News and Publications from the Marlene Hess Center

News & Press Releases

Publications

The following research was partially supported by funding from the Marlene Hess Center.

2026:

A MERTK-Targeting antibody-drug conjugate selectively depletes M2 tumor-associated macrophages and MERTK-expressing cancer cells by Shugaku Takeda, Subhasree Sridhar, Daniel Schefer, Celia Andreu-Agullo, Pui C. Lo, Minhee Lee, Robert Busby, David M. Darst, Anne Assmus, Suresh Anaganti, Nils Halberg, Benjamin N. Ostendorf, Ivo C. Lorenz, Sohail F. Tavazoie, Masoud F. Tavazoie, and Isabel Kurth. Published in Cancer Research, 2026, https://doi.org/10.1158/0008-5472.CAN-25-2998

MERTK is a receptor tyrosine kinase predominantly expressed on M2 macrophages that plays a critical role in the clearance of apoptotic cells and maintenance of an immune-suppressive phenotype. M2 macrophages are highly abundant in the tumor microenvironment where they facilitate tumor progression and resistance to immunotherapy. MERTK is also overexpressed in cancer cells, where it can drive cancer survival and metastasis through induction of proliferation and anti-apoptotic signaling programs. Here we developed an antibody-drug conjugate (ADC) that simultaneously targets MERTK-expressing M2 tumor associated macrophages and cancer cells. The ADC comprised the monoclonal antibody RGX-019 that binds human MERTK, combined with a monomethyl auristatin E (MMAE) toxic payload. The unconjugated antibody had intrinsic activity to suppress M2 cytokine expression by macrophages, block in vitro colony formation of cancer cells, and inhibit in vivo tumor growth and metastasis. When MMAE was conjugated to the antibody, the ADC exhibited superior in vitro cytotoxicity and in vivo anti-tumor efficacy in MERTK-expressing tumors. Tumor growth inhibition in humanized mice was associated with depletion of tumor-associated M2 macrophages. Furthermore, unlike other MERTK-targeting small molecules or antibodies, no retinal toxicity of RGX-019-MMAE was observed in vivo. These findings reveal that combined therapeutic targeting of MERTK in cancer cells and M2 macrophages offers enhanced opportunities for anti-tumor efficacy in a wide range of MERTK-expressing tumors.

Molecular determinants of Smc5/6 association with DNA junctions by Jeremy T-H. Chang, Victoria Miller-Browne, Gabriella N. L. Chua, Jian Zheng, Emily C. Beckwitt, Shibai Li, Bryce J. Katch, Michael E. O’Donnell, Shixin Liu, and Xiaolan Zhao. Published in Nature Communications, 2026, https://doi.org/10.1038/s41467-025-67999-5

Smc5/6 is an essential genome maintenance complex that interacts with double-stranded (ds) DNA, single-stranded (ss) DNA, and ss-dsDNA junctions. DNA association underlies Smc5/6’s functions in managing intermediates generated during genome replication and repair. However, the mechanisms of this activity are not fully understood. Here, we report a single-molecule study examining Smc5/6 association with a dsDNA substrate containing a ssDNA gap with defined 3’ and 5’ junctions. We found that Smc5/6 associates with both 3’ and 5’ junctions but prefers the 3’ junction in the presence of the ssDNA-binding complex RPA. Further, Smc5/6’s junction association frequency and dwell time are regulated by two non-SMC subcomplexes and DNA binding residues of Smc6. Moreover, Smc5/6 prefers binding to junction sites free of the sliding clamp PCNA over those occupied with it. These results suggest that Smc5/6 utilizes its multiple structural modules to associate with junction sites in coordination with other genome maintenance factors.

Cell type-specific proximity labeling of organ secretomes reveals energy balance-dependent proteomic remodeling by Kaja Plucińska, Charlotte R. Wayne, Henry Sanford, Boby Mathew, Nathalie Ropek, Stephanie M. Adaniya, Corey Model, Nicolás Gómez-Banoy, Ksenia Morozova, Xiongwen Cao, Jeffrey M. Friedman, Ken H. Loh, Paul Cohen, and Ekaterina V. Vinogradova. Published on bioRxiv: The Preprint Server for Biology, 2026, https://doi.org/10.64898/2026.01.11.698831

Intercellular communication is critical for maintaining organismal metabolic homeostasis. Here, we present a new method enabling temporally controlled, cell type-specific labeling of secreted and membrane proteins in key metabolic tissues. The method employs a genetically encoded proximity-labeling strategy by targeting a Cre-dependent TurboID ligase to the endoplasmic reticulum (ER) in ES cell-derived mice. Expression of TurboID in liver, adipose tissue, and spleen enabled the characterization of organ-specific ER proteomes at baseline and in response to fasting, inflammation, and dietary obesity, revealing tissue-and perturbation-specific changes and augmenting our understanding of how the proteomes of individual tissues change to regulate systemic energy balance. This comprehensive resource represents an important advance toward understanding both how cell-to-cell communication changes in response to energy homeostasis and how it contributes to these alterations. This method is broadly applicable and provides a means for identifying biomarkers and therapeutic targets across a wide range of tissues.

A commensally regulated immune rheostat fine-tunes skin barrier fitness by Anita Gola, Rohith Srinivas, Elias G. Rodig, Marina Schernthanner, Merve Deniz Abdusselamoglu, Matthew T. Tierney, Natalie J. Alexander, Kevin A. U. Gonzales, Sairaj M. Sajjath, Luis F. Soto-Ugaldi, Alain R. Bonny, and Elaine Fuchs. Published on bioRxiv: The Preprint Server for Biology, 2026, https://doi.org/10.64898/2026.01.07.698149

At the skin’s surface, the epidermis must balance stem cell renewal with barrier maintenance to withstand environmental stress and shield against pathogens. Here, we identify a microbial-immune–epithelial feedback mechanism that integrates environmental information into stem cell regulation. Specifically, we show that Langerhans cells—an intra-epithelial macrophage population— orchestrate this circuit by producing prostaglandin E₂, which restrains stem cell proliferation, promotes epidermal differentiation and maintains barrier integrity during homeostasis. Upon pathway disruption, stem cells become overactivated, impairing differentiation and compromising barrier function. Upstream, Langerhans cell activity is tuned by the local microbial environment in a rheostat-like fashion, coupling commensal sensing to stem cell control. Our findings provide a general framework for how barrier tissues achieve adaptive homeostasis amid continual external challenge.

A post-translational regulatory map of chronic antigen-driven human T cell dysfunction by Hiroyuki Kojima, Charlotte R. Wayne, Luis F. Somarribas Patterson, Henry Sanford, Tzu-Jou Chen, Ya-Hui Lin, Joshua D. Schoenfeld, Lisa H. F. McGary, Yan-Ting Chen, Korbinian N. Kropp, Beatrice Zhang, Jahan Rahman, Tiffany L. Zhang, Nathalie Ropek, Cameron Roberts, Yuxi Ai, Kartikeya M. Menon, A. Ari Hakimi, Jiankun Lyu, Christopher A. Klebanoff, Omar Abdel-Wahab, Santosha A. Vardhana, and Ekaterina V. Vinogradova. Published on bioRxiv: The Preprint Server for Biology, 2026, https://doi.org/10.64898/2026.03.04.709614

T cells exposed to persistent antigen in the context of chronic viral infections or cancer lose self-renewal and cytotoxic capacity. Several transcriptional, epigenetic, and metabolic drivers of this process have been identified. However, the post-transcriptional regulatory mechanisms influencing the proteome of dysfunctional T cells are not well understood. Here we present a time-resolved molecular landscape of human T cells during the development of chronic antigen-driven dysfunction. Persistent T cell receptor stimulation significantly remodeled the proteome, including changes in canonical T cell exhaustion-associated proteins and proteins related to mitochondrial function, redox homeostasis, nucleotide metabolism, and cell-cycle progression. Dysfunctional T cells displayed activation of stress response pathways that were recapitulated in vivo; targeting these pathways altered the cytotoxic capacity of T cells during persistent tumor exposure. Our comprehensive proteomic resource reveals unique post-transcriptional changes in dysfunctional T cells and lays the groundwork for novel cysteine-directed therapeutics to enhance cancer immunotherapy.

An immunocompetent murine model of virus-elicited liver fibrosis and hepatocellular carcinoma by Mariana Nogueira Batista, Juliano Bordignon, Ana Luiza Pamplona Mosimann, Tesia Bobrowski, Hsuan-An Chen, Gabriel Tobin-Xet, Erika A. Barrall, Nataliya Prokhnevska, Abishek Balachandra Vaidya, Tyler Lewy, Kenneth H. Dinnon III, Leon Louis Seifert, Briana Zeck, Corrine Quirk, Yu-Jui Ho, Aveline Filiol, Raphael Wolfisberg, Caroline Jiang, Bruno Cogliati, Luis Chiriboga, Neil Theise, Margaret R. MacDonald, Alice Kamphorst, Troels K. H. Scheel, Timothy P. Sheahan, Eva Billerbeck, Scott Lowe, Brad R. Rosenberg, and Charles M. Rice. Published in the Journal of Hepatology, 2026, https://doi.org/10.1016/j.jhep.2026.02.020

Hepatocellular carcinoma (HCC) is the third deadliest cancer worldwide. Over 75% of HCC cases are associated with chronic viral infections. Mechanistic studies and preclinical therapeutic development for virus-associated HCC have been limited by a paucity of small animal models of chronic hepatotropic virus infection that faithfully recapitulate human disease. Here we demonstrate the induction of chronic hepatitis, progressive liver fibrosis, and HCC in immunocompetent laboratory mice upon chronic viral infection with Norway rat hepacivirus (NrHV) – a virus closely related to hepatitis C virus (HCV). NrHV-elicited tumors resemble HCV-associated tumors and liver transcriptome analyses reveal numerous similarities between chronic NrHV and HCV. These findings establish an experimentally tractable, physiologically relevant, and immunocompetent mouse model of virus-elicited progressive liver fibrosis and oncogenesis.

 

2025:

A commonly inherited human PCSK9 germline variant drives breast cancer metastasis via LRP1 receptor by Wenbin Mei, Schayan Faraj Tabrizi, Christopher Godina, Anthea F. Lovisa, Karolin Isaksson, Helena Jernström, and Sohail F. Tavazoie. Published in Cell, Volume 188, Issue 2, 2025, Pages 371-389.e28, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2024.11.009

Identifying patients at risk for metastatic relapse is a critical medical need. We identified a common missense germline variant in proprotein convertase subtilisin/kexin type 9 (PCSK9) (rs562556, V474I) that is associated with reduced survival in multiple breast cancer patient cohorts. Genetic modeling of this gain-of-function single-nucleotide variant in mice revealed that it causally promotes breast cancer metastasis. Conversely, host PCSK9 deletion reduced metastatic colonization in multiple breast cancer models. Host PCSK9 promoted metastatic initiation events in lung and enhanced metastatic proliferative competence by targeting tumoral low-density lipoprotein receptor related protein 1 (LRP1) receptors, which repressed metastasis-promoting genes XAF1 and USP18. Antibody-mediated therapeutic inhibition of PCSK9 suppressed breast cancer metastasis in multiple models. In a large Swedish early-stage breast cancer cohort, rs562556 homozygotes had a 22% risk of distant metastatic relapse at 15 years, whereas non-homozygotes had a 2% risk. Our findings reveal that a commonly inherited genetic alteration governs breast cancer metastasis and predicts survival—uncovering a hereditary basis underlying breast cancer metastasis.

A non-catalytic role for RFC in PCNA-mediated processive DNA synthesis by Gabriella N.L. Chua, Emily C. Beckwitt, Victoria Miller-Browne, Olga Yurieva, Dan Zhang, Bryce J. Katch, Nina Y. Yao, John W. Watters, Kaitlin Abrantes, Ryogo Funabiki, Xiaolan Zhao, Michael E. O’Donnell and Shixin Liu. Published in Cell, 2026, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2025.12.029.

The ring-shaped sliding clamp proliferating cell nuclear antigen (PCNA) enables DNA polymerases to perform processive DNA synthesis during replication and repair. The loading of PCNA onto DNA is catalyzed by the ATPase clamp-loader replication factor C (RFC). Using a single-molecule platform to visualize the dynamic interplay between PCNA and RFC on DNA, we unexpectedly discovered that RFC continues to associate with PCNA after loading, contrary to the conventional view. Functionally, this clamp-loader/clamp (CLC) complex is required for processive DNA synthesis by polymerase ẟ (Polẟ), as the PCNA-Polẟ assembly is inherently unstable. This architectural role of RFC is dependent on the BRCA1 C-terminal homology (BRCT) domain of Rfc1, and mutation of its DNA-binding residues causes sensitivity to genotoxic stress in vivo. We further showed that flap endonuclease I (FEN1) can also stabilize the PCNA-Polẟ interaction and mediate robust synthesis. Overall, our work revealed that, beyond their canonical enzymatic functions, PCNA-binding proteins harbor non-catalytic functions important for DNA replication and genome maintenance.

Kinetic control of mammalian transcription elongation by Yukun Wang, Xizi Chen, Maximilian Kümmecke, John W. Watters, Joel E. Cohen, Yanhui Xu and Shixin Liu. Published in Nature Structural & Molecular Biology, 2025, https://doi.org/10.1038/s41594-025-01707-1

Transcription elongation by RNA polymerase II (Pol II) is an integral step in eukaryotic gene expression. The speed of Pol II is controlled by a multitude of elongation factors, but the exact regulatory mechanisms remain incompletely understood, especially for higher eukaryotes. Here we develop a single-molecule platform to visualize the dynamics of individual mammalian transcription elongation complexes (ECs) reconstituted from purified proteins. This platform allows us to follow the elongation and pausing behavior of EC in real time and unambiguously determine the role of each elongation factor in the kinetic control of Pol II. We find that the mammalian EC harbors multiple speed gears dictated by its associated factors and phosphorylation status. Moreover, the elongation factors are not functionally redundant but act hierarchically and synergistically to achieve optimal elongation activity. We propose that such elaborate kinetic regulation underlies the major speed-changing events during the transcription cycle and enables cells to adapt to a changing environment.

Molecular interplay between the DNA damage checkpoint kinase Mec1-Ddc2 and its activator Dpb11 on gapped DNA by Emily C. Beckwitt, Gabriella N. L. Chua, Shixin Liu, and Michael E. O’Donnell. Published on Published on bioRxiv: The Preprint Server for Biology, 2025, https://doi.org/10.1101/2025.11.28.691181

The eukaryotic DNA damage and replication stress checkpoint is an essential component of the DNA damage response and crucial for genome maintenance. In budding yeast, the apical kinase Mec1 (ATR ortholog), along with binding partner Ddc2 (ATRIP ortholog), senses persistent RPA-bound ssDNA in the cell. Mec1 is activated by interaction with a Mec1-activating protein. One such activator, Dpb11 (TopBP1 ortholog), is recruited to a 5’ ss-dsDNA junction via the 9-1-1 checkpoint clamp. Due to their differential DNA binding preferences, it remains to be determined how Mec1 encounters its activators on damaged DNA. Using real-time single-molecule imaging of checkpoint proteins binding to dsDNA containing a long ssDNA gap, we show that, even in the absence of 9-1-1, Dpb11 binds to ssDNA and localizes to ss-dsDNA junctions in an RPA-dependent manner. Importantly, we directly visualize that Dpb11 recruits Mec1-Ddc2 to ss-dsDNA junctions. Additionally, single-molecule force spectroscopy was used to demonstrate that Dpb11 can interact with multiple DNA sites simultaneously to form bridges both alone and in the presence of RPA, stabilizing ssDNA loops and reducing the end-to-end distance of gapped DNA. Taken together, these data support a model in which Dpb11 facilitates Mec1 colocalization with its activators both directly by recruiting Mec1 to gap junctions and indirectly by decreasing the effective gap length.