nanoparticles. Qin Zhang, PhD, Robert Coffey, MD, and colleagues were motivated by previous advances in the lab regarding the role of EVs in cancer to determine if smaller particles existed with similar functions. Dr. Coffey and his team discovered a new nanoparticle, termed the supermere, with functional relevance not only to cancer but to many other diseases, resulting in a publication at the end of 2021 in Nature Cell Biology (Zhang Q et al. 2021).
