"SenNet Recommendations for Detecting Senescent Cells in Different Tissues"
Featured in the June 2024 issue of Nature Reviews Molecular Cell Biology
“The SenNet Biomarkers Working Group was formed to provide recommendations for the use of cellular senescence markers to identify and characterize senescent cells in tissues. Here, we provide recommendations for detecting senescent cells in different tissues based on a comprehensive analysis of existing literature reporting senescence markers in 14 tissues in mice and humans.”
Consortium News & Updates
SenNet members: please submit Consortium news, updates, or event notices for publication by emailing help@sennetconsortium.org.
CODCC Recent News
- Buck Institute Team is named semifinalist of XPRIZE Heatlhspan: $101 million global competition aims to revolutionize how we approach aging. Read more here.
- The Brain Image Library, HuBMAP, CFDE, and others will host a virtual Spatial Omics workshop on May 12–16, 2025, featuring hands-on training with Giotto, SPArrOW, and Harpy tools. Participants will use real-world data on Pittsburgh Supercomputing Center systems; register by 5/1/25.
- At the Knowledge Graphs symposium at the Bio-IT World Conference & Expo, SenNet PI Jonathan C. Silverstein presented the UBKG Knowledge Graph (KG) that serves as data backend for both the SenNet and HuBMAP Data Portal. PI Katy Börner presented the Human Reference Atlas KG that serves as data backend for the HRA Portal. (April 2025).
- “MRI detection of senescent cells in porcine knee joints with a β-galactosidase responsive Gd-chelate” is in press with Nature Publishing Group (NPJ) Imaging, featuring the research of SenNet scientists. Check back for a link to the publication soon! (April 2025).
- “Human BioMolecular Atlus Program (HuBMAP): 3D Human Reference Atlas Construction and Usage” was published in Nature Methods on March 13, 2025, featuring the work of several SenNet authors. Read here. Additional supporting information can be found here. (March 2025).
- The HDIVE Lab at Harvard Medical School is pleased to announce “VUES on Spatial Biology – The Future of 3D Tissue Maps” on March 11, 2025. This in person event will be held at Harvard Medical School. Registration is free, and more information can be found here. (March 2025).
- The 2025 HuBMAP JumpStart Fellowship is now accepting applications, offering junior investigators working on human atlasing projects the opportunity to take a leadership role in conducting synergistic, collaborative research projects within the HuBMAP Consortium. Apply and find more info here! (February 2025).
- SenNet research sites at Indiana University and Columbia University collaborate on a senescent cell VR demo, featuring Andreas Bueckle, PhD, and Hemali Phatnani, PhD. Click to view here. (December 2024).
- “SenNet recommendations for detecting senescent cells in different tissues” has been published in Nature Reviews Molecular Cell Biology. Click to view the entire article. (December 2024).
- SenNet is featured in the Nature article “How to kill the ‘zombie’ cells that make you age” by Carissa Wong. View the entire article here. (May 2024).
- Pitt’s high-performance computing upgrade signals accelerated translational research. Read more here. (March 2024).
- Computer hardware gift from Dell enhances SenNet Consortium research infrastructure. Read more here. (March 2024).
Working Group 2025 Updates
- Data Coordination – Chair: Jonathan Silverstein
- Data Submission Guide includes multi-omic maps.
- Reminder: use CEDAR for all sample and assay metadata
- Bulk upload is working for all data (7 uploads not accounted above)
- All SenNet data is to be submitted upon production, do not wait for analysis.
- Benchmarking – Chair: Vilas Menon
- Cross-consortium meeting recent meeting
- Working on metrics/analysis
- March will discuss other consortia benchmarking metrics
- Generally this is early days and collecting expertise and metrics increasing biological complexity coming
- Outreach – Chair: Kay Metis
- SenNet YouTube https://www.youtube.com/@SenNetConsortium
- CUSP Videos and promo video’https://www.youtube.com/watch?v=30c88kn-6q8
- Associate Membership discussed, no new policy required, consensus to have each candidate presented by a SenNet Member to Steering Committee
- Senescence Biomarkers – Chair: Nicola Neretti
- Science talk last meeting regarding functional senescence
- Biomarkers review in late phases with editorial requests – get your materials in NOW – Nicola/Vidyani working through it
- Its compendium of senescence markers by tissue and source (mouse/human) – there is database of these now and it will be published with the paper and draft is online from sennetconsortium.org resources page
- Publication – Chair: Rong Fan
- Publications package coming together for Cell – upcoming more info to come
- Please use the CODCC publication tracker: https://docs.google.com/spreadsheets/d/18LhZGCoyKvkfmAM5hGOZpd6IDxK10AD0Movtsi2x1KQ/edit#gid=0
- Committee integrating package and routing tracker
- Policy – Chair: Vidyani Suryadevara
- Associate Membership discussed – no new policy required – voting procedures of consortium allow appropriate regulation of membership
- -omics/Mapping WG are merging. Chairs: Sheng Li & Rong Fan
- Imaging/Mapping – Joao Passos retired from chairing Imaging to lead the Benchmarking project
- -omics and Image Mapping WG is new name chaired by Sheng Li and Joao Passos
- Focus upon integration of spatial technologies / analysis – e.g., Xenium and others
- Speakers being invited
- This group is generally also posting the presentations on SenNet YouTube Channel
- -omics perspective paper in revising phase – computational analysis and organ specific sections (few sections remaining)
- Human Reference Atlas WG (previously ASCT+B) – Chair: Katy Borner
- Patty Lee provided update on 5×5
- Additional digital objects may be in the green by Apr 1
- Would like additional external reviewers for any of the ASCT+B items below:
- Junior Investigators – Chairs: Birgit Schilling & Lexi Rindone
- The Division of Aging Builogy at the NIA is holding a virtual workshop titled, “Cellular Quiescence, Senescence, and Death in Aging and Longevity.” The workshop will be help on Tuesday, 4/23/24 from 10am-5:30pm EST. If you would like to attend, please register using this link before 4/23/24.
- Poster sessions desirable for April meeting – organizing group informed
- Mentoring lunch desirable for April meeting – organizing group informed
- Intent to continue to encourage JIs attending consortium meetings
General Consortium Updates
Akoya Biosciences launches an imaging contest–submissions are due by May 31, 2024. To enter the contest, click here.
The Common Fund Data Ecosystem Public Webinar Series will take place on 4/26/24.
The 2024 scverse Hackathon in Boston, MA is accepting applicants until March 24.
CUSP 2023 Graduate Hillina Berhane accepts a postbac fellowship at the NIH!
SenNet remembers Dr. Judith Campisi (1949-2024).
Registration open for the NIH-CZI Junior Investigators Atlas Builders Meeting on March 17-19, 2024. The conference topic is “Cellular and Molecular Human Atlases in Health and Disease.”
The 6th release of the Human Reference Atlas (HRA) is now available via https://humanatlas.io/. See details on what data, tools, training materials were updated/added in the Release Notes at https://humanatlas.io/release-
Sign up for HuBMAP’s 12/19/23 VUES Seminar with Jeremy Kriegel! Topic is: “Development of User Personas: Who is the User in Your Stories?”
Kaggle Competition Launched: “SenNet + HOA – Hacking the Human Vasculature in 3D”
HTAN Jamboree & HuBMAP Jumpstart Program
Collection of Articles Reports Advances in Building Cellular Organization Maps of the Human Body
NIH launches program to map a rare type of non-dividing cells implicated in human health and disease
Molecular Atlas of Senescent Cells Could Chart Way to Therapies for Age-Related Diseases and Cancer
Pitt teams tapped to develop ‘Google Maps’ of cells important in aging
$125 Million in Grants to Study Cellular Aging to Be Coordinated from Pittsburgh
CMU CompBio Researchers Take Leading Roles in NIH SenNet Program
Buck Institute awarded $12.7 million from NIH to join SenNet, Cellular Senescence Network
$7.5 million to study elusive cell type important in aging, cancer, other diseases
Senescent Cell Tissue Mapping Will Facilitate Study of Aging and Chronic Diseases
Archived Consortium News & Updates
CODCC Updates
- The Human Reference Atlas is hosting a 24-hour online webinar titled “What is a Multiscale Human,” starting at 12:00pm on Dec. 14. Visit this page to register and attend.
- Thomas Höllt, PhD from the Delft University of Technology will be speaking on “Visual Analytics for Spatially resolved High-Dimensional Data – Methods and Applications in Biology.” Register to attend here.
- Join the NHLBI for a virtual workshop on November 7-8, 2024, from 10:30am-4:00pm EST, focused on progenitor resilience and the early onset of chronic lung diseases. More details and registration can be found here.
- VUES Webinar: “Democratizing the analysis and visualization of omics datasets using Multi-Dimensional Viewer” with speaker Stephen Taylor, PhD. Presented on 10/15/24 at 11:00am EST. More info and registration here.
- The 2024 HuBMAP Fall Hackathon kicks off on Sep. 20, 2024. Applications are accepted until Aug. 30. Click here for more information.
- The Buck Institute presents “Cellular Senescence: The Road to Immortality?” on Monday, Aug. 12 as a part of the Judy Campisi Inaugural Symposium. Free virtual passes are available now: click here.
- Katy Börner and Bruce Herr will present A Tour of the Human Reference Atlas v.2.1 during the Common Fund Data Ecosystem’s Public Webinar Series on July 26, 1:00-2:00pm EST. Please register here.
- The 2024 SenNet Annual Meeting webpage is now live: click to view meeting and registration information.
- The NIH Common Fund is requesting research applications (RFA-RM-24-006) encouraging the use of Common Fund data. To be eligible, the proposed research must substantially leverage data from at least two Common Fund programs (a full list of eligible Common Fund data sets is listed in the Notice of Funding Opportunity). Applications are due June 27, 2024 by 5:00 PM local time of the applicant organization. More information can be found on the Common Fund Data Ecosystem website.
- The CUSP 2024 cohort has been announced! Click to learn about our incoming students.
- Fall 2024 Meeting: The SenNet Fall Meeting will take place September 9-10 in San Diego, near Sanford Burnham Prebys Medical Discover Institute. More meeting information coming soon. All meeting participants must register to attend–link will be emailed to all SenNet members and posted here. SenNet members will be able to attend by Zoom if they require.
- The SenNet Interview Series continues with interviews with Laura Niedernhofer, Simon Melov, Patty Lee, and Hemali Phatnani. Email help@sennetconsortium.org if you’d like to be interviewed!
- The 6th release of the Human Reference Atlas (HRA) is now available via https://humanatlas.io/. See details on what data, tools, training materials were updated/added in the Release Notes at https://humanatlas.io/release-
notes/v2.0. - Sign up for HuBMAP’s 12/19/23 VUES Seminar with Jeremy Kriegel! Topic is: “Development of User Personas: Who is the User in Your Stories?”
- Duke Cancer Institute (DCI) is looking to host post-doctoral candidates to present their research, meet faculty and learn about postdoctoral training programs, on March 25-26, 2024. Flights, hotel, meals and transportation will be sponsored by Duke. Application deadline is by January 1. More details attached!
- The HRA team is hosting a “24 Hour Macroscopes: Interactive Data Visualizations Event” on Dec 9-10. The evolving agenda is now available at https://tinyurl.com/24h-Macroscopes. Last year’s event can be seen here: https://humanatlas.io/events/2022-24h/
- SenNet YouTube page is live: https://www.youtube.com/@SenNetConsortium. Currently posted are the first three SenNet Interview Series videos, with spotlight on Lexi Rindone, Peter Adams, and Andi Bueckle.
- Talks from the 2023 Fall SenNet meeting are in the conference folder with in the SenNet All shared drive – if you missed the conference. SenNet Science Talks will be public moving forward, but Q&A will be edited out.
CUSP Updates
- 2/15/24: Applications for the summer 2024 CUSP cohort are now closed.
- 11/15/23: Call for labs is out and communication has been sent out to PIs. CUSP page and application is live. Visit https://sennetconsortium.org/internship/ Reach out to the SenNet Help Desk for more information.
Working Group Updates
- Benchmarking (Dec. 2023):
- The SenNet Benchmarking Group is collecting information on past, current, and future benchmarking efforts within the consortium. Our goal is to put together a consortium-wide document of recommendations, approaches, and best practices to benchmark experimental and computational workflows being used.
- Survey link can be found here: https://universityrochester.co1.qualtrics.com/jfe/form/SV_cwJbv9JoXbUOD5k
- Data Coordination (Dec. 2023):
- December 2023 Data Coordination Commitment
- June 2024 Data Coordination Commitment
- Migrating metadata to the Cedar platform
- Data sets may require an abstract to explain the experimental design and goals to help harmonize the analysis of senescent cells and the products of the TMCs delivered to CODCC.
- Human Reference Atlas (Dec. 2023):
- Meets the first Wednesday of each month at 11:00amET: All are welcome!
- Zoom link: https://iu.zoom.us/j/82011829401?pwd=aTlVT2loUllnVWZldDFXdUdEN2hGZz09
- All past meeting slides may be found here: https://drive.google.com/drive/folders/1MLHQBFHHpXeZVm0kUGiukwI_3_EOygIz
- Imaging/Mapping (Dec. 2023):
- Joao is looking for someone to replace him as the WG chair as he focuses on the Benchmarking project
- If you would like to volunteer, please reach out to the SenNet Help Desk
- Option to merge with Omics WG
- Junior Investigators (Jan. 2024):
- 2024 US NAM Catalyst Award Competition is live! Applications open.
- Check the WG notes for more information.
- Omics/Mapping (Jan. 2024):
- The Omics/Mapping working group is now hosting a monthly Seminar series. Reach out to Sheng.Li@jax.org for more information or to schedule your talk.
- SenNet Omics perspective table 1 on consortium-wide TMCs/TDAs 18 organ-/tissue-specific single-cell and spatial omics considerations (Laura and Sheng):
- Table1_Organ-specific_omics_considerations
- Primary organ/tissue types: adipose (Laura & Ming); muscle (Ben, Xu, and Nathan); placenta (Paul)
- Outreach (Dec. 2023):
- If you’re interested in joining the Outreach Working Group, email help@sennetconsortium.org.
- Publication (12/4/23):
- Planning for a publication package. There is a publication package spreadsheet. Please fill this out with as much detail as possible
- Invitation to submit a perspective to Nature Review Genetics. Volunteers who want to contribute are welcome. Please contact Allie Pybas pybas002@umn.edu
- Senescence Biomarkers (12/4/23):
- SenGuiDe: SenNet guidelines for detecting senescent cells across tissues
- Revised version circulated this week for resubmission on Friday
- Please deposit validated antibodies to the WG table
- The benchmarking project team members will meet during the senescence biomarkers WG this month. December 6th from 2:30 pm – 3:30 pm EST. Meetings will rotate between the omics, imaging, benchmarking, and biomarker WG regular meetings.