Publications

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Thillaiappan, NB;Smith, HA;Atakpa-Adaji, P;Taylor, CW.
Nature communications,
12
(1)
, 4514
(2021)
Regulation of IP3 receptors (IP3Rs) by IP3 and Ca2+ allows regenerative Ca2+ signals, the smallest being Ca2+ puffs, which arise from coordinated openings of a few clustered IP3Rs. Cells express thousands of mostly mobile IP3Rs, yet Ca2+ puffs occur at a few immobile IP3R clusters. By imaging cells with endogenous IP3Rs tagged with EGFP, we show that KRas-induced actin-interacting protein (KRAP) tethers IP3Rs to actin beneath the plasma membrane. Loss of KRAP abolishes Ca2+ puffs and the global increases in cytosolic Ca2+ concentration evoked by more intense stimulation. Over-expressing KRAP immobilizes additional IP3R clusters and results in more Ca2+ puffs and larger global Ca2+ signals. Endogenous KRAP determines which IP3Rs will respond: it tethers IP3R clusters to actin alongside sites where store-operated Ca2+ entry occurs, licenses IP3Rs to evoke Ca2+ puffs and global cytosolic Ca2+ signals, implicates the actin cytoskeleton in IP3R regulation and may allow local activation of Ca2+ entry.
Dessalles, CA;Ramon-Lozano, C;Babataheri, A;Barakat, AI.
Biofabrication,
(2021)
In the microvasculature, blood flow-derived forces are key regulators of vascular structure and function. Consequently, the development of hydrogel-based microvessel-on-chip systems that strive to mimic the in vivo cellular organization and mechanical environment has received great attention in recent years. However, despite intensive efforts, current microvessel-on-chip systems suffer from several limitations, most notably failure to produce physiologically relevant wall strain levels. In this study, a novel microvessel-on-chip based on the templating technique and using luminal flow actuation to generate physiologically relevant levels of wall shear stress and circumferential stretch is presented. Normal forces induced by the luminal pressure compress the surrounding soft collagen hydrogel, dilate the channel, and create large circumferential strain. The fluid pressure gradient in the system drives flow forward and generates realistic pulsatile wall shear stresses. Rigorous characterization of the system reveals the crucial role played by the poroelastic behavior of the hydrogel in determining the magnitudes of the wall shear stress and strain. The experimental measurements are combined with an analytical model of flow in both the lumen and the porous hydrogel to provide an exceptionally versatile user manual for an application-based choice of parameters in microvessels-on-chip. This unique strategy of flow actuation adds a dimension to the capabilities of microvessel-on-chip systems and provides a more general framework for improving hydrogel-based in vitro engineered platforms.Creative Commons Attribution license.
O'Connor, JT;Stevens, AC;Shannon, EK;Akbar, FB;LaFever, KS;Narayanan, NP;Gailey, CD;Hutson, MS;Page-McCaw, A.
Developmental cell,
56
(15)
, 2160-2175.e5
(2021)
The presence of a wound triggers surrounding cells to initiate repair mechanisms, but it is not clear how cells initially detect wounds. In epithelial cells, the earliest known wound response, occurring within seconds, is a dramatic increase in cytosolic calcium. Here, we show that wounds in the Drosophila notum trigger cytoplasmic calcium increase by activating extracellular cytokines, Growth-blocking peptides (Gbps), which initiate signaling in surrounding epithelial cells through the G-protein-coupled receptor Methuselah-like 10 (Mthl10). Latent Gbps are present in unwounded tissue and are activated by proteolytic cleavage. Using wing discs, we show that multiple protease families can activate Gbps, suggesting that they act as a generalized protease-detector system. We present experimental and computational evidence that proteases released during wound-induced cell damage and lysis serve as the instructive signal: these proteases liberate Gbp ligands, which bind to Mthl10 receptors on surrounding epithelial cells, and activate downstream release of calcium.
Benítez-Mateos, AI;Bertella, S;Behaghel de Bueren, J;Luterbacher, JS;Paradisi, F.
ChemSusChem,
14
(15)
, 3198-3207
(2021)
Lignin has emerged as an attractive alternative in the search for more eco-friendly and less costly materials for enzyme immobilization. In this work, the terephthalic aldehyde-stabilization of lignin is carried out during its extraction to develop a series of functionalized lignins with a range of reactive groups (epoxy, amine, aldehyde, metal chelates). This expands the immobilization to a pool of enzymes (carboxylase, dehydrogenase, transaminase) by different binding chemistries, affording immobilization yields of 64-100 %. As a proof of concept, a ω-transaminase reversibly immobilized on polyethyleneimine-lignin is integrated in a packed-bed reactor. The stability of the immobilized biocatalyst is tested in continuous-flow deamination reactions and maintains the same conversion for 100 cycles. These results outperform previous stability tests carried out with the enzyme covalently immobilized on methacrylic resins, with the advantage that the reversibility of the immobilized enzyme allows recycling and reuse of lignin beyond the enzyme inactivation. Additionally, an in-line system also based on lignin is added into the downstream process to separate the reaction products by catch-and-release. These results demonstrate a fully closed-loop sustainable flow-biocatalytic system based exclusively on lignin.
Di Giulio, S;Colicchia, V;Pastorino, F;Pedretti, F;Fabretti, F;Nicolis di Robilant, V;Ramponi, V;Scafetta, G;Moretti, M;Licursi, V;Belardinilli, F;Peruzzi, G;Infante, P;Goffredo, BM;Coppa, A;Canettieri, G;Bartolazzi, A;Ponzoni, M;Giannini, G;Petroni, M.
Oncogene,
(2021)
MYCN drives aggressive behavior and refractoriness to chemotherapy, in several tumors. Since MYCN inactivation in clinical settings is not achievable, alternative vulnerabilities of MYCN-driven tumors need to be explored to identify more effective and less toxic therapies. We previously demonstrated that PARP inhibitors enhance MYCN-induced replication stress and promote mitotic catastrophe, counteracted by CHK1. Here, we showed that PARP and CHK1 inhibitors synergized to induce death in neuroblastoma cells and in primary cultures of SHH-dependent medulloblastoma, their combination being more effective in MYCN amplified and MYCN overexpressing cells compared to MYCN non-amplified cells. Although the MYCN amplified IMR-32 cell line carrying the p.Val2716Ala ATM mutation showed the highest sensitivity to the drug combination, this was not related to ATM status, as indicated by CRISPR/Cas9-based correction of the mutation. Suboptimal doses of the CHK1 inhibitor MK-8776 plus the PARP inhibitor olaparib led to a MYCN-dependent accumulation of DNA damage and cell death in vitro and significantly reduced the growth of four in vivo models of MYCN-driven tumors, without major toxicities. Our data highlight the combination of PARP and CHK1 inhibitors as a new potential chemo-free strategy to treat MYCN-driven tumors, which might be promptly translated into clinical trials.
Nasteska, D;Cuozzo, F;Viloria, K;Johnson, EM;Thakker, A;Bany Bakar, R;Westbrook, RL;Barlow, JP;Hoang, M;Joseph, JW;Lavery, GG;Akerman, I;Cantley, J;Hodson, L;Tennant, DA;Hodson, DJ.
JCI insight,
6
(16)
(2021)
The α-ketoglutarate-dependent dioxygenase, prolyl-4-hydroxylase 3 (PHD3), is an HIF target that uses molecular oxygen to hydroxylate peptidyl prolyl residues. Although PHD3 has been reported to influence cancer cell metabolism and liver insulin sensitivity, relatively little is known about the effects of this highly conserved enzyme in insulin-secreting β cells in vivo. Here, we show that the deletion of PHD3 specifically in β cells (βPHD3KO) was associated with impaired glucose homeostasis in mice fed a high-fat diet. In the early stages of dietary fat excess, βPHD3KO islets energetically rewired, leading to defects in the management of pyruvate fate and a shift from glycolysis to increased fatty acid oxidation (FAO). However, under more prolonged metabolic stress, this switch to preferential FAO in βPHD3KO islets was associated with impaired glucose-stimulated ATP/ADP rises, Ca2+ fluxes, and insulin secretion. Thus, PHD3 might be a pivotal component of the β cell glucose metabolism machinery in mice by suppressing the use of fatty acids as a primary fuel source during the early phases of metabolic stress.
Monmeyran, A;Benyoussef, W;Thomen, P;Dahmane, N;Baliarda, A;Jules, M;Aymerich, S;Henry, N.
NPJ biofilms and microbiomes,
7
(1)
, 64
(2021)
Multispecies microbial adherent communities are widespread in nature and organisms, although the principles of their assembly and development remain unclear. Here, we test the possibility of establishing a simplified but relevant model of multispecies biofilm in a non-invasive laboratory setup for the real-time monitoring of community development. We demonstrate that the four chosen species (Bacillus thuringiensis, Pseudomonas fluorescens, Kocuria varians, and Rhodocyclus sp.) form a dynamic community that deterministically reaches its equilibrium after ~30 h of growth. We reveal the emergence of complexity in this simplified community as reported by an increase in spatial heterogeneity and non-monotonic developmental kinetics. Importantly, we find interspecies interactions consisting of competition for resources-particularly oxygen-and both direct and indirect physical interactions. The simplified experimental model opens new avenues to the study of adherent bacterial communities and their behavior in the context of rapid global change.
Garone, MG;Birsa, N;Rosito, M;Salaris, F;Mochi, M;de Turris, V;Nair, RR;Cunningham, TJ;Fisher, EMC;Morlando, M;Fratta, P;Rosa, A.
Communications biology,
4
(1)
, 1025
(2021)
Mutations in the RNA-binding protein (RBP) FUS have been genetically associated with the motoneuron disease amyotrophic lateral sclerosis (ALS). Using both human induced pluripotent stem cells and mouse models, we found that FUS-ALS causative mutations affect the activity of two relevant RBPs with important roles in neuronal RNA metabolism: HuD/ELAVL4 and FMRP. Mechanistically, mutant FUS leads to upregulation of HuD protein levels through competition with FMRP for HuD mRNA 3’UTR binding. In turn, increased HuD levels overly stabilize the transcript levels of its targets, NRN1 and GAP43. As a consequence, mutant FUS motoneurons show increased axon branching and growth upon injury, which could be rescued by dampening NRN1 levels. Since similar phenotypes have been previously described in SOD1 and TDP-43 mutant models, increased axonal growth and branching might represent broad early events in the pathogenesis of ALS.
Sujkowski, A;Wessells, R.
Cells,
10
(9)
(2021)
Chronic exercise is widely recognized as an important contributor to healthspan in humans and in diverse animal models. Recently, we have demonstrated that Sestrins, a family of evolutionarily conserved exercise-inducible proteins, are critical mediators of exercise benefits in flies and mice. Knockout of Sestrins prevents exercise adaptations to endurance and flight in Drosophila, and similarly prevents benefits to endurance and metabolism in exercising mice. In contrast, overexpression of dSestrin in muscle mimics several of the molecular and physiological adaptations characteristic of endurance exercise. Here, we extend those observations to examine the impact of dSestrin on preserving speed and increasing lysosomal activity. We find that dSestrin is a critical factor driving exercise adaptations to climbing speed, but is not absolutely required for exercise to increase lysosomal activity in Drosophila. The role of Sestrin in increasing speed during chronic exercise requires both the TORC2/AKT axis and the PGC1α homolog spargel, while dSestrin requires interactions with TORC1 to cell-autonomously increase lysosomal activity. These results highlight the conserved role of Sestrins as key factors that drive diverse physiological adaptations conferred by chronic exercise.
Merigliano, C;Burla, R;La Torre, M;Del Giudice, S;Teo, H;Liew, CW;Chojnowski, A;Goh, WI;Olmos, Y;Maccaroni, K;Giubettini, M;Chiolo, I;Carlton, JG;Raimondo, D;Vernì, F;Stewart, CL;Rhodes, D;Wright, GD;Burke, BE;Saggio, I.
PLoS genetics,
17
(8)
, e1009757
(2021)
To complete mitosis, the bridge that links the two daughter cells needs to be cleaved. This step is carried out by the endosomal sorting complex required for transport (ESCRT) machinery. AKTIP, a protein discovered to be associated with telomeres and the nuclear membrane in interphase cells, shares sequence similarities with the ESCRT I component TSG101. Here we present evidence that during mitosis AKTIP is part of the ESCRT machinery at the midbody. AKTIP interacts with the ESCRT I subunit VPS28 and forms a circular supra-structure at the midbody, in close proximity with TSG101 and VPS28 and adjacent to the members of the ESCRT III module CHMP2A, CHMP4B and IST1. Mechanistically, the recruitment of AKTIP is dependent on MKLP1 and independent of CEP55. AKTIP and TSG101 are needed together for the recruitment of the ESCRT III subunit CHMP4B and in parallel for the recruitment of IST1. Alone, the reduction of AKTIP impinges on IST1 and causes multinucleation. Our data altogether reveal that AKTIP is a component of the ESCRT I module and functions in the recruitment of ESCRT III components required for abscission.
Church, ME;Ceja, G;McGeehan, M;Miller, MC;Farias, P;Sánchez, MD;Swain, GP;Assenmacher, CA;Stopa, EG;Vite, CH;Bar-Or, A;Alvarez, JI.
Journal of immunology,
(2021)
Multiple sclerosis (MS) is an idiopathic demyelinating disease in which meningeal inflammation correlates with accelerated disease progression. The study of meningeal inflammation in MS has been limited because of constrained access to MS brain/spinal cord specimens and the lack of experimental models recapitulating progressive MS. Unlike induced models, a spontaneously occurring model would offer a unique opportunity to understand MS immunopathogenesis and provide a compelling framework for translational research. We propose granulomatous meningoencephalomyelitis (GME) as a natural model to study neuropathological aspects of MS. GME is an idiopathic, progressive neuroinflammatory disease of young dogs with a female bias. In the GME cases examined in this study, the meninges displayed focal and disseminated leptomeningeal enhancement on magnetic resonance imaging, which correlated with heavy leptomeningeal lymphocytic infiltration. These leptomeningeal infiltrates resembled tertiary lymphoid organs containing large B cell clusters that included few proliferating Ki67+ cells, plasma cells, follicular dendritic/reticular cells, and germinal center B cell-like cells. These B cell collections were confined in a specialized network of collagen fibers associated with the expression of the lympho-organogenic chemokines CXCL13 and CCL21. Although neuroparenchymal perivascular infiltrates contained B cells, they lacked the immune signature of aggregates in the meningeal compartment. Finally, meningeal B cell accumulation correlated significantly with cortical demyelination reflecting neuropathological similarities to MS. Hence, during chronic neuroinflammation, the meningeal microenvironment sustains B cell accumulation that is accompanied by underlying neuroparenchymal injury, indicating GME as a novel, naturally occurring model to study compartmentalized neuroinflammation and the associated pathology thought to contribute to progressive MS.
Cordella, F;Sanchini, C;Rosito, M;Ferrucci, L;Pediconi, N;Cortese, B;Guerrieri, F;Pascucci, G;Antonangeli, F;Peruzzi, G;Giubettini, M;Basilico, B;Pagani, F;Grimaldi, A;D’Alessandro, G;Limatola, C;Ragozzino, D;Di Angelantonio, S.
Cells,
(2021)
‘Dysbiosis’ of the adult gut microbiota, in response to challenges such as infection, altered diet, stress, and antibiotics treatment has been recently linked to pathological alteration of brain func-tion and behavior. Moreover, gut microbiota composition constantly controls microglia matura-tion as revealed by morphological observations and gene expression analysis. However, it is un-clear whether gut microbiota influences microglia functional properties and crosstalk with neu-rons, known to shape and modulate synaptic development and function. Here, we investigated how antibiotic mediated alteration of the gut microbiota influences microglial and neuronal functions in adult mice hippocampus. Hippocampal microglia from adult mice treated with oral antibiotics exhibited increased microglia density, altered basal patrolling activity, and impaired process rearrangement in response to damage. Patch clamp recordings at CA3-CA1 synapses revealed that antibiotics treatment alters neuronal functions, reducing spontaneous postsynaptic glutamatergic currents and decreasing synaptic connectivity, without reducing dendritic spines density. The effect of dysbiosis on neuronal functions are mediated by microglia-neuron cross-talk through the CX3CL1-CX3CR1 axis, as antibiotics treatment of CX3CR1 deficient mice, mod-ulates microglia density and processes rearrangement leaving unaltered synaptic function. To-gether, our findings show that the antibiotics alteration of gut microbiota impairs synaptic effi-cacy, probably through CX3CL1-CX3CR1 signaling supporting microglia as a major player in in the gut-brain axis, and in particular in the gut microbiota-to-neuron communication pathway.
Kilik, U;Yu, Q;Holtackers, R;Seimiya, M.
bioRxiv,
(2021)
Methods to generate human intestinal tissue from pluripotent stem cells (PSCs) open new inroads into modeling intestine development and disease. However, current protocols require organoid transplantation into an immunocompromised mouse to achieve matured and differentiated epithelial cell states. Inspired by developmental reconstructions from primary tissues, we establish a regimen of inductive cues that enable stem cell maturation and epithelial differentiation entirely in vitro. We show that the niche factor Neuregulin1 (NRG1) promotes morphological change from proliferative epithelial cysts to matured epithelial tissue in three-dimensional cultures. Single-cell transcriptome analyses reveal differentiated epithelial cell populations, including diverse secretory and absorptive lineages. Comparison to multi-organ developmental and adult intestinal cell atlases confirm the specificity and maturation state of cell populations. Altogether, this work opens a new direction to use in vitro matured epithelium from human PSCs to study human intestinal epithelium development, disease, and evolution in controlled culture environments.
Heckman, CA;Ademuyiwa, OM;Cayer, ML.
bioRxiv,
(2021)
During directional locomotion, cells must reorient themselves in response to attractive or repulsive cues. Filopodia are narrow actin-based protrusions whose prevalence at the leading edge of a migrating cell is related to the persistence of locomotion. Although there is a marked absence of calcium-binding components in their structure, they responded to store-operated calcium entry (SOCE). Here, we used a two-phase protocol to determine how they responded. In the first phase, extracellular calcium was removed and ER calcium lowered by blocking reuptake through the calcium pump. This was known to activate stromal interacting molecule (STIM) and cause its microtubule-mediated translocation to the cell surface. In the second phase, extracellular calcium and calcium influx into the ER were restored. ER depletion caused filopodia to increase, followed by a spontaneous decrease that was blocked by inhibiting endocytosis. The intracellular calcium concentration increased during depletion, while the size of the exchangeable compartment of vesicles, measured by fluid-phase marker uptake, shrank. When SOCE mediators and the aquaporin, AQP4, were localized, STIM and transient receptor potential canonical (TPRC) channels occupied vesicular profiles side-by-side in linear arrays. STIM1 was translocated, as expected. TRPC1 was initially in a rapidly recycling pool (RRP) where it partially colocalized with Vamp2. Calcium restoration caused TRPC1 exocytosis, while STIM1 reverted toward its original pattern associated with the ER. The exchangeable compartment was restored and this enabled filopodia extension, which was blocked by inhibitors of TRPC1/4/5 and endocytosis. That vesicle recycling was essential for extension during calcium readdition was indicated by reversal of the effect of endocytosis inhibitors in the depletion and readdition phases. The results suggest that SOCE regulates the size of the RRP in epithelial cells, and vesicle recycling is the immediate mechanism affecting filopodia extension. The conclusions are discussed in light of factors regulating protrusion formation, namely surface tension and vesicle trafficking.
Torromino, G;Loffredo, V;Cavezza, D;Esposito, F.
bioRxiv,
(2021)
Memory can be challenged by increasing both its required duration and the amount of information to be encoded, namely the memory load. The dorsal hippocampus (dHP) has been involved in memory consolidation, which is the stabilization of a trace from short-term (STM) to long-term memory (LTM), as well as in the ability to process high information load. However, how memory load influences memory consolidation, and the underlying neural mechanisms, are yet unknown. To address this question, we used male and female mice that, despite having in our Different Object recognition Task (DOT) the same STM capacity of 6 objects, spontaneously show differences in the number of objects directly transferred to LTM, when tested over longer delays. Males memorize all 6 objects encoded, while females remember only up to 4, both at 1 and 24 h delays. Interestingly, males activate more the dHP (as measured by c-Fos expression), while females the thalamic nucleus reuniens (RE). Optogenetic inhibition of the RE-dHP pathway during off-line memory consolidation favors 6-object LTM retention in females by removing inhibitory control over dHP activation, while chemogenetic RE-activation impairs it in males. Our data represent a first demonstration of a sub-cortical control of dHP recruitment, that might underlie its sex-dependent activation during incidental memory, with potential also for clinical application.
Eberle, AB;Schranz, K;Nasif, S;Grollmus, L.
bioRxiv,
(2021)
The RNA helicase UPF1 is best known for its key role in mRNA surveillance but has been implicated in additional cellular processes both in the nucleus and in the cytoplasm. In human cells, the vast majority of UPF1 resides in the cytoplasm and only small amounts can be detected in the nucleus at steady state. It was previously shown that its export from the nucleus to the cytoplasm is Crm1-dependent, yet neither the nuclear export signal (NES) nor the nuclear localization signal (NLS) has been identified. Here, we provide evidence for a noncanonical NLS in UPF1, map the NES to amino acids 89-105 and show that L103 and F105 are essential for UPF1’s export to the cytoplasm. Examination of additional UPF1 mutants revealed that a functional helicase domain but not the association with RNA is crucial for the shuttling capacity of UPF1.
Lemma, B;Mitchell, NP;Subramanian, R.
arXiv,
(2021)
Mixtures of microtubules and molecular motors form active materials with diverse dynamical behaviors that vary based on their constituents’ molecular properties. We map the non-equilibrium phase diagram of microtubules and tip-accumulating kinesin-4 molecular motors. We find that kinesin-4 can drive either global contractions or turbulent-like extensile dynamics, depending on the concentrations of both microtubules and a bundling agent. We also observe a range of spatially heterogeneous non-equilibrium phases, including finite-sized radial asters, 1D wormlike chains, extended 2D bilayers, and system-spanning 3D active foams. Finally, we describe intricate kinetic pathways that yield microphase separated structures and arise from the inherent frustration between the orientational order of filamentous microtubules and the positional order of tip-accumulating molecular motors. Our work shows that the form of active stresses and phases in cytoskeletal networks are not solely dictated by the properties of individual motors and filaments, but are also contingent on the constituent’s concentrations and spatial arrangement.
Lequyer, J;Philip, R;Sharma, A;Pelletier, L.
arXiv,
(2021)
In the last several years deep learning based approaches have come to dominate many areas of computer vision, and image denoising is no exception. Neural networks can learn by example to map noisy images to clean images. However, access to noisy/clean or even noisy/noisy image pairs isn’t always readily available in the desired domain. Recent approaches have allowed for the denoising of single noisy images without access to any training data aside from that very image. But since they require both training and inference to be carried out on each individual input image, these methods require significant computation time. As such, they are difficult to integrate into automated microscopy pipelines where denoising large datasets is essential but needs to be carried out in a timely manner. Here we present Noise2Fast, a fast single image blind denoiser. Our method is tailored for speed by training on a four-image dataset produced using a unique form of downsampling we refer to as “checkerboard downsampling”. Noise2Fast is faster than all tested approaches and is more accurate than all except Self2Self, which takes well over 100 times longer to denoise an image. This allows for a combination of speed and flexibility that was not previously attainable using any other method.
Brighi, C;Salaris, F;Soloperto, A;Cordella, F;Ghirga, S;de Turris, V;Rosito, M;Porceddu, PF;D'Antoni, C;Reggiani, A;Rosa, A;Di Angelantonio, S.
Cell Death & Disease,
12
(5)
, 1-22
(2021)
Fragile X syndrome (FXS) is a neurodevelopmental disorder, characterized by intellectual disability and sensory deficits, caused by epigenetic silencing of the FMR1 gene and subsequent loss of its protein product, fragile X mental retardation protein (FMRP). Delays in synaptic and neuronal development in the cortex have been reported in FXS mouse models; however, the main goal of translating lab research into pharmacological treatments in clinical trials has been so far largely unsuccessful, leaving FXS a still incurable disease. Here, we generated 2D and 3D in vitro human FXS model systems based on isogenic FMR1 knock-out mutant and wild-type human induced pluripotent stem cell (hiPSC) lines. Phenotypical and functional characterization of cortical neurons derived from FMRP-deficient hiPSCs display altered gene expression and impaired differentiation when compared with the healthy counterpart. FXS cortical cultures show an increased number of GFAP positive cells, likely astrocytes, increased spontaneous network activity, and depolarizing GABAergic transmission. Cortical brain organoid models show an increased number of glial cells, and bigger organoid size. Our findings demonstrate that FMRP is required to correctly support neuronal and glial cell proliferation, and to set the correct excitation/inhibition ratio in human brain development.
Bonnal, RJP;Rossetti, G;Lugli, E;De Simone, M;Gruarin, P;Brummelman, J;Drufuca, L;Passaro, M;Bason, R;Gervasoni, F;Della Chiara, G;D'Oria, C;Martinovic, M;Curti, S;Ranzani, V;Cordiglieri, C;Alvisi, G;Mazza, EMC;Oliveto, S;Silvestri, Y;Carelli, E;Mazzara, S;Bosotti, R;Sarnicola, ML;Godano, C;Bevilacqua, V;Lorenzo, M;Siena, S;Bonoldi, E;Sartore-Bianchi, A;Amatu, A;Veronesi, G;Novellis, P;Alloisio, M;Giani, A;Zucchini, N;Opocher, E;Ceretti, AP;Mariani, N;Biffo, S;Prati, D;Bardelli, A;Geginat, J;Lanzavecchia, A;Abrignani, S;Pagani, M.
Nature immunology,
22
(6)
, 735-745
(2021)
Regulatory T (Treg) cells are a barrier for tumor immunity and a target for immunotherapy. Using single-cell transcriptomics, we found that CD4+ T cells infiltrating primary and metastatic colorectal cancer and non-small-cell lung cancer are highly enriched for two subsets of comparable size and suppressor function comprising forkhead box protein P3+ Treg and eomesodermin homolog (EOMES)+ type 1 regulatory T (Tr1)-like cells also expressing granzyme K and chitinase-3-like protein 2. EOMES+ Tr1-like cells, but not Treg cells, were clonally related to effector T cells and were clonally expanded in primary and metastatic tumors, which is consistent with their proliferation and differentiation in situ. Using chitinase-3-like protein 2 as a subset signature, we found that the EOMES+ Tr1-like subset correlates with disease progression but is also associated with response to programmed cell death protein 1-targeted immunotherapy. Collectively, these findings highlight the heterogeneity of Treg cells that accumulate in primary tumors and metastases and identify a new prospective target for cancer immunotherapy.