Plus: Applications open for the next round of Investigators at New York Biohub

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Nexus - News from Chan Zuckerberg Biohub Network
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Getting ahead of disease with protein monitoring


What if we didn’t have to wait for patients to suffer symptoms before intervening to treat disease? That’s the vision outlined in a new Science review co-authored by Chicago Biohub President Shana Kelley (pictured above), which explores the potential of continuous protein monitoring to revolutionize the way we approach health care. Inspired, in part, by the success of glucose-monitoring devices that have dramatically improved diabetes care, Kelley and her colleagues imagine a future in which implantable or wearable devices keep watch over key proteins in our bodies, and sound the alarm when changing concentrations of particular proteins indicate something might be going wrong, allowing patients to get help before an illness has done noticeable damage. The review explores how advances in areas like biochemical sensing, bioelectronics, and machine learning are helping create a path towards realizing this vision and highlights remaining barriers that need to be addressed. To hear Kelley discuss the concept, check out her recent appearances on the podcasts “Behind the Breakthroughs” and “Ground Truths.”

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Investigator Spotlight

CZ Biohub SF Investigator Lucy Shapiro

Meet Lucy Shapiro

 

Last month, CZ Biohub SF Investigator Lucy Shapiro was awarded the 2025 Lasker-Koshland Award for Special Achievement in Medical Science; the Lasker Awards are widely considered the nation’s most prestigious honors for biomedical and clinical research. During her 55-year career in biomedical sciences, Shapiro’s work has revolutionized our understanding of bacterial cell organization and demonstrated how linear DNA can encode three-dimensional regulatory mechanisms. Her collaborative approach to research helped lay the foundation for the field of systems biology, an interdisciplinary area that applies computational and mathematical analysis to understanding biological systems. Shapiro was also an early architect of the San Francisco Biohub, the first female department chair at three universities, an advisor to the White House on issues from bioterrorism to pandemic preparedness, and a mentor to more than 70 students and postdocs. 

 

Learn more.

News & Events

CZI’s new benchmarking suite provides the emerging field of virtual cell modeling with the capabilities to readily assess both biological relevance and technical performance.

Accelerating AI in biology with community-driven benchmarks

 

In collaboration with industry partners and a community working group, CZI released its new benchmarking suite, the first suite of tools to enable robust and broad task-based benchmarking to drive the development of virtual cell models. This standardized tool kit provides model developers and biologists with the capabilities to readily assess both the biological relevance and technical performance of these models, reducing what previously took developers weeks of tedious and error-prone manual work to a matter of hours.

 

Read more on our blog.
CZ_Biohub_NewYork_InvestigatorAward_2

Apply now: NY Biohub Investigator Award Program

 

Designed to identify and support visionary scientists to pursue their most innovative and high-impact projects that align with the organization’s mission, the Investigator Award Program supports research focused on deciphering the molecular language of immune cells, enabling these cells to be deployed for disease detection, prevention, and treatment. To be eligible, applicants must hold a faculty position at one of the New York Biohub’s partnering institutions (Columbia University, The Rockefeller University, or Yale University).

 

Learn more and apply.

Reminder: One Month Left to Apply for RFAs Focused on Immune System

 

These funding opportunities for two-year research projects are in the areas of synthetic biology for immunology and spatial omics for instrumented tissues. PIs from a range of institutions are eligible, and early-career researchers are encouraged to apply! The deadline for applications is Nov. 13. 

 

Find details here for the synthetic biology RFA and here for the spatial omics RFA.

life / science

STORIES FROM THE CZ BIOHUB NETWORK

Sjoukje van der Stegen (center) speaks about immune cell strategies at the 2025 Spring CZI Affiliate Symposium meeting in New York. Credit: Angelina Katsanis.

A deep look at the immune system

 

Sjoukje van der Stegen (pictured above, center) imagines a world where immunotherapy is as accessible as any prescription drug. As lead of the Immune Cell Engineering and Development Platform at the New York Biohub, she is working to generate immune cells from induced pluripotent stem cells, or iPSCs, which can be created from skin or blood cells. With iPSCs it’s possible to produce large numbers of immune cells of many different varieties and to engineer them so they don’t provoke rejection by patients’ bodies. This would allow treatments to be produced en masse for “off-the-shelf” use, instead of needing to be personalized for each patient.

 

Read more.

In the News

TIME
Why AI companies are racing to build a virtual human cell

Virtual cells can accelerate drug discovery, advance understanding of cancer, and even provide fundamental new insights to scientists. In a piece covering efforts of several organizations to build digital representations of a cell, including Google’s DeepMind, Arc Institute, and Wellcome Sanger Institute, journalist Veronique Greenwood quotes Theo Karaletsos, senior director of AI at CZI, and Stephen Quake, the former head of science at CZI, on the promise of AI in advancing these efforts.

 

Read more.

      MIT Technology Review
      How healthy am I? My immunome knows the score.

      In formulating the New York Biohub’s goal to bioengineer immune cells for the early detection and treatment of disease, Yale systems immunologist John Tsang was an early contributor, serving on the steering committee. Now, as a New York Biohub Lead Investigator and Director of the Yale Center for Systems and Engineering Immunology, he’s leading an ambitious effort to decipher the human immunome, a collection of the trillions of cells, proteins, and other biomolecules that serve to keep us healthy. The Human Immunome Project aims to build the largest ever dataset of human immunological profiles, ultimately enabling researchers to build predictive models of the immune system.

       

      Read more.

          UCSF News Center
          Why does female fertility decline so fast? The key is the ovary

          A comprehensive study combining a new imaging technique with single-cell sequencing published in Science reveals a new understanding of how ovaries in mice and humans age. Led by Diana Laird, a San Francisco Biohub Investigator and UCSF professor of Obstetrics, Gynecology & Reproductive Sciences, working with the SF Biohub Genomics Platform led by Norma Neff, the team made a number of discoveries about the ovarian environment, including finding an unexpected cell type – glial cells, which are typically associated with nerves. This suggests a new role for the nervous system in ovarian health. The study could be key to developing strategies for extended fertility and healthier aging.

           

          Read more. This work was also covered in The Scientist and New Scientist.

              Stanford Report 
              Soft bioelectronic fiber can track hundreds of biological events simultaneously

              “Soft” bioelectronic implants are much in demand for both research and clinical applications. Flexible, minimally invasive, and biocompatible, these devices could act as sensors to precisely monitor activity in tissues. Now, by tightly rolling up integrated circuits into a sort of bioelectronic jelly roll, San Francisco Biohub Investigator Zhenan Bao and colleagues have created “Spiral-NeuroString,” an innovative device that packs a pile of functions into an implant the width of a human hair. NeuroString, which was described last month in Nature, incorporates hundreds to thousands of channels for powerful multimodal recording capabilities and can deliver electrical stimuli, drugs, and even light stimulation.

               

              Read more.

                  University of Illinois Urbana-Champaign News
                  Long-term alcohol use suspends liver cells in limbo, preventing regeneration

                  To support the liver’s remarkable ability to regenerate, mature liver cells undergo shifts in gene expression and revert to fetal-like states capable of multiplying into new cells before once again resuming their normal, mature roles. Now, a new study co-led by Chicago Biohub Investigator Auinash Kalsotra shows that long-term alcohol use can cause liver cells to get stuck between these two states — leaving them neither capable of regenerating nor doing their normal jobs in the liver. This state of limbo occurs because chronic inflammation disrupts RNA splicing, which, in turn, prevents key proteins from reaching their proper locations in the cell. 

                   

                  Read more.

                      The Scientist
                      Mass spectrometry reveals protein subcellular localization

                      To carry out their roles effectively, a cell’s proteins must be in the right place at the right time. New tools that allow scientists to map each protein's location within a cell are therefore critical to understand how cells respond to changing conditions. In a recent interview with The Scientist, Josh Elias, Mass Spectrometry Platform Leader at the SF Biohub, describes how Biohub researchers are using mass spectrometry to pinpoint where proteins are positioned within cells and track how those positions shift under different conditions, offering new clues into how cells change in circumstances of stress, infection, or other challenges. 

                       

                      Read more and go here to see a video on the Organelle Profiling tool. 

                          Biohub Buzz

                          • If you are in the Bay Area, check out the Bay Area Science Festival on Oct. 25! It’s Northern California’s largest free science event, featuring over 100 engaging demos, games, talks, and more! Visit the Biohub booth to learn about zebrafish and organelles!
                          • Last month SF Biohub’s Rapid Response team conducted an intensive, two-week long sequencing workshop at the Rwanda Military Referral Teaching Hospital in Kigali, Rwanda. This week, the Biohub team is back in Kigali for the 2025 Genomic Frontiers symposium, where President Emeritus Joe DeRisi will discuss real-world applications of genomic technology in tackling both infectious and non-communicable diseases. 
                          • If you’ll be in Toronto for the November meeting of the American Society of Tropical Medicine & Hygiene, make sure to stop by the Biohub booth, where we’ll be showcasing cool tools, like Remoscope, an automated label-free malaria detection instrument, and Well-Lit, a device that helps eliminate errors when pipetting samples from barcoded tubes into multi-well plates, and when transferring samples from one multi-well plate to another.

                          Select Recent Publications

                          Contributors listed in bold are or were affiliated with the CZ Biohub Network.

                          Royal Society of Chemistry   |   SEPTEMBER 26, 2025

                          Single-cell western blotting of cytoplasmic cytokeratin 8 proteoforms


                          Anna Fomitcheva Khartchenko, Trinh Lam, Amy E. Herr.

                          bioRxiv   |   SEPTEMBER 26, 2025

                          Complex assembly and activity states as multifaceted protein attributes explaining phenotypic variability


                          George Rosenberger, Peng Xue, Isabell Bludau, Claudia Martelli, Evan Williams, Ben C. Collins, Andrea Califano, Yansheng Liu, Ruedi Aebersold.

                          Nature Neuroscience   |   SEPTEMBER 17, 2025

                          Rapid learning of neural circuitry from holographic ensemble stimulation enabled by model-based compressed sensing


                          Marcus A. Triplett, Marta Gajowa, Benjamin Antin, Masato Sadahiro, Hillel Adesnik, Liam Paninski.

                          ACS Sensors   |   SEPTEMBER 16, 2025

                          Dual-chronoamperometry drift correction for electrochemical sensors


                          Kimberly T. Riordan, Kefan Yang, Ethan Brazelton, Mohammed Ali Eslami, Ashley Copenhaver, Fatemeh Esmaeili, Connor D. Flynn, Zhenwei Wu, Scott E. Isaacson, Dingran Chang, Maria D. Cabezas, Vuslat Juska, Jagotamoy Das, Edward H. Sargent, Shana O. Kelley.

                          Journal of Clinical Investigation   |   SEPTEMBER 16, 2025

                          Double-positive T cells form heterotypic clusters with circulating tumor cells to foster cancer metastasis


                          David Scholten, Lamiaa El-Shennawy, Yuzhi Jia, Youbin Zhang, Elizabeth Hyun, Carolina Reduzzi, Andrew D. Hoffmann, Hannah F. Almubarak, Fangjia Tong, Nurmaa K. Dashzeveg, Yuanfei Sun, Joshua R. Squires, Janice Lu, Leonidas C. Platanias, Clive H. Wasserfall, William J. Gradishar, Massimo Cristofanilli, Deyu Fang, Huiping Liu.

                          Nature Reviews Drug Discovery  I   SEPTEMBER 15, 2025

                          Microsystem technologies for accelerating the discovery and translation of immunotherapies

                           

                          Zongjie Wang, Claire Liu, Kangfu Chen, Joseph Song, Shana O. Kelley.

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                          The Chan Zuckerberg Biohub Network is a group of nonprofit research institutes that bring together physicians, scientists, and engineers with the goal of pursuing grand scientific challenges on a 10- to 15-year time horizon. These institutes partner with Chan Zuckerberg Science in its goal to understand the mysteries of the cell and how cells interact within systems. This collaboration will bring us closer to our mission to cure, prevent, or manage all disease by the end of the century. To learn more, visit www.czbiohub.org.

                           

                           

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