bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2025–02–23
thirty-two papers selected by
Fawaz Alzaïd, Sorbonne Université
  1. Moving epigenetic inheritance into the space age: Evidence that 3D genome organization is required for the establishment of epigenetic memory.
  2. Meningeal Treg cells keep brain in balance.
  3. Insufficient evidence for natural selection associated with the Black Death.
  4. Putting the brakes on mitochondrial fusion to prevent escape of mitochondrial DNA.
  5. Fc-engineered large molecules targeting blood-brain barrier transferrin receptor and CD98hc have distinct central nervous system and peripheral biodistribution.
  6. A human gene makes mice squeak differently - did it contribute to language?
  7. How chronic stress warps decision-making.
  8. FGF21 keeps the thymus young.
  9. Dual regulation of mitochondrial fusion by Parkin-PINK1 and OMA1.
  10. Identification and characterization of cell niches in tissue from spatial omics data at single-cell resolution.
  11. How to bring health and happiness to your lab.
  12. What's next for the World Health Organization? US exit could reshape agency.
  13. AIF3 splicing variant elicits mitochondrial malfunction via the concurrent dysregulation of electron transport chain and glutathione-redox homeostasis.
  14. Single-molecule live-cell RNA imaging with CRISPR-Csm.
  15. Migraine is more than a headache - a radical rethink offers hope to one billion people.
  16. WNK1-dependent water influx is required for CD4+ T cell activation and T cell-dependent antibody responses.
  17. Integrating the environmental and genetic architectures of aging and mortality.
  18. Racial bias eliminated when ratings switch from five stars to thumbs up or down.
  19. AI tool diagnoses diabetes, HIV and COVID from a blood sample.
  20. An innate drive to save a life.
  21. How leading a postdoc network boosted my career prospects.
  22. Safeguard repressor locks hepatocyte identity and blocks liver cancer.
  23. Why retractions data could be a powerful tool for cleaning up science.
  24. CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association.
  25. Functional analysis of NLRP3 variants provides insight into inflammasome regulation.
  26. Snapshots of acyl carrier protein shuttling in human fatty acid synthase.
  27. Activity-based sensing reveals elevated labile copper promotes liver aging via hepatic ALDH1A1 depletion.
  28. Here's how to bag a hefty research prize to turbocharge innovation.
  29. Evaluation of polygenic scores for hypertrophic cardiomyopathy in the general population and across clinical settings.
  30. DNA methylation differences between cord and adult white blood cells reflect postnatal immune cell maturation.
  31. Clinical Research and Public Health in the JCI.
  32. Disease diagnostics using machine learning of B cell and T cell receptor sequences.
  1. Mol Cell. 2025 Feb 20. pii: S1097-2765(25)00100-5. [Epub ahead of print]85(4): 667-669
    Moving epigenetic inheritance into the space age: Evidence that 3D genome organization is required for the establishment of epigenetic memory.
    Jessica J Hawes, Alyson Ashe.
      In this issue, Fitz-James et al.1 use genetic manipulations to show that transient interchromosomal contacts between distant regulatory elements, mediated by the transcription factor GAF, can initiate transgenerational epigenetic inheritance in D. melanogaster.
    DOI:  https://doi.org/10.1016/j.molcel.2025.01.033
  2. Nat Rev Immunol. 2025 Feb 14.
    Meningeal Treg cells keep brain in balance.
    Alexandra Flemming.
      
    DOI:  https://doi.org/10.1038/s41577-025-01148-3
  3. Nature. 2025 Feb;638(8051): E19-E22
    Insufficient evidence for natural selection associated with the Black Death.
    Alison R Barton, Cindy G Santander, Pontus Skoglund, Ida Moltke, David Reich, Iain Mathieson.
      
    DOI:  https://doi.org/10.1038/s41586-024-08496-5
  4. Nature. 2025 Feb 19.
    Putting the brakes on mitochondrial fusion to prevent escape of mitochondrial DNA.
    Kate McArthur, Michael T Ryan.
      
    Keywords:  Cell biology
    DOI:  https://doi.org/10.1038/d41586-025-00303-z
  5. Nat Commun. 2025 Feb 20. 16(1): 1822
    Fc-engineered large molecules targeting blood-brain barrier transferrin receptor and CD98hc have distinct central nervous system and peripheral biodistribution.
    Nathalie Khoury, Michelle E Pizzo, Claire B Discenza, David Joy, David Tatarakis, Mihail Ivilinov Todorov, Moritz Negwer, Connie Ha, Gabrielly L De Melo, Lily Sarrafha, Matthew J Simon, Darren Chan, Roni Chau, Kylie S Chew, Johann Chow, Allisa Clemens, Yaneth Robles-Colmenares, Jason C Dugas, Joseph Duque, Doris Kaltenecker, Holly Kane, Amy Leung, Edwin Lozano, Arash Moshkforoush, Elysia Roche, Thomas Sandmann, Mabel Tong, Kaitlin Xa, Yinhan Zhou, Joseph W Lewcock, Ali Ertürk, Robert G Thorne, Meredith E K Calvert, Y Joy Yu Zuchero.
      Blood brain barrier-crossing molecules targeting transferrin receptor (TfR) and CD98 heavy chain (CD98hc) are widely reported to promote enhanced brain delivery of therapeutics. Here, we provide a comprehensive and unbiased biodistribution characterization of TfR and CD98hc antibody transport vehicles (ATVTfR and ATVCD98hc) compared to control IgG. Mouse whole-body tissue clearing reveals distinct organ localization for each molecule. In the brain, ATVTfR and ATVCD98hc achieve enhanced exposure and parenchymal distribution even when brain exposures are matched between ATV and control IgG in bulk tissue. Using a combination of cell sorting and single-cell RNAseq, we reveal that control IgG is nearly absent from parenchymal cells and is distributed primarily to brain perivascular and leptomeningeal cells. In contrast, ATVTfR and ATVCD98hc exhibit broad and unique parenchymal cell-type distribution. Finally, we profile in detail brain region-specific biodistribution of ATVTfR in cynomolgus monkey brain and spinal cord. Taken together, this in-depth multiscale characterization will guide platform selection for therapeutic targets of interest.
    DOI:  https://doi.org/10.1038/s41467-025-57108-x
  6. Nature. 2025 Feb 18.
    A human gene makes mice squeak differently - did it contribute to language?
    Ewen Callaway.
      
    Keywords:  Genetics; Language
    DOI:  https://doi.org/10.1038/d41586-025-00518-0
  7. Nature. 2025 Feb 19.
    How chronic stress warps decision-making.
    Traci Watson.
      
    Keywords:  Brain; Medical research; Neuroscience
    DOI:  https://doi.org/10.1038/d41586-025-00502-8
  8. Nat Aging. 2025 Feb 19.
    FGF21 keeps the thymus young.
    Yousuke Takahama.
      
    DOI:  https://doi.org/10.1038/s43587-025-00814-4
  9. Nature. 2025 Feb 19.
    Dual regulation of mitochondrial fusion by Parkin-PINK1 and OMA1.
    Tatsuya Yamada, Arisa Ikeda, Daisuke Murata, Hu Wang, Cissy Zhang, Pratik Khare, Yoshihiro Adachi, Fumiya Ito, Pedro M Quirós, Seth Blackshaw, Carlos López-Otín, Thomas Langer, David C Chan, Anne Le, Valina L Dawson, Ted M Dawson, Miho Iijima, Hiromi Sesaki.
      Mitochondrial stress pathways protect mitochondrial health from cellular insults1-8. However, their role under physiological conditions is largely unknown. Here, using 18 single, double and triple whole-body and tissue-specific knockout and mutant mice, along with systematic mitochondrial morphology analysis, untargeted metabolomics and RNA sequencing, we discovered that the synergy between two stress-responsive systems-the ubiquitin E3 ligase Parkin and the metalloprotease OMA1-safeguards mitochondrial structure and genome by mitochondrial fusion, mediated by the outer membrane GTPase MFN1 and the inner membrane GTPase OPA1. Whereas the individual loss of Parkin or OMA1 does not affect mitochondrial integrity, their combined loss results in small body size, low locomotor activity, premature death, mitochondrial abnormalities and innate immune responses. Thus, our data show that Parkin and OMA1 maintain a dual regulatory mechanism that controls mitochondrial fusion at the two membranes, even in the absence of extrinsic stress.
    DOI:  https://doi.org/10.1038/s41586-025-08590-2
  10. Nat Commun. 2025 Feb 16. 16(1): 1693
    Identification and characterization of cell niches in tissue from spatial omics data at single-cell resolution.
    Jingyang Qian, Xin Shao, Hudong Bao, Yin Fang, Wenbo Guo, Chengyu Li, Anyao Li, Hua Hua, Xiaohui Fan.
      Deciphering the features, structure, and functions of the cell niche in tissues remains a major challenge. Here, we present scNiche, a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution. We benchmark scNiche with both simulated and biological datasets, and demonstrate that scNiche can effectively and robustly identify cell niches while outperforming other existing methods. In spatial proteomics data from human triple-negative breast cancer, scNiche reveals the influence of the microenvironment on cellular phenotypes, and further dissects patient-specific niches with distinct cellular compositions or phenotypic characteristics. By analyzing mouse liver spatial transcriptomics data across normal and early-onset liver failure donors, scNiche uncovers disease-specific liver injury niches, and further delineates the niche remodeling from normal liver to liver failure. Overall, scNiche enables decoding the cellular microenvironment in tissues from single-cell spatial omics data.
    DOI:  https://doi.org/10.1038/s41467-025-57029-9
  11. Nature. 2025 Feb 21.
    How to bring health and happiness to your lab.
    Adam Levy.
      
    Keywords:  Careers; Lab life; Psychiatric disorders
    DOI:  https://doi.org/10.1038/d41586-025-00538-w
  12. Nature. 2025 Feb 19.
    What's next for the World Health Organization? US exit could reshape agency.
    David Adam.
      
    Keywords:  Policy; Public health
    DOI:  https://doi.org/10.1038/d41586-025-00449-w
  13. Nat Commun. 2025 Feb 20. 16(1): 1804
    AIF3 splicing variant elicits mitochondrial malfunction via the concurrent dysregulation of electron transport chain and glutathione-redox homeostasis.
    Mi Zhou, Shuiqiao Liu, Yanan Wang, Bo Zhang, Ming Zhu, Jennifer E Wang, Veena Rajaram, Yisheng Fang, Weibo Luo, Yingfei Wang.
      Genetic mutations in apoptosis-inducing factor (AIF) have a strong association with mitochondrial disorders; however, little is known about the aberrant splicing variants in affected patients and how these variants contribute to mitochondrial dysfunction and brain development defects. We identified pathologic AIF3/AIF3-like splicing variants in postmortem brain tissues of pediatric individuals with mitochondrial disorders. Mutations in AIFM1 exon-2/3 increase splicing risks. AIF3-splicing disrupts mitochondrial complexes, membrane potential, and respiration, causing brain development defects. Mechanistically, AIF is a mammalian NAD(P)H dehydrogenase and possesses glutathione reductase activity controlling respiratory chain functions and glutathione regeneration. Conversely, AIF3, lacking these activities, disassembles mitochondrial complexes, increases ROS generation, and simultaneously hinders antioxidant defense. Expression of NADH dehydrogenase NDI1 restores mitochondrial functions partially and protects neurons in AIF3-splicing mice. Our findings unveil an underrated role of AIF as a mammalian mitochondrial complex-I alternative NAD(P)H dehydrogenase and provide insights into pathologic AIF-variants in mitochondrial disorders and brain development.
    DOI:  https://doi.org/10.1038/s41467-025-57081-5
  14. Nat Biotechnol. 2025 Feb 18.
    Single-molecule live-cell RNA imaging with CRISPR-Csm.
    Chenglong Xia, David Colognori, Xueyang Stephen Jiang, Ke Xu, Jennifer A Doudna.
      Understanding the diverse dynamic behaviors of individual RNA molecules in single cells requires visualizing them at high resolution in real time. However, single-molecule live-cell imaging of unmodified endogenous RNA has not yet been achieved in a generalizable manner. Here, we present single-molecule live-cell fluorescence in situ hybridization (smLiveFISH), a robust approach that combines the programmable RNA-guided, RNA-targeting CRISPR-Csm complex with multiplexed guide RNAs for direct and efficient visualization of single RNA molecules in a range of cell types, including primary cells. Using smLiveFISH, we track individual native NOTCH2 and MAP1B transcripts in living cells and identify two distinct localization mechanisms including the cotranslational translocation of NOTCH2 mRNA at the endoplasmic reticulum and directional transport of MAP1B mRNA toward the cell periphery. This method has the potential to unlock principles governing the spatiotemporal organization of native transcripts in health and disease.
    DOI:  https://doi.org/10.1038/s41587-024-02540-5
  15. Nature. 2025 Feb;638(8051): 600-602
    Migraine is more than a headache - a radical rethink offers hope to one billion people.
    Fred Schwaller.
      
    Keywords:  Brain; Drug discovery; Medical research
    DOI:  https://doi.org/10.1038/d41586-025-00456-x
  16. Nat Commun. 2025 Feb 21. 16(1): 1857
    WNK1-dependent water influx is required for CD4+ T cell activation and T cell-dependent antibody responses.
    Joshua Biggs O'May, Lesley Vanes, Leonard L de Boer, David A Lewis, Harald Hartweger, Simone Kunzelmann, Darryl Hayward, Miriam Llorian, Robert Köchl, Victor L J Tybulewicz.
      Signaling from the T cell antigen receptor (TCR) on CD4+ T cells plays a critical role in adaptive immune responses by inducing T cell activation, proliferation, and differentiation. Here we demonstrate that WNK1, a kinase implicated in osmoregulation in the kidney, is required in T cells to support T-dependent antibody responses. We show that the canonical WNK1-OXSR1-STK39 kinase signaling pathway is required for TCR signaling in CD4+ T cells, their subsequent entry into the cell cycle, and suppression of the ATR-mediated G2/M cell cycle checkpoint. We show that the WNK1 pathway regulates ion influx leading to water influx, potentially through AQP3, and that water influx is required for TCR-induced signaling and cell cycle entry. Thus, TCR signaling via WNK1, OXSR1, STK39 and AQP3 leads to water entry that is essential for CD4+ T cell proliferation and hence T cell-dependent antibody responses.
    DOI:  https://doi.org/10.1038/s41467-025-56778-x
  17. Nat Med. 2025 Feb 19.
    Integrating the environmental and genetic architectures of aging and mortality.
    M Austin Argentieri, Najaf Amin, Alejo J Nevado-Holgado, William Sproviero, Jennifer A Collister, Sarai M Keestra, Midas M Kuilman, Bigina N R Ginos, Mohsen Ghanbari, Aiden Doherty, David J Hunter, Alexandra Alvergne, Cornelia M van Duijn.
      Both environmental exposures and genetics are known to play important roles in shaping human aging. Here we aimed to quantify the relative contributions of environment (referred to as the exposome) and genetics to aging and premature mortality. To systematically identify environmental exposures associated with aging in the UK Biobank, we first conducted an exposome-wide analysis of all-cause mortality (n = 492,567) and then assessed the associations of these exposures with a proteomic age clock (n = 45,441), identifying 25 independent exposures associated with mortality and proteomic aging. These exposures were also associated with incident age-related multimorbidity, aging biomarkers and major disease risk factors. Compared with information on age and sex, polygenic risk scores for 22 major diseases explained less than 2 percentage points of additional mortality variation, whereas the exposome explained an additional 17 percentage points. Polygenic risk explained a greater proportion of variation (10.3-26.2%) compared with the exposome for incidence of dementias and breast, prostate and colorectal cancers, whereas the exposome explained a greater proportion of variation (5.5-49.4%) compared with polygenic risk for incidence of diseases of the lung, heart and liver. Our findings provide a comprehensive map of the contributions of environment and genetics to mortality and incidence of common age-related diseases, suggesting that the exposome shapes distinct patterns of disease and mortality risk, irrespective of polygenic disease risk.
    DOI:  https://doi.org/10.1038/s41591-024-03483-9
  18. Nature. 2025 Feb 19.
    Racial bias eliminated when ratings switch from five stars to thumbs up or down.
    Lauren Rivera.
      
    Keywords:  Human behaviour; Society; Sociology
    DOI:  https://doi.org/10.1038/d41586-025-00304-y
  19. Nature. 2025 Feb 20.
    AI tool diagnoses diabetes, HIV and COVID from a blood sample.
    Miryam Naddaf.
      
    Keywords:  Diseases; Immunology; Machine learning
    DOI:  https://doi.org/10.1038/d41586-025-00528-y
  20. Science. 2025 Feb 21. 387(6736): 827-828
    An innate drive to save a life.
    William M Sheeran, Zoe R Donaldson.
      In mice, two brain regions drive the impulse to revive an unconscious companion.
    DOI:  https://doi.org/10.1126/science.adv3731
  21. Nature. 2025 Feb 20.
    How leading a postdoc network boosted my career prospects.
    Tracy Wietecha.
      
    Keywords:  Careers; Education; Institutions
    DOI:  https://doi.org/10.1038/d41586-025-00207-y
  22. Nat Genet. 2025 Feb 19.
    Safeguard repressor locks hepatocyte identity and blocks liver cancer.
      
    DOI:  https://doi.org/10.1038/s41588-025-02082-9
  23. Nature. 2025 Feb;638(8051): 581
    Why retractions data could be a powerful tool for cleaning up science.
      
    Keywords:  Authorship; Ethics; Institutions; Policy; Publishing
    DOI:  https://doi.org/10.1038/d41586-025-00509-1
  24. Nat Struct Mol Biol. 2025 Feb 21.
    CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association.
    Ruofan Yu, Shelby Roseman, Allison P Siegenfeld, Zachary Gardner, Son C Nguyen, Khoa A Tran, Eric F Joyce, Rajan Jain, Brian B Liau, Ian D Krantz, Katherine A Alexander, Shelley L Berger.
      Recent findings indicate that nuclear speckles, a distinct type of nuclear body, interact with certain chromatin regions in a ground state. Here, we report that the chromatin structural factors CTCF and cohesin are required for full ground-state association between DNA and nuclear speckles. We identified a putative speckle-targeting motif (STM) within cohesin subunit RAD21 and demonstrated that the STM is required for chromatin-nuclear speckle association, disruption of which also impaired induction of speckle-associated genes. Depletion of the cohesin-releasing factor WAPL, which stabilizes cohesin on chromatin, resulted in reinforcement of DNA-speckle contacts and enhanced inducibility of speckle-associated genes. Additionally, we observed disruption of chromatin-nuclear speckle association in patient-derived cells with Cornelia de Lange syndrome, a congenital neurodevelopmental disorder involving defective cohesin pathways. In summary, our findings reveal a mechanism for establishing the ground state of chromatin-speckle association and promoting gene inducibility, with relevance to human disease.
    DOI:  https://doi.org/10.1038/s41594-024-01465-6
  25. Nat Immunol. 2025 Feb 20.
    Functional analysis of NLRP3 variants provides insight into inflammasome regulation.
    Bénédicte F Py.
      
    DOI:  https://doi.org/10.1038/s41590-025-02093-y
  26. Nature. 2025 Feb 20.
    Snapshots of acyl carrier protein shuttling in human fatty acid synthase.
    Kollin Schultz, Pedro Costa-Pinheiro, Lauren Gardner, Laura V Pinheiro, Julio Ramirez-Solis, Sarah M Gardner, Kathryn E Wellen, Ronen Marmorstein.
      The mammalian fatty acid synthase (FASN) enzyme is a dynamic multienzyme that belongs to the megasynthase family. In mammals, a single gene encodes six catalytically active domains and a flexibly tethered acyl carrier protein (ACP) domain that shuttles intermediates between active sites for fatty acid biosynthesis1. FASN is an essential enzyme in mammalian development through the role that fatty acids have in membrane formation, energy storage, cell signalling and protein modifications. Thus, FASN is a promising target for treatment of a large variety of diseases including cancer, metabolic dysfunction-associated fatty liver disease, and viral and parasite infections2,3. The multi-faceted mechanism of FASN and the dynamic nature of the protein, in particular of the ACP, have made it challenging to understand at the molecular level. Here we report cryo-electron microscopy structures of human FASN in a multitude of conformational states with NADPH and NADP+ plus acetoacetyl-CoA present, including structures with the ACP stalled at the dehydratase (DH) and enoyl-reductase (ER) domains. We show that FASN activity in vitro and de novo lipogenesis in cells is inhibited by mutations at the ACP-DH and ACP-ER interfaces. Together, these studies provide new molecular insights into the dynamic nature of FASN and the ACP shuttling mechanism, with implications for developing improved FASN-targeted therapeutics.
    DOI:  https://doi.org/10.1038/s41586-025-08587-x
  27. Nat Commun. 2025 Feb 20. 16(1): 1794
    Activity-based sensing reveals elevated labile copper promotes liver aging via hepatic ALDH1A1 depletion.
    Zhenxiang Zhao, Melissa Y Lucero, Shengzhang Su, Eric J Chaney, Jiajie Jessica Xu, Michael Myszka, Jefferson Chan.
      Oxidative stress plays a key role in aging and related diseases, including neurodegeneration, cancer, and organ failure. Copper (Cu), a redox-active metal ion, generates reactive oxygen species (ROS), and its dysregulation contributes to aging. Here, we develop activity-based imaging probes for the sensitive detection of Cu(I) and show that labile hepatic Cu activity increases with age, paralleling a decline in ALDH1A1 activity, a protective hepatic enzyme. We also observe an age-related decrease in hepatic glutathione (GSH) activity through noninvasive photoacoustic imaging. Using these probes, we perform longitudinal studies in aged mice treated with ATN-224, a Cu chelator, and demonstrate that this treatment improves Cu homeostasis and preserves ALDH1A1 activity. Our findings uncover a direct link between Cu dysregulation and aging, providing insights into its role and offering a therapeutic strategy to mitigate its effects.
    DOI:  https://doi.org/10.1038/s41467-025-56585-4
  28. Nature. 2025 Feb;638(8051): 845-847
    Here's how to bag a hefty research prize to turbocharge innovation.
    Rachel Brazil.
      
    Keywords:  Careers; Funding; Scientific community; Society
    DOI:  https://doi.org/10.1038/d41586-025-00461-0
  29. Nat Genet. 2025 Feb 18.
    Evaluation of polygenic scores for hypertrophic cardiomyopathy in the general population and across clinical settings.
    HCM GWAS Collaborators
      Hypertrophic cardiomyopathy (HCM) is an important cause of morbidity and mortality, with pathogenic variants found in about a third of cases. Large-scale genome-wide association studies (GWAS) demonstrate that common genetic variation contributes to HCM risk. Here we derive polygenic scores (PGS) from HCM GWAS and genetically correlated traits and test their performance in the UK Biobank, 100,000 Genomes Project, and clinical cohorts. We show that higher PGS significantly increases the risk of HCM in the general population, particularly among pathogenic variant carriers, where HCM penetrance differs 10-fold between those in the highest and lowest PGS quintiles. Among relatives of HCM probands, PGS stratifies risks of developing HCM and adverse outcomes. Finally, among HCM cases, PGS strongly predicts the risk of adverse outcomes and death. These findings support the broad utility of PGS across clinical settings, enabling tailored screening and surveillance and stratification of risk of adverse outcomes.
    DOI:  https://doi.org/10.1038/s41588-025-02094-5
  30. Commun Biol. 2025 Feb 14. 8(1): 237
    DNA methylation differences between cord and adult white blood cells reflect postnatal immune cell maturation.
    Meaghan J Jones, Chaini Konwar, Rebecca Asiimwe, Louie Dinh, Hamid Reza Razzaghian, Olivia de Goede, Julia L MacIsaac, Alexander M Morin, Kurt P Kolsun, Kristina Gervin, Robert Lyle, Raymond T Ng, Devin C Koestler, Janine F Felix, Pascal M Lavoie, Wendy P Robinson, Sara Mostafavi, Michael S Kobor.
      Epigenetic modifications such as DNA methylation are both cell type and developmental age specific. Here, we show that the immunological maturation of blood cell types influences DNA methylation changes from naive cord blood to fully functional adult blood. Lymphoid cells in adult blood showed more variability than in cord blood suggesting an antigen-dependent maturation of DNA methylation in lymphoid cells throughout the lifespan. Fewer DNA methylation changes between cord and adult blood were observed in myeloid cells, particularly in monocytes, which demonstrated the least number of DNA methylation changes between cord and adult blood. We also noted differences in epigenetic ages by immune cell types within the same individuals, specifically in cord blood where monocytes were epigenetically oldest compared to the other cell types. In addition, we provide a publicly available resource to the community as an R Shiny web application to interactively explore epigenetic patterns between naive cord white blood cells and fully functional adult white blood cells for six immune cell types.
    DOI:  https://doi.org/10.1038/s42003-025-07661-4
  31. J Clin Invest. 2025 Feb 17. pii: e190119. [Epub ahead of print]135(4):
    Clinical Research and Public Health in the JCI.
    Elizabeth M McNally.
      
    DOI:  https://doi.org/10.1172/JCI190119
  32. Science. 2025 Feb 21. 387(6736): eadp2407
    Disease diagnostics using machine learning of B cell and T cell receptor sequences.
    Maxim E Zaslavsky, Erin Craig, Jackson K Michuda, Nidhi Sehgal, Nikhil Ram-Mohan, Ji-Yeun Lee, Khoa D Nguyen, Ramona A Hoh, Tho D Pham, Katharina Röltgen, Brandon Lam, Ella S Parsons, Susan R Macwana, Wade DeJager, Elizabeth M Drapeau, Krishna M Roskin, Charlotte Cunningham-Rundles, M Anthony Moody, Barton F Haynes, Jason D Goldman, James R Heath, R Sharon Chinthrajah, Kari C Nadeau, Benjamin A Pinsky, Catherine A Blish, Scott E Hensley, Kent Jensen, Everett Meyer, Imelda Balboni, Paul J Utz, Joan T Merrill, Joel M Guthridge, Judith A James, Samuel Yang, Robert Tibshirani, Anshul Kundaje, Scott D Boyd.
      Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system's own record of antigen exposures encoded by receptors on B cells and T cells. We analyzed immune receptor datasets from 593 individuals to develop MAchine Learning for Immunological Diagnosis, an interpretive framework to screen for multiple illnesses simultaneously or precisely test for one condition. This approach detects specific infections, autoimmune disorders, vaccine responses, and disease severity differences. Human-interpretable features of the model recapitulate known immune responses to severe acute respiratory syndrome coronavirus 2, influenza, and human immunodeficiency virus, highlight antigen-specific receptors, and reveal distinct characteristics of systemic lupus erythematosus and type-1 diabetes autoreactivity. This analysis framework has broad potential for scientific and clinical interpretation of immune responses.
    DOI:  https://doi.org/10.1126/science.adp2407
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