Continued commitment to all stages of the physician-scientist career path
This issue features a collection of Physician-Scientist Development articles that highlight the work, challenges, and goals faced along the physician-scientist career path. It is introduced by an Editorial from Oliver Eickelberg, Christopher S. Williams, and Kyu Y. Rhee. The cover image is a collage of drawings that were produced by children who were prompted to illustrate what comes to mind when they think of a physician-scientist. Illustrations were provided by Demetri Kitsios, Liam Snyder, Elizabeth Neal, and Jocelyn L. (clockwise from the top right).
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Editorial
Oliver Eickelberg, … , Christopher S. Williams, Kyu Y. Rhee Published April 8, 2025
Citation Information: JCI Insight. 2025;10(7):e193355. https://doi.org/10.1172/jci.insight.193355.
×Abstract
Authors
Oliver Eickelberg, Christopher S. Williams, Kyu Y. Rhee
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Physician-Scientist Development
Lawrence F. Brass, … , Aislinn Wallace, Myles H. Akabas Published March 4, 2025
Citation Information: JCI Insight. 2025;10(7):e184493. https://doi.org/10.1172/jci.insight.184493.
×Abstract
MD-PhD programs prepare physicians for research-focused careers. The challenge for admissions committees is to select from among their applicants those who will achieve this goal, becoming leaders in academic medicine and biomedical research. Although holistic practices are encouraged, the temptation remains to use metrics such as grade point average, Medical College Admission Test scores, and postbaccalaureate gap length, combined with race and ethnicity, age at college graduation, and sex to select whom to interview and admit. Here, we asked whether any of these metrics predict performance in training or career paths after graduation. Data were drawn from the National MD-PhD Program Outcomes Study with information on 4,659 alumni and 593 MD-PhD graduates of the Albert Einstein College of Medicine and the University of Pennsylvania. The Penn-Einstein dataset included admissions committee summative scores, attrition, and the number and impact of PhD publications. Output metrics included time to degree, eventual employment in workplaces consistent with MD-PhD training goals, and self-reported research effort. Data were analyzed using machine learning and multivariate linear regression. The results show that none of the applicant metrics, individually or collectively, predicted in-program performance, future research effort, or eventual workplace choices even when comparisons were limited to those in the top and bottom quintiles.
Authors
Lawrence F. Brass, Maurizio Tomaiuolo, Aislinn Wallace, Myles H. Akabas
Amara L. Plaza-Jennings, … , Robert Fallar, Valerie Parkas Published April 8, 2025
Citation Information: JCI Insight. 2025;10(7):e185839. https://doi.org/10.1172/jci.insight.185839.
×Abstract
MD-PhD programs provide interdisciplinary training in medicine and research. Undergraduate pre-health advisors (PHAs) play a critical role in counseling prospective applicants, yet there have been no studies to our knowledge of MD-PhD pre-health advising. Here we surveyed 280 PHAs from US colleges and universities using both qualitative and quantitative measures that assessed their real-world advising behaviors as well as standardized evaluation of 1 of 2 fictional MD-PhD applicants, identical except for gender. We identified 3 factors that influenced advising behaviors: experience advising MD-PhD applicants, attitudes toward MD-PhD programs, and gender bias. Those PHAs with less experience and who held negative attitudes toward MD-PhD programs were less likely to initiate discussions about MD-PhD programs with qualified applicants and less likely to recommend the fictional applicants apply to MD-PhD programs. Finally, there was subtle gender bias that favored the male applicant. PHAs face challenges in advising MD-PhD applicants because there are relatively few MD-PHD applicants overall and there is a lack of resources to guide them. Addressing these challenges by strengthening collaborations with PHAs and providing comprehensive information about the value of and applicant qualifications for MD-PhD programs is crucial to enhancing MD-PhD advising, mitigating effects of bias, and expanding the pool of qualified applicants.
Authors
Amara L. Plaza-Jennings, Christie B. Ryba, Jessica Tan, Jennifer E.L. Diaz, Grace E. Mosley, Talia H. Swartz, Margaret H. Baron, Robert Fallar, Valerie Parkas
Gary Koretzky Published April 8, 2025
Citation Information: JCI Insight. 2025;10(7):e192637. https://doi.org/10.1172/jci.insight.192637.
×Abstract
Efforts dating back to the 1950s have sought to formalize educating physician-scientists, individuals trained in both science and medicine and who devote the bulk of their professional time to investigative work. The return on investment has been huge, because, as a group, these individuals have made outsized contributions to advancing human health. However, efforts at supporting the physician-scientist career path have been accompanied by repeated concerns regarding the lack of intentional support needed to sustain trainees and faculty. This Perspective reviews the history of the career path, highlighting both opportunities and challenges, and offers seven recommendations with the potential to both promote its vitally and reinvigorate its future at all its stages.
Authors
Gary Koretzky
Kyu Y. Rhee, … , ASCI Research Pathways Working Group, Christopher S. Williams Published April 8, 2025
Citation Information: JCI Insight. 2025;10(7):e192689. https://doi.org/10.1172/jci.insight.192689.
×Abstract
The Alliance for Academic Internal Medicine (AAIM) first convened a workshop in 2015 that brought a small group of internal medicine program directors together who recognized the growing success of early-phase physician-scientist training programs but the unclear path afterward for these trainees. The meeting subsequently evolved into what is now the annual American Society for Clinical Investigation/AAIM/Burroughs Wellcome Fund (ASCI/AAIM/BWF) Physician-Scientist Pathways Workshop, which continues to bring stakeholders together to discuss the obstacles to success that physician-scientists face at all stages of their careers. This perspective presents the history and goals of the workshop, with an emphasis on the most recent meeting in 2024, and looks ahead to the work that still needs to be done to ensure a robust physician-scientist workforce.
Authors
Kyu Y. Rhee, Charles W. Emala, Emily Jane Gallagher, Don C. Rockey, Patrick J. Hu, Jatin M. Vyas, Daniel P. Cook, Tiffany C. Scharschmidt, Olujimi A. Ajijola, ASCI Research Pathways Working Group, Christopher S. Williams
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Research Articles
Yanying Yang, … , Zhouli Cheng, Duojiao Wu Published March 5, 2025
Citation Information: JCI Insight. 2025;10(7):e174600. https://doi.org/10.1172/jci.insight.174600.
×Abstract
This study aimed to explore the potential correlation between the metabolic intermediate L-2-hydroxyglutarate (L-2-HG) and T cell exhaustion, as well as the underlying mechanisms involved. In this study, we investigated the presence of exhausted T (Tex) cells in patients under certain conditions: HIV infection, chronic leukemia, and hepatocellular carcinoma. To gain insights into the epigenetic signatures and transcriptome changes in Tex cells, we employed a combination of RNA-seq and ATAC-seq analyses. To evaluate the impact of L-2-HG on mitochondrial function, differentiation, and antitumor capacity of Tex cells, we utilized in vitro cell culture experiments and animal tumor models. We observed mitochondrial depolarization and metabolic dysfunction in Tex cells, accompanied by a significant reduction in L-2-HG levels. Moreover, altered epigenetic characteristics were observed in Tex cells, including a substantial increase in H3K27me3 abundance. Culturing Tex cells with L-2-HG demonstrated improved mitochondrial metabolism, reduced H3K27me3 abundance, and enhanced memory T cell differentiation. In a mouse melanoma tumor model, L-2-HG–treated CD8+ T cells for adoptive therapy led to significantly reduced tumor volume and significantly enhanced effector function of T cells. The study revealed that L-2-HG acted as an immune metabolite through epigenetic modifications of Tex cells.
Authors
Yanying Yang, Xiaoyan Li, Fangming Liu, Mingyue Ma, Ying Yang, Chengchao Ruan, Yan Lu, Xiaoyang Li, Xiangdong Wang, Yinghong Shi, Zheng Zhang, Hua Wang, Zhouli Cheng, Duojiao Wu
Alicia M. Soucy, … , Charles W. Frevert, Joseph P. Mizgerd Published February 25, 2025
Citation Information: JCI Insight. 2025;10(7):e177084. https://doi.org/10.1172/jci.insight.177084.
×Abstract
The role of mesenchymal cells during respiratory infection is not well defined, including whether, which, and how the different types of mesenchymal cells respond. We collected all mesenchymal cells from lung single-cell suspensions of mice that were naive (after receiving only saline vehicle), pneumonic (after intratracheal instillation of pneumococcus 24 hours previously), or resolved from infection (after nonlethal pneumococcal infections 6 weeks previously) and performed single-cell RNA sequencing. Cells clustered into 5 well-separated groups based on their transcriptomes: matrix fibroblasts, myofibroblasts, pericytes, smooth muscle cells, and mesothelial cells. Fibroblasts were the most abundant and could be further segregated into Pdgfra+Npnt+Ces1d+Col13a1+ alveolar fibroblasts and Cd9+Pi16+Sca1+Col14a1+ adventitial fibroblasts. The cells from naive and resolved groups overlapped in dimension reduction plots, suggesting the mesenchymal cells returned to baseline transcriptomes after resolution. During pneumonia, all mesenchymal cells responded with altered transcriptomes, revealing a core response that had been conserved across cell types as well as distinct mesenchymal cell type–specific responses. The different subsets of fibroblasts induced similar gene sets, but the alveolar fibroblasts responded more strongly than the adventitial fibroblasts. These data demonstrated diverse and specialized immune activities of lung mesenchymal cells during pneumonia.
Authors
Alicia M. Soucy, Jourdan E. Brune, Archana Jayaraman, Anukul T. Shenoy, Filiz T. Korkmaz, Neelou S. Etesami, Bradley E. Hiller, Ian M.C. Martin, Wesley N. Goltry, Catherine T. Ha, Nicholas A. Crossland, Joshua D. Campbell, Thomas G. Beach, Katrina E. Traber, Matthew R. Jones, Lee J. Quinton, Markus Bosmann, Charles W. Frevert, Joseph P. Mizgerd
Camilla Tondello, … , Richard A. Kroczek, Urs Christen Published February 27, 2025
Citation Information: JCI Insight. 2025;10(7):e178743. https://doi.org/10.1172/jci.insight.178743.
×Abstract
Type 1 diabetes (T1D) is precipitated by the autoimmune destruction of the insulin-producing β cells in the pancreatic islets of Langerhans. Chemokines have been identified as major conductors of islet infiltration by autoaggressive leukocytes, including antigen-presenting cells and islet autoantigen–specific T cells. We have previously generated a road map of gene expression in the islet microenvironment during T1D in a mouse model and found that most of the chemokine axes are chronically upregulated during T1D. The XCL1/XCR1 chemokine axis is of particular interest, since XCR1 is exclusively expressed on conventional DCs type 1 (cDC1) that excel by their high capacity for T cell activation. Here, we demonstrate that cDC1-expressing XCR1 are present in and around the islets of patients with T1D and of individuals with islet autoantibody positivity. Furthermore, we show that XCL1 plays an important role in the attraction of highly potent DCs expressing XCR1 to the islets in an inducible mouse model for T1D. XCL1-deficient mice display a diminished infiltration of XCR1+ cDC1 and, subsequently, a reduced magnitude and activity of islet autoantigen–specific T cells, resulting in a profound decrease in T1D incidence. Interference with the XCL1/XCR1 chemokine axis might constitute a novel therapy for T1D.
Authors
Camilla Tondello, Christine Bender, Gregory J. Golden, Deborah Puppe, Elisa Blickberndt, Monika Bayer, Giulia K. Buchmann, Josef Pfeilschifter, Malte Bachmann, Edith Hintermann, Ralf P. Brandes, Michael R. Betts, Richard A. Kroczek, Urs Christen
Jessica Day, … , Gordon S. Lynch, Ian P. Wicks Published March 4, 2025
Citation Information: JCI Insight. 2025;10(7):e179928. https://doi.org/10.1172/jci.insight.179928.
×Abstract
The deleterious consequences of chronic synovitis on cartilage, tendon, and bone in rheumatoid arthritis (RA) are well described. In contrast, its effects on periarticular skeletal muscle are under-studied. Furthermore, while TNF inhibition is an effective therapy for RA synovitis, it exacerbates fibrosis in muscle injury models. We aimed to investigate whether myositis and muscle fibrosis are features of inflammatory arthritis and evaluate whether targeted RA therapies influence these disease features. Periarticular muscle was analyzed in murine models of poly- and monoarticular inflammatory arthritis: serum transfer–induced arthritis, collagen-induced arthritis, K/BxN, and antigen-induced arthritis (AIA). Periarticular myositis and an increase in muscle fibroadipocyte progenitors (FAPs) were observed in all models, despite diverse arthritogenic mechanisms. Periarticular muscle fibrosis was observed from day 15 in AIA. Neither etanercept nor baricitinib suppressed periarticular myositis or subsequent fibrosis compared to vehicle, despite reducing arthritis. Notably, etanercept failed to prevent muscle fibrosis even when initiated early, but this was not linked to increased FAP survival or collagen production. Corroborating these data, radiographic and histological analyses revealed periarticular myositis in patients with RA. We conclude that periarticular myositis and fibrosis are under-recognized features of inflammatory arthritis. Targeted RA therapies may not prevent periarticular muscle sequelae, despite controlling arthritis.
Authors
Jessica Day, Cynthia Louis, Kristy Swiderski, Angus Stock, Huon Wong, Wentao Yao, Bonnia Liu, Suba Nadesapillai, Gordon S. Lynch, Ian P. Wicks
Emanuel Holm, … , Silvia Remeseiro, Andreas Hörnblad Published April 8, 2025
Citation Information: JCI Insight. 2025;10(7):e179990. https://doi.org/10.1172/jci.insight.179990.
×Abstract
Metabolic dysfunction–associated steatotic liver disease (MASLD) is the most common chronic liver disease worldwide for which there is only one approved treatment. Adenosine monophosphate–activated protein kinase (AMPK) is an interesting therapeutic target since it acts as a central regulator of cellular metabolism. Despite efforts to target AMPK, no direct activators have yet been approved for treatment of this disease. This study investigated the effect of the AMPK activator ATX-304 in a preclinical mouse model of progressive fatty liver disease. The data demonstrated that ATX-304 diminishes body fat mass, lowers blood cholesterol levels, and mitigates general liver steatosis and the development of liver fibrosis, but with pronounced local heterogeneities. The beneficial effects of ATX-304 treatment were accompanied by a shift in the liver metabolic program, including increased fatty acid oxidation, reduced lipid synthesis, as well as remodeling of cholesterol and lipid transport. We also observed variations in lipid distribution among liver lobes in response to ATX-304, and a shift in the zonal distribution of lipid droplets upon treatment. Taken together, our data suggested that ATX-304 holds promise as a potential treatment for MASLD.
Authors
Emanuel Holm, Isabeau Vermeulen, Saba Parween, Ana López-Pérez, Berta Cillero-Pastor, Michiel Vandenbosch, Silvia Remeseiro, Andreas Hörnblad
Susanne Rueger, … , Kathrin Held, Julia Roider Published April 8, 2025
Citation Information: JCI Insight. 2025;10(7):e180309. https://doi.org/10.1172/jci.insight.180309.
×Abstract
People living with HIV treated during acute infection are the group for whom achieving functional cure appears most viable. Follicular CD8+ T cells could contribute to HIV reservoir clearance by accessing B cell follicles through CXCR5 expression. This study examines peripheral follicular CD8+ T cells using flow cytometry, transcriptome analyses, and functional assays in people treated during acute (n = 37) and chronic (n = 18) infection, as well as in individuals naturally controlling HIV (n = 20) and living without HIV (n = 10). Our results reveal that early, as opposed to late, treatment initiation preserves antiviral effector functions of follicular CD8+ T cells, which are further enhanced by PD1 inhibition. We also identify a correlation between follicular CD8+ T cells and intact proviral HIV DNA levels in acute, but not chronic, infection. Longitudinal transcriptomic analysis of peripheral effector cells after 48 weeks of suppressive therapy indicated traits of recent antigen exposure, suggesting potential recirculation into lymphoid tissue. These findings underscore the pivotal role of follicular CD8+ T cells in anti-HIV responses and support investigating targeted cure strategies, such as anti-PD1 therapy, especially in individuals initiating treatment during acute infection.
Authors
Susanne Rueger, Eva Gruener, Danni Wang, Faiaz Shaik Abdool, Veronica Ober, Theresa Vallée, Renate Stirner, Raffaele Conca, Immanuel Andrä, Lisa Rogers, Robert Zahn, Elke Gersbacher, Joanna Eger, Ramona Pauli, Nils Postel, Christoph D. Spinner, Jörg J. Vehreschild, Melanie Stecher, Hans Nitschko, Josef Eberle, Johannes R. Bogner, Ulrich Seybold, Rika Draenert, Al Leslie, Henrik N. Kløverpris, Christof Geldmacher, Maximilian Muenchhoff, Kathrin Held, Julia Roider
×Abstract
Intervertebral disc degeneration (IDD) is associated with low back pain, a leading cause of disability worldwide. Fibrosis of nucleus pulposus (NP) is a principal component of IDD, featuring an accumulation of myofibroblast-like cells. Previous study indicates that matrix metalloproteinase 12 (MMP12) expression is upregulated in IDD, but its role remains largely unexplored. We here showed that TGF-β1 could promote myofibroblast-like differentiation of human NP cells along with an induction of MMP12 expression. Intriguingly, MMP12 knockdown not only ameliorated the myofibroblastic phenotype but also increased chondrogenic marker expression. Transcriptome analysis revealed that the MMP12-mediated acquisition of myofibroblast phenotype was coupled to processes related to fibroblast activation and osteogenesis and to pathways mediated by MAPK and Wnt signaling. Injury induced mouse IDD showed NP fibrosis with marked increase of collagen deposition and αSMA-expressing cells. In contrast, MMP12-KO mice exhibited largely reduced collagen I and III but increased collagen II and aggrecan deposition, indicating an inhibition of NP fibrosis along with an enhanced cartilaginous matrix remodeling. Consistently, an increase of SOX9+ and CNMD+ but decrease of αSMA+ NP cells was found in the KO. Altogether, our findings suggest a pivotal role of MMP12 in myofibroblast generation, thereby regulating NP fibrosis in IDD.
Authors
Yi Sun, Wai-Kit Tam, Manyu Zhu, Qiuji Lu, Mengqi Yu, Yuching Hsu, Peng Chen, Peng Zhang, Minmin Lyu, Yongcan Huang, Zhaomin Zheng, Xintao Zhang, Victor Y. Leung
Sebastian Steinhauser, … , Jonathan D. Brown, Christian Kolter Published February 25, 2025
Citation Information: JCI Insight. 2025;10(7):e182232. https://doi.org/10.1172/jci.insight.182232.
×Abstract
Metabolic dysfunction–associated steatotic liver disease (MASLD) — characterized by excess accumulation of fat in the liver — now affects one-third of the world’s population. As MASLD progresses, extracellular matrix components including collagen accumulate in the liver, causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply characterized cohort of patients spanning the full histopathologic spectrum of MASLD. CRISPR-based genetic KO of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation, we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of MASLD-associated liver fibrosis.
Authors
Sebastian Steinhauser, David Estoppey, Dennis P. Buehler, Yanhua Xiong, Nicolas Pizzato, Amandine Rietsch, Fabian Wu, Nelly Leroy, Tiffany Wunderlin, Isabelle Claerr, Philipp Tropberger, Miriam Müller, Alexandra Vissieres, Lindsay M. Davison, Eric Farber-Eger, Quinn S. Wells, Quanhu Sheng, Sebastian Bergling, Sophia Wild, Pierre Moulin, Jiancong Liang, Wayne J. English, Brandon Williams, Judith Knehr, Marc Altorfer, Alejandro Reyes, Johannes Voshol, Craig Mickanin, Dominic Hoepfner, Florian Nigsch, Mathias Frederiksen, Charles R. Flynn, Barna D. Fodor, Jonathan D. Brown, Christian Kolter
×Abstract
The sentinel lymph node (SLN) is the first lymph node encountered by a metastatic cancer cell and serves as a predictor of poor prognosis, as cases with clinically occult SLN metastases are classified as stage III with elevated rates of recurrence and diminished overall survival. However, the dynamics of immune infiltrates in SLNs remain poorly characterized. Here, using an unbiased cellular indexing of transcriptomes and epitopes by sequencing technique, we profiled 97,777 cells from SLN tissues obtained from patients with stages I/II and III cutaneous melanoma. We described the transcriptional programs of a multitude of T, B, and myeloid cell subtypes in SLNs. Based on the proportions of cell types, we determined that SLN subtypes stratified along a naive → activated axis; patients with a “high activated” signature score appeared to be undergoing a robust melanoma antigen–driven adaptive immune response and, thus, could be responsive to immunotherapy. Additionally, we identified transcriptomic signatures of SLN-infiltrating dendritic cell subsets that compromise antitumor immune responses. Our analyses provide valuable insights into tumor-driven immune changes in the SLN tissue, offering a powerful tool for the informed design of immune therapies for patients with high-risk melanoma.
Authors
Eric Engelbrecht, Bryce F. Stamp, Lewis Chew, Omar Sadi Sarkar, Phillip Harter, Sabine J. Waigel, Eric C. Rouchka, Julia Chariker, Andrei Smolenkov, Jason Chesney, Kelly McMasters, Corey T. Watson, Kavitha Yaddanapudi
×Abstract
Lipid metabolism is closely linked with antitumor immunity and autoimmune disorders. However, the precise role of lipid metabolism in uveitis pathogenesis is not clear. In our study, we analyzed the single-cell RNA-Seq (scRNA-Seq) data from cervical draining lymph nodes (CDLNs) of mice with experimental autoimmune uveitis (EAU), revealing an increased abundance of fatty acids in Th17 cells. Subsequent scRNA-Seq analysis identified the upregulation of DGAT1 expression in EAU and its marked reduction under various immunosuppressive agents. Suppression of DGAT1 prevented the conversion of fatty acids into neutral lipid droplets, resulting in the accumulation of lipid peroxidation and subsequent reduction in the proportion of Th17 cells. Inhibiting lipid peroxidation by Ferrostatin-1 effectively restored Th17 cell numbers that were decreased by DGAT1 inhibitor. Moreover, we validated the upregulation of DGAT1 in CD4+ T cells from patients with Vogt-Koyanagi-Harada (VKH) disease, a human uveitis. Inhibiting DGAT1 induced lipid peroxidation in human CD4+ T cells and reduced the proportion of Th17 cells. Collectively, our study focused on elucidating the regulatory mechanisms underlying Th17 cell survival and proposed that targeting DGAT1 may hold promise as a therapeutic approach for uveitis.
Authors
Tianfu Wang, Runping Duan, Zhaohuai Li, Bowen Zhang, Qi Jiang, Loujing Jiang, Jianjie Lv, Wenru Su, Lei Feng
Lue Ping Zhao, … , Daniel E. Geraghty, Åke Lernmark Published March 4, 2025
Citation Information: JCI Insight. 2025;10(7):e184348. https://doi.org/10.1172/jci.insight.184348.
×Abstract
HLA-DR genes are associated with the progression from stage 1 and stage 2 to onset of stage 3 type 1 diabetes (T1D), after accounting HLA-DQ genes with which they are in high linkage disequilibrium. Based on an integrated cohort of participants from 2 completed clinical trials, this investigation finds that, sharing a haplotype with the DRB1*03:01 (DR3) allele, DRB3*01:01:02 and *02:02:01 have respectively negative and positive associations with the progression. Furthermore, we uncovered 2 residues (β11, β26, participating in pockets 6 and 4, respectively) on the DRB3 molecule responsible for the progression among DR3 carriers; motif RY and LF respectively delay and promote the progression (hazard ratio [HR] = 0.73 and 2.38, P = 0.039 and 0.017, respectively). Two anchoring pockets 6 and 4 probably bind differential autoantigenic epitopes. We further investigated the progression association with the motifs RY and LF among carriers of DR3 and found that carriers of the motif LF have significantly faster progression than carriers of RY (HR = 1.48, P = 0.019 in unadjusted analysis; HR = 1.39, P = 0.047 in adjusted analysis), results of which provide an impetus to examine the possible role of specific DRB3-binding peptides in the progression to T1D.
Authors
Lue Ping Zhao, George K. Papadopoulos, Jay S. Skyler, William W. Kwok, George P. Bondinas, Antonis K. Moustakas, Ruihan Wang, Chul-Woo Pyo, Wyatt C. Nelson, Daniel E. Geraghty, Åke Lernmark
×Abstract
Using transcriptomic profiling at single-cell resolution, we investigated cell-intrinsic and cell-extrinsic signatures associated with pathogenesis and inflammation-driven fibrosis in both adult and pediatric patients with localized scleroderma (LS). We performed single-cell RNA-Seq on adult and pediatric patients with LS and healthy controls. We then analyzed the single-cell RNA-Seq data using an interpretable factor analysis machine learning framework, significant latent factor interaction discovery and exploration (SLIDE), which moves beyond predictive biomarkers to infer latent factors underlying LS pathophysiology. SLIDE is a recently developed latent factor regression-based framework that comes with rigorous statistical guarantees regarding identifiability of the latent factors, corresponding inference, and FDR control. We found distinct differences in the characteristics and complexity in the molecular signatures between adult and pediatric LS. SLIDE identified cell type–specific determinants of LS associated with age and severity and revealed insights into signaling mechanisms shared between LS and systemic sclerosis (SSc), as well as differences in onset of the disease in the pediatric compared with adult population. Our analyses recapitulate known drivers of LS pathology and identify cellular signaling modules that stratify LS subtypes and define a shared signaling axis with SSc.
Authors
Aaron BI Rosen, Anwesha Sanyal, Theresa Hutchins, Giffin Werner, Jacob S. Berkowitz, Tracy Tabib, Robert Lafyatis, Heidi Jacobe, Jishnu Das, Kathryn S. Torok
Anna B. Morris, … , Colleen S. Kraft, Mandy L. Ford Published April 8, 2025
Citation Information: JCI Insight. 2025;10(7):e186259. https://doi.org/10.1172/jci.insight.186259.
×Abstract
While the inhibitory receptor FcγRIIB has been shown to be upregulated on activated CD8+ T cells in both mice and humans, its effect on T cell fate during infection has not been fully elucidated. We identified an increase in FcγRIIB-expressing CD8+ T cells in patients with COVID-19 relative to healthy controls as well as in mouse models of viral infection. Despite its well-known role as an Fc receptor, FcγRIIB also ligates the immunosuppressive cytokine Fgl2, resulting in CD8+ T cell apoptosis. Both chronic LCMV infection in mice and COVID-19 in humans resulted in a significant increase in plasma Fgl2. Transfer of CD8+ T cells into a Fgl2-replete, but not Fgl2-devoid, environment resulted in elimination of FcγRIIB+, but not FcγRIIB–, CD8+ T cells. Similarly, plasma Fgl2 was directly proportional to CD8+ T cell lymphopenia in patients with COVID-19. RNA-Seq analysis demonstrated that Fgl2 was produced by murine virus–specific CD8+ T cells, with an increase in Fgl2 in CD8+ T cells elicited during chronic versus acute viral infection. Fgl2 was also upregulated in CD8+ T cells from patients with COVID-19 versus healthy controls. In summary, CD8+ T cell production of Fgl2 during viral infection underpinned an FcγRIIB-mediated loss of CD8+ T cell immunity in both mice and humans.
Authors
Anna B. Morris, Max W. Adelman, Kelsey B. Bennion, Catherine D. Martinez, Kem-Maria McCook, Michael H. Woodworth, Charles R. Langelier, Nadine Rouphael, Christopher D. Scharer, Cheryl L. Maier, Colleen S. Kraft, Mandy L. Ford
×Abstract
The functional plasticity of tumor-infiltrating lymphocyte B–cells (TIL-B) spans from antitumor responses to noncanonical immune suppression. Yet, how the tumor microenvironment (TME) influences TIL-B development is still underappreciated. Our current study integrated single-cell transcriptomics and B cell receptor (BCR) sequencing to profile TIL-B phenotypes and clonalities in hepatocellular carcinoma (HCC). Using trajectory and gene regulatory network analysis, we were able to characterize plasma cells and memory and naive B cells within the HCC TME and further revealed a downregulation of BCR signaling genes in plasma cells and a subset of inflammatory TNF+ memory B cells. Within the TME, a nonswitched memory B cell subset acquired an age-associated B cell phenotype (TBET+CD11c+) and expressed higher levels of PD-L1, CD25, and granzyme B. We further demonstrated that the presence of HCC tumor cells could confer suppressive functions on peripheral blood B cells that in turn, dampen T cell costimulation. To the best of our knowledge, these findings represent novel mechanisms of noncanonical immune suppression in HCC. While previous studies identified atypical memory B cells in chronic hepatitis and across several solid cancer types, we further highlighted their potential role as regulatory B cells (Bregs) within both the TME and peripheral blood of HCC patients.
Authors
Shi Yong Neo, Timothy Wai Ho Shuen, Shruti Khare, Joni Chong, Maichan Lau, Niranjan Shirgaonkar, Levene Chua, Junzhe Zhao, Keene Lee, Charmaine Tan, Rebecca Ba, Janice Lim, Joelle Chua, Hui Shi Cheong, Hui Min Chai, Chung Yip Chan, Alexander Yaw Fui Chung, Peng Chung Cheow, Prema Raj Jeyaraj, Jin Yao Teo, Ye Xin Koh, Aik Yong Chok, Pierce Kah Hoe Chow, Brian Goh, Wei Keat Wan, Wei Qiang Leow, Tracy Jie Zhen Loh, Po Yin Tang, Jayanthi Karunanithi, Nye Thane Ngo, Tony Kiat Hon Lim, Shengli Xu, Ramanuj Dasgupta, Han Chong Toh, Kong-Peng Lam
Marcel Arias-Badia, … , Wendy Ritacco, Lawrence Fong Published February 27, 2025
Citation Information: JCI Insight. 2025;10(7):e187921. https://doi.org/10.1172/jci.insight.187921.
×Abstract
While immune checkpoint inhibition (CPI) has reshaped cancer treatment, the majority of patients with cancer do not benefit from this approach, which can also cause immune-related adverse events. Induction of IFN-γ responses is thought be necessary for antitumor immunity, but growing evidence also implicates IFN-γ as a tumor-intrinsic mediator of CPI resistance. CPI-induced IFN-γ mediates activation-induced cell death in T cells as an immune-intrinsic mechanism of resistance. In this study, we found that transient block of IFN-γ signaling through administration of the JAK1 inhibitor ABT-317 enhanced antitumor T cell responses with CPI in preclinical models. Importantly, sequential but not concomitant ABT-317 treatment led to significantly reduced toxicity and improved tumor efficacy. Sequential treatment reduced activation-induced T cell death and enhanced expansion of tumor-reactive T cell subsets with increased effector function in vivo and ex vivo. Only CPI in combination with ABT-317 also enhanced memory responses by protecting mice from tumor rechallenge. These results demonstrate that JAK inhibition within a discrete time window following CPI addresses an immune-intrinsic mechanism of therapeutic resistance.
Authors
Marcel Arias-Badia, PeiXi Chen, Yee May Lwin, Aahir Srinath, Aram Lyu, Zenghua Fan, Serena S. Kwek, Diamond N. Luong, Ali Setayesh, Mason Sakamoto, Matthew Clark, Averey Lea, Rachel M. Wolters, Andrew Goodearl, Fiona A. Harding, Jacob V. Gorman, Wendy Ritacco, Lawrence Fong
Sheng Tang, … , Sarah Weckhuysen, Gemma L. Carvill Published February 13, 2025
Citation Information: JCI Insight. 2025;10(7):e188014. https://doi.org/10.1172/jci.insight.188014.
×Abstract
Dravet syndrome is a developmental and epileptic encephalopathy associated with pathogenic variants in SCN1A. Most disease-causing variants are located within coding regions, but recent work has shed light on the role of noncoding variants associated with a poison exon in intron 20 of SCN1A. Discovery of the SCN1A poison exon known as 20N has led to the first potential disease-modifying therapy for Dravet syndrome in the form of an antisense oligonucleotide. Here, we demonstrate the existence of 2 additional poison exons in introns 1 and 22 of SCN1A through targeted, deep-coverage long-read sequencing of SCN1A transcripts. We show that inclusion of these poison exons is developmentally regulated in the human brain, and that deep intronic variants associated with these poison exons lead to their aberrant inclusion in vitro in a minigene assay or in iPSC-derived neurons. Additionally, we show that splice-modulating antisense oligonucleotides can ameliorate aberrant inclusion of poison exons. Our findings highlight the role of deep intronic pathogenic variants in disease and provide additional therapeutic targets for precision medicine in Dravet syndrome and other SCN1A-related disorders.
Authors
Sheng Tang, Hannah Stamberger, Jeffrey D. Calhoun, Sarah Weckhuysen, Gemma L. Carvill
×Abstract
Successful allograft-specific tolerance induction would eliminate the need for daily immunosuppression and improve posttransplant quality of life. Adoptive cell therapy with regulatory T cells expressing donor-specific chimeric antigen receptors (CAR Tregs) is a promising strategy but, as monotherapy, cannot prolong survival with allografts with multiple MHC mismatches. Using an HLA-A2–transgenic haplo-mismatched heart transplantation model in immunocompetent C57BL/6 recipients, we showed that HLA-A2–specific CAR (A2.CAR) Tregs were able to synergize with a low dose of anti-CD154 to enhance graft survival. Using haplo-mismatched grafts expressing the 2W-OVA transgene and tetramer-based tracking of 2W- and OVA-specific T cells, we showed that in mice with accepted grafts, A2.CAR Tregs inhibited donor-specific T cell, B cell, and antibody responses and promoted a substantial increase in endogenous FOXP3+ Tregs with indirect donor specificity. By contrast, in mice where A2.CAR Tregs failed to prolong graft survival, FOXP3– A2.CAR T cells preferentially accumulated in rejecting allografts, and endogenous donor-specific responses were not controlled. This study therefore provides evidence for synergy between A2.CAR Tregs and CD154 blockade to promote infectious tolerance in immunocompetent recipients of haplo-mismatched heart grafts and defines features of A2.CAR Tregs when they fail to reshape host immunity toward allograft tolerance.
Authors
Samarth S. Durgam, Isaac Rosado-Sánchez, Dengping Yin, Madeleine Speck, Majid Mojibian, Ismail Sayin, Grace E. Hynes, Maria-Luisa Alegre, Megan K. Levings, Anita S. Chong
Kacy S. Yount, … , Natalie Stanley, Toni Darville Published February 27, 2025
Citation Information: JCI Insight. 2025;10(7):e189388. https://doi.org/10.1172/jci.insight.189388.
×Abstract
Chlamydia trachomatis (CT) is the most common bacterial sexually transmitted infection globally. Understanding natural immunity to CT will inform vaccine design. This study aimed to profile immune cells and associated functional features in CT-infected women and determine immune profiles associated with reduced risk of ascended endometrial CT infection and CT reinfection. PBMCs from CT-exposed women were profiled by mass cytometry, and random forest models identified key features that distinguished outcomes. CT+ participants exhibited higher frequencies of CD4+ Th2, Th17, and Th17 double-negative (Th17 DN) CD4+ T effector memory (TEM) cells than uninfected participants with decreased expression of T cell activation and differentiation markers. Minimal differences were detected between women with or without endometrial CT infection. Participants who remained follow-up negative (FU–) showed higher frequencies of CD4+ T central memory (TCM) Th1, Th17, Th1/17, and Th17 DN but reduced CD4+ TEM Th2 cells than FU+ participants. Expression of markers associated with central memory and Th17 lineage was increased on T cell subsets among FU– participants. These data indicate that peripheral T cells exhibit distinct features associated with resistance to CT reinfection. The highly plastic Th17 lineage appears to contribute to protection. Addressing these immune nuances could promote efficacy of CT vaccines.
Authors
Kacy S. Yount, Chi-Jane Chen, Avinash Kollipara, Chuwen Liu, Neha V. Mokashi, Xiaojing Zheng, C. Bruce Bagwell, Taylor B. Poston, Harold C. Wiesenfeld, Sharon L. Hillier, Catherine M. O’Connell, Natalie Stanley, Toni Darville
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Abstract
Fibroblasts are central to pathogenesis of systemic sclerosis (SSc). However, studies of conventional explant fibroblast cultures incompletely reflect disease biology and treatment response. We isolated a second non-migratory “resident” population of fibroblasts from skin biopsies after outgrowth of explant “migratory” cells. These non-motile resident fibroblasts were compared with migratory cells from the same biopsy, using functional studies, bulk and scRNAseq, and localised in situ by multichannel immunofluorescence. Migratory and resident fibroblast populations in SSc showed distinct pro-fibrotic characteristics and gene expression for pathogenic pathways differing by stage and autoantibody subgroup. TGFβ signalling was highly active in migratory fibroblasts in early stage dcSSc. Conversely, resident fibroblasts had less upregulated TGFβ signalling, especially in late dcSSc. Increased chemokine expression was a hallmark of resident fibroblasts at all stages. In vitro studies confirmed differential response to TGFβ1 and CCL2 between migratory and resident cells. We suggest that migratory fibroblasts are especially important in early skin disease whereas non-migratory fibroblasts may have a regulatory role and contribute more to fibrosis in later stage disease. Thus, we have identified a pathogenic fibroblast population in SSc, not isolated by conventional explant culture, that could play an important role in fibrosis and be targeted therapeutically.
Authors
Kristina E.N. Clark, Shiwen Xu, Moustafa Attar, Voon H. Ong, Christopher D. Buckley, Christopher P. Denton
Abstract
Degenerative retinal disorders leading to irreversible photoreceptor death are a common cause of blindness. Optogenetic gene therapy aims to restore vision in affected individuals by introducing light sensitive opsins into the surviving neurons of the inner retina. While up until now the main focus of optogenetic therapy has been on terminally blind individuals, treating at stages where residual native vision is present could have several advantages. Yet, it is still unknown how residual native and optogenetic vision would interact if present at the same time. Using transgenic mice expressing the optogenetic tool ReaChR in ON-bipolar cells, we herein examine this interaction through electroretinography (ERG) and visually evoked potentials (VEP). We find that optogenetic responses show a peculiar ERG signature and are enhanced in retinas without photoreceptor loss. Conversely, native responses are dampened in the presence of ReaChR. Moreover, in VEP recordings we find that optogenetic responses reach the cortex asynchronous to the native response. These findings should be taken into consideration when planning future clinical trials and may direct future preclinical research to optimize optogenetic approaches for visual restoration. The identified ERG signatures moreover may serve to track treatment efficiency in clinical trials.
Authors
Eleonora Carpentiero, Steven Hughes, Jessica Rodgers, Nermina Xhaferri, Sumit Biswas, Michael J. Gilhooley, Mark W. Hankins, Moritz Lindner
Abstract
Bronchiolitis obliterans syndrome (BOS) is a progressive, fatal obstructive lung that occurs following lung transplant, where it is termed chronic lung allograft dysfunction BOS (CLAD-BOS), or as the primary manifestation of pulmonary chronic graft versus host disease (cGVHD-BOS) following allogeneic hematopoietic stem cell transplant. Disease pathogenesis is poorly understood, however chronic alloreactivity is common to both conditions, suggesting a shared pathophysiology. We performed single-cell RNA-Seq (scRNA-Seq) on explanted human lungs from 4 CLAD-BOS patients, 3 cGVHD-BOS patients, and 3 deceased controls to identify cell types, genes, and pathways enriched in BOS to better understand disease mechanisms. In both forms of BOS, we found an expanded population of CD8+ tissue resident memory T-cells (TRM), which was distinct to BOS compared to other chronic lung diseases. In addition, BOS samples expressed genes and pathways associated with macrophage chemotaxis and proliferation, including in non-immune cell populations. We also identify dysfunctional stromal cells in BOS, characterized by pro and anti-fibrotic gene programs. These data suggest substantial cellular and molecular overlap between CLAD- and cGVHD-BOS and therefore, common pathways for possible therapeutic intervention.
Authors
Patrick W. Mellors, Ana N. Nottingham, Bruno Casino Remondo, Maksim Shestov, Joseph D. Planer, Andrew R. Peterson, Yun Ying, Su Zhou, Jason D. Christie, Joshua M. Diamond, Edward Cantu, Maria C. Basil, Saar Gill
Abstract
We defined injury-induced transcriptome states in 4502 kidney transplant biopsies taken 1 day to 45 years post-transplant using genome-wide microarrays. Injury was measured by injury-induced gene sets and classifiers previously developed in transplants. In principal component analysis, PC1 correlated with both acute and chronic kidney injury and related inflammation, and PC2 with time post-transplant. PC3 was a novel dimension that correlated with epithelial remodeling pathways. Both PC1 and PC3 correlated with reduced survival, PC1 effects strongly increasing with time whereas PC3 effects being time-independent. In this model, we studied the expression of genes annotated in native kidneys in epithelial cells with failed repair: 12 “New” gene sets previously defined in single nucleus RNA sequencing of native kidneys with AKI (Genome Med.14(1):103). The “New4” gene sets reflecting epithelial-mesenchymal transition (EMT) correlated with injury PC1, lower eGFR, higher donor age, and future failure as strongly as any gene sets previously derived in transplants, independent of nephron segment of origin and graft rejection. These results suggest that there are two distinct dimensions in kidney transplant response to injury: PC1, AKI-induced changes, failed repair, and inflammation; and PC3, a response involving epithelial remodeling without inflammation. Increasing kidney age amplifies PC1 and particularly PC3.
Authors
Philip F. Halloran, Jessica Chang, Martina Mackova, Katelynn Madill-Thomsen, Enver Akalin, Tarek Alhamad, Sanjiv Anand, Miha Arnol, Rajendra Baliga, Mirosław Banasik, Christopher Blosser, Georg Böhmig, Daniel Brennan, Jonathan Bromberg, Klemens Budde, Andrzej Chamienia, Kevin Chow, Michał Ciszek, Declan de Freitas, Dominika Dęborska-Materkowska, Alicja Debska-Ślizień, Arjang Djamali, Leszek Domański, Magdalena Durlik, Gunilla Einecke, Farsad Eskandary, Richard Fatica, Iman Francis, Justyna Fryc, John Gill, Jagbir Gill, Maciej Glyda, Sita Gourishankar, Marta Gryczman, Gaurav Gupta, Petra Hruba, Peter Hughes, Arskarapurk Jittirat, Zeljka Jurekovic, Layla Kamal, Mahmoud Kamel, Sam Kant, Nika Kojc, Joanna Konopa, James Lan, Roslyn Mannon, Arthur Matas, Joanna Mazurkiewicz, Marius Miglinas, Thomas Mueller, Marek Myślak, Seth Narins, Beata Naumnik, Anita Patel, Agnieszka Perkowska-Ptasińska, Michael Picton, Grzegorz Piecha, Emilio Poggio, Silvie Rajnochová Bloudíčková, Thomas Schachtner, Soroush Shojai, Majid Sikosana, Janka Slatinská, Katarzyna Smykal-Jankowiak, Željka Veceric Haler, Ondrej Viklicky, Ksenija Vucur, Matthew R. Weir, Andrzej Wiecek, Zbigniew Włodarczyk, Harold Yang, Ziad Zaky, Patrick T. Gauthier, Christian Hinze
Abstract
Invasive aspergillosis is characterized by lung hemorrhage and release of extracellular heme, which promotes fungal growth. Heme can also mediate tissue injury directly, and both fungal growth and lung injury may induce hemorrhage. To assimilate these interdependent processes, we hypothesized that, during aspergillosis, heme mediates direct lung injury independent of fungal growth, leading to worse infection outcomes, and the scavenger protein, hemopexin, mitigates these effects. Mice with neutropenic aspergillosis were found to have a time-dependent increase in lung extracellular heme and a corresponding hemopexin induction. Hemopexin deficiency resulted in markedly increased lung injury, fungal growth, and lung hemorrhage. Using a computational model of the interactions of Aspergillus, heme, and the host, we predicted a critical role for heme-mediated generation of neutrophil-extracellular traps in this infection. We tested this prediction using a fungal strain unable to grow at body temperature, and found that extracellular heme and fungal exposure synergize to induce lung injury by promoting NET release, and disruption of NETs was sufficient to attenuate lung injury and fungal burden. These data implicate heme-mediated NETosis in both lung injury and fungal growth during aspergillosis, resulting in a detrimental positive feedback cycle that can be interrupted by scavenging heme or disrupting NETs.
Authors
Ganlin Qu, Henrique A.L. Ribeiro, Angelica L. Solomon, Luis Sordo Vieira, Yana Goddard, Nickolas G. Diodati, Arantxa V. Lazarte, Matthew Wheeler, Reinhard Laubenbacher, Borna Mehrad
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