Marcel P. Bruchez

Background: Failure of adoptive cell therapies (ACTs) is associated with insufficient persistence within the patient, inability to infiltrate tumor sites, and cell-intrinsic loss of functionality. One of the key factors responsible for T cell dysfunction are metabolic barriers such as nutrient competition, low oxygen tension and damaging byproducts in the tumor microenvironment. This leads to a T cell metabolic deregulation affecting their ability to find and kill cancer cell targets properly and effectively. Therefore, elucidating the metabolic pressures experienced in the TME could provide new therapeutic targets to improve ACTs. Reactive Oxidative Species (ROS) accumulation in the TME have detrimental effects on T cell function and anti-tumor response, although the precise targets of ROS are unclear. There are accumulating data showing that mitochondrial ROS can have profound effects on the telomere status of cells. However, there is little evidence describing the role or oxidative stress on telomere health, or the importance of telomere function in immune cells. Our current study demonstrates that tumor infiltrating lymphocytes (TIL) accumulate DNA damage at telomeres, most prominently in terminally exhausted T cells. Furthermore, inducing ROS accumulation at telomeres alone drives T cell dysfunction. Importantly we discovered that alleviating ROS specifically at telomeres improves the response to adoptive cell therapies in a mouse tumor model. Methods: In this study we perform telomeric and centromeric FISH assays to analyze TIL for DNA damage accumulation. We used a chemo-optogenetic FAPS-TAPS to generate singlet oxygen and consequent 8-oxo-guanine lesions specifically at telomeres.¹ We tethered the antioxidant protein GPX1 to TRF1, subunit of the Shelterin Complex at telomeres, to generate a telomere-guided ROS scavenger. Results: Telo-FISH analysis demonstrates an accumulation of telomeric DNA damage in TIL from B16 mouse tumors shown by the presence of 53BP1 and ƔH2AX at telomeres. Our data show that mitochondria and telomeric ROS cause the accumulation of DNA damage at telomeres, as well as the development of telomere fragility. These cells ultimately become dysfunctional showing a diminished capability for cytokine production. Importantly, localizing the ROS scavenger GPX1 directly to telomeres reduced telomere fragility and improved the function of therapeutic T cells in the B16 melanoma. Conclusions: Our data suggest that dysfunctional T cells in cancer are not classically senescent, bearing short telomeres, but rather harbor damaged telomeres due to exposure to oxidative stress. Telomeric damage is sufficient to drive a dysfunctional state in newly activated T cells. Protecting telomeres through expression of a telomere-targeted antioxidant protein may preserve T cell function in the tumor microenvironment and drive superior responses to adoptive cell therapies. Citation Format: Dayana Rivadeneira, Sanjana Thosar, Victoria Dean, William Gunn, Konstantinos Lontos, Marcel Bruchez, Patricia Opresko, Greg Delgoffe. Neutralizing oxidative damage at telomeres prevents T cell dysfunction and improves adoptive cell therapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr A020.

Background Failure of adoptive cell therapies (ACTs) is associated with insufficient persistence within the patient, inability to infiltrate tumor sites, and cell-intrinsic loss of functionality. One of the key factors responsible for T cell dysfunction are metabolic barriers such as nutrient competition, low oxygen tension and damaging byproducts in the tumor microenvironment. This leads to a T cell metabolic deregulation affecting their ability to find and kill cancer cell targets effectively. Therefore, elucidating the metabolic pressures experienced in the TME could provide new therapeutic targets to improve ACTs. Reactive Oxidative Species (ROS) accumulation in the TME have detrimental effects on T cell function and anti-tumor response, although the precise targets of ROS are unclear. There are accumulating data showing that mitochondrial ROS can have profound effects on the telomere status of cells. However, there is little evidence describing the role or oxidative stress on telomere health, or the importance of telomere function in immune cells. Our current study demonstrates that tumor infiltrating lymphocytes (TIL) accumulate DNA damage at telomeres. Furthermore, inducing ROS accumulation at telomeres alone drives T cell dysfunction. Importantly we discovered that alleviating ROS specifically at telomeres improves the response to adoptive cell therapies in a mouse tumor model. Methods We perform telomeric and centromeric FISH assays to analyze TIL for DNA damage accumulation. We used a chemo-optogenetic FAPS-TAPS to generate oxidative lesions specifically at telomeres.¹ We tethered the antioxidant protein GPX1 to the telomere shelterin TRF1 to generate a telomere-guided ROS scavenger. Results Telo-FISH analysis demonstrates an accumulation of telomeric DNA damage in TIL from B16 mouse tumors shown by the presence of 53BP1 and γH2AX at telomeres (figure 1A). Our data show that mitochondria and telomeric ROS cause the accumulation of DNA damage at telomeres, as well as the development of telomere fragility (figure 1B). These cells ultimately become dysfunctional showing a diminished capability for cytokine production. Importantly, localizing the ROS scavenger GPX1 directly to telomeres reduced telomere fragility and improved the function of therapeutic T cells in the B16 melanoma (figure 1C). Conclusions Our data suggest that dysfunctional T cells in cancer are not classically senescent, bearing short telomeres, but rather harbor damaged telomeres due to exposure to oxidative stress. Telomeric damage is sufficient to drive a dysfunctional state in newly activated T cells. Protecting telomeres through expression of a telomere-targeted antioxidant protein may preserve T cell function in the tumor microenvironment and drive superior responses to adoptive cell therapies. Reference Fouquerel E, Barnes RP, Uttam S, Watkins SC, Bruchez MP, Opresko PL. Targeted and persistent 8-oxoguanine base damage at telomeres promotes telomere loss and crisis. Mol Cell. 2019 Jul 11;75(1):117–130.e6. doi: 10.1016/j.molcel.2019.04.024. Epub 2019 May 14. PMID: 31101499; PMCID: PMC6625854. (A) Tumor infiltrating lymphocytes from B16 tumors and spleen sorted on PD1-Tim3 expression. FISH analysis of Telomere (Telo) and DNA damage response elements 53BP1 and γH2AX. (B) Activated T cells expression TRF1-FAP get oxidative damage induced at telomeres by chemoptogenetic method. T cells are arrested and perform metaphase spreads for telomere fragility analysis. (C) Therapeutic T cells co-expressing ROS scavenger GPX and TRF1 (telomere specific) transferred Into B16 tumor bearing mice. Control T cells express control plasmid PMIA.

Neuronal dense-core vesicles (DCVs) contain neuropeptides and much larger proteins that affect synaptic growth and plasticity. Rather than using full collapse exocytosis that commonly mediates peptide hormone release by endocrine cells, DCVs at the Drosophila neuromuscular junction release their contents via fusion pores formed by kiss-and-run exocytosis. Here, we used fluorogen-activating protein (FAP) imaging to reveal the permeability range of synaptic DCV fusion pores and then show that this constraint is circumvented by cAMP-induced extra fusions with dilating pores that result in DCV emptying. These Ca2+-independent full fusions require PKA-R2, a PKA phosphorylation site on Complexin and the acute presynaptic function of Rugose, the homolog of mammalian neurobeachin, a PKA-R2 anchor implicated in learning and autism. Therefore, localized Ca2+-independent cAMP signaling opens dilating fusion pores to release large cargoes that cannot pass through the narrower fusion pores that mediate spontaneous and activity-dependent neuropeptide release. These results imply that the fusion pore is a variable filter that differentially sets the composition of proteins released at the synapse by independent exocytosis triggers responsible for routine peptidergic transmission (Ca2+) and synaptic development (cAMP).

The liver restores its mass and architecture after injury. Yet, investigating morphogenetic cell behaviours and signals that repair tissue architecture at high spatiotemporal resolution remains challenging. We developed LiverZap, a tuneable chemoptogenetic liver injury model in zebrafish. LiverZap employs formation of a binary FAP-TAP photosensitiser followed by brief near-infrared illumination inducing hepatocyte-specific death and recapitulating mammalian liver injury types. The tool enables local hepatocyte ablation and extended live imaging of regenerative cell behaviours, critical for studying cellular interactions at the interface of healthy and damaged tissue. Applying LiverZap, we show that targeted hepatocyte ablation in a small region-of-interest is unexpectedly sufficient to trigger Liver Progenitor-like Cell (LPC)-mediated regeneration, challenging the current understanding of LPC activation. Associated dynamic bilary network rearrangement and E-cadherin relocalisation suggest modulation of cell adhesion as an integral step of LPC-mediated liver regeneration. This precisely targetable live cell ablation model will enable addressing of key regeneration paradigms.

Oxidative nuclear DNA damage increases in all tissues with age in multiple animal models, as well as in humans. However, the increase in DNA oxidation varies from tissue to tissue, suggesting that certain cells/tissues may be more vulnerable to DNA damage than others. The lack of a tool that can control dosage and spatiotemporal induction of oxidative DNA damage, which accumulates with age, has severely limited our ability to understand how DNA damage drives aging and age-related diseases. To overcome this, here we developed a chemoptogenetic tool that produces 8-oxoguanine (8-oxoG) at DNA in a whole organism, Caenorhabditis elegans. This tool uses di-iodinated malachite green (MG-2I) photosensitizer dye that generates singlet oxygen, ¹O₂, upon fluorogen activating peptide (FAP) binding and excitation with far-red light. Using our chemoptogenetic tool, we are able to control generation of singlet oxygen ubiquitously or in a tissue-specific manner, including in neurons and muscle cells. To induce oxidative DNA damage, we targeted our chemoptogenetic tool to histone, his-72, that is expressed in all cell types. Our results show that a single exposure to dye and light is able to induce DNA damage, promote embryonic lethality, lead to developmental delay, and significantly reduce lifespan. Our chemoptogenetic tool will now allow us to assess the cell autonomous versus non-cell autonomous role of DNA damage in aging, at an organismal level.

Neuronal dense-core vesicles (DCVs) contain neuropeptides and much larger proteins that affect synaptic growth and plasticity. Rather than using full collapse exocytosis that is common in endocrine cells, DCVs at a native intact synapse, the Drosophila neuromuscular junction, release their contents via fusion pores formed by kiss and run exocytosis. Here fluorogen activating protein (FAP) imaging reveals the permeability range of synaptic DCV fusion pores and then shows that this constraint is circumvented by cAMP-induced extra fusions with dilating pores that result in DCV emptying. These Ca ²⁺ -independent full fusions require PKA-R2, a PKA phosphorylation site on the fusion clamp protein complexin and the acute presynaptic function of Rugose/Neurobeachin, a PKA-R2 anchor implicated in learning and autism. Therefore, localized Ca ²⁺ -independent cAMP signaling opens dilating fusion pores to release large cargo proteins that cannot pass through the narrower fusion pores that normally dominate spontaneous and Ca ²⁺ -evoked synaptic protein release. Hence, two independent exocytosis triggers (Ca ²⁺ and cAMP) vary the composition of released proteins at the synapse by differentially adjusting DCV fusion pores.

A need in synthetic biology is the ability to precisely and efficiently make flexible fully designed vectors that addresses challenging cloning strategies of single plasmids that rely on combinatorial co-expression of a multitude of target and bait fusion reporters useful in projects like library screens. For these strategies, the regulatory elements and functional components need to correspond perfectly to project specific sequence elements that facilitate easy exchange of these elements. This requires systematic implementation and building on recent improvements in Golden Gate (GG) that ensures high cloning efficiency for such complex vectors. Currently, this is not addressed in the variety of molecular GG cloning techniques in synthetic biology. Here, we present the bottom-up design and plasmid synthesis to prepare 10 kb functional yeast secrete and display plasmids that uses an optimized version of GG in combination with fluorogen-activating protein reporter technology. This allowed us to demonstrate nanobody/target protein interactions in a single cell, as detected by cell surface retention of secreted target proteins by cognate nanobodies. This validates the GG constructional approach and suggests a new approach for discovering protein interactions. Our GG assembly platform paves the way for vector-based library screening and can be used for other recombinant GG platforms.

Optical imaging of targeted compartments within living animals has been widely adopted in many research areas. In particular, various fluorescence-based probes and emerged photoacoustic molecules that enable sensitive and specific imaging through tissue have greatly advanced clinically relevant studies. However, delivery and signal penetration have placed requirements on the performance of conventional optical probes. Here, we use hallow tantalum oxide (TaO_x) nanoparticles to enclose fluorogen-activating protein (FAP) for the in vivo fluorescence and photoacoustic imaging of cancer cells. We found that the TaO_x shell can provide a natural cover for the enclosed fluorogen/FAP complexes, protecting them from photobleaching and common biodegradation. Moreover, we have developed a near-infrared excitable tetrafluorinated photoacoustic fluorogen for the specific and persistent photoacoustic imaging of tumors. We believe that this enclosing and delivery strategy of optical biomolecules will be an attractive alternative for bioimaging.

Recent advantages of genetically encoded fluorescent probes have led to the development of fluorogen‐activating proteins (FAPs). This technology has two components: a non‐fluorescent single chain antibody (SCA) that can be fused to a protein of interest and fluorogens, which in our case are derivatives of malachite green that are non‐fluorescent when free in solution. When the SCA and fluorogen bind, there is a 20,000‐fold fluorescent increase relative to unbound dye. The FAP‐technology has two major advantages to standard fluorescent probes: i) the fluorogen exists as either a membrane‐permeant or impermeant form and this allows for selective labeling of cell surface proteins and (2) since SCA does not fluoresce when it is not bound by dye and so there is no background fluorescence during the imaging of other markers until after the fluorogen is added. Although developed in yeast, this technology surprisingly has not been applied in this model system until our recent studies. In order to make this technology more available to the yeast community, we have optimized the SCA sequence for yeast expression, created a series for FAP‐tagged plasmid constructs, and generated a suite of intracellular localization markers to aid in cell biology studies in yeast. We further employ the FAP technology to study the trafficking of the G‐protein coupled receptor Ste3 and its regulation by the alpha‐arrestins, an important class of trafficking adaptor.

Human immunodeficiency virus type 1 (HIV-1) capsid binds host proteins during infection, including cleavage and polyadenylation specificity factor 6 (CPSF6) and cyclophilin A (CypA). We observe that HIV-1 infection induces higher-order CPSF6 formation, and capsid-CPSF6 complexes cotraffic on microtubules. CPSF6-capsid complex trafficking is impacted by capsid alterations that reduce CPSF6 binding or by excess cytoplasmic CPSF6 expression, both of which are associated with decreased HIV-1 infection. Higher-order CPSF6 complexes bind and disrupt HIV-1 capsid assemblies in vitro. Disruption of HIV-1 capsid binding to CypA leads to increased CPSF6 binding and altered capsid trafficking, resulting in reduced infectivity. Our data reveal an interplay between CPSF6 and CypA that is important for cytoplasmic capsid trafficking and HIV-1 infection. We propose that CypA prevents HIV-1 capsid from prematurely engaging cytoplasmic CPSF6 and that differences in CypA cellular localization and innate immunity may explain variations in HIV-1 capsid trafficking and uncoating in CD4⁺ T cells and macrophages. IMPORTANCE HIV is the causative agent of AIDS, which has no cure. The protein shell that encases the viral genome, the capsid, is critical for HIV replication in cells at multiple steps. HIV capsid has been shown to interact with multiple cell proteins during movement to the cell nucleus in a poorly understood process that may differ during infection of different cell types. In this study, we show that premature or too much binding of one human protein, cleavage and polyadenylation specificity factor 6 (CPSF6), disrupts the ability of the capsid to deliver the viral genome to the cell nucleus. Another human protein, cyclophilin A (CypA), can shield HIV capsid from premature binding to CPSF6, which can differ in CD4⁺ T cells and macrophages. Better understanding of how HIV infects cells will allow better drugs to prevent or inhibit infection and pathogenesis.