Simone Puccio
Researcher
Area of interest:
Over the past years, Dr. Simone Puccio has dedicated his professional career to the application of bioinformatics, computational biology, and high-dimensional data analysis to biomedical research. His work has focused on the development and implementation of advanced computational approaches for the analysis of genomics, transcriptomics, epigenomics, metagenomics, and single-cell datasets, with particular attention to cancer immunology, host–pathogen interactions, and translational medicine.
Dr. Puccio obtained his Master’s Degree in Bioinformatics from the University of Tor Vergata in Rome, graduating cum laude, and later completed a PhD in Molecular and Translational Medicine at the University of Milan. During his doctoral studies, he developed computational tools for the analysis of interactome-sequencing data and the identification of Helicobacter pylori epitopes involved in host immune-response modulation. He further strengthened his expertise in data science by completing a First Level Specialising Master in Business Intelligence and Big Data Analytics at the University of Milan-Bicocca.
His research experience includes positions at the National Council of Research in Milan, Humanitas Research Hospital, and Temple University in Philadelphia. At Temple University, he contributed to projects in Alzheimer’s disease, neuronal toxicity, chronic obstructive pulmonary disease, and proteomics. At the CNR Institute of Biomedical Technologies, he worked on next-generation sequencing data analysis in genomics, transcriptomics, and proteomics, with a particular focus on Helicobacter pylori pathogenesis and persistence. He later joined the Laboratory of Translational Immunology at Humanitas Research Hospital, where he contributed to projects investigating stem-like T cell differentiation and strategies to improve anti-tumor CAR T cell activity.
Dr. Puccio is currently a bioinformatician at the CNR Institute for Genetic and Biomedical Research in Milan. His work combines scientific programming, statistical analysis, workflow development, and multi-omics integration to support experimental and clinical research. He is highly experienced in RNA-seq, ChIP-seq, ATAC-seq, single-cell transcriptomics, high-dimensional cytometry, and cancer genomics, and he develops scalable pipelines using tools such as Python, R, Bioconductor, UNIX/bash, Nextflow, Snakemake, Docker, and Galaxy.
Throughout his career, Dr. Puccio has contributed to numerous peer-reviewed publications in leading scientific journals, including Nature Communications, Nature Immunology, Journal of Clinical Investigation, Cancer Immunology Research, Circulation Research, and others. He has also contributed to the development of bioinformatics platforms and software resources, including WOPPER, InteractomeSeq and CRUSTY, supporting the analysis and visualization of complex biological datasets.
Most significant publications:
2026
Gattinoni, Luca; Inchingolo, Gabriele; Harrer, Dennis C; Susana, Alberto; Puccio, Simone; Slavkovic-Lukic, Dragana; Natrakul, Danielle A; Strieder, Nicholas; Heuser-Loy, Christoph; Baldwin, Jeremy G; Fioravanti, Jessica; Ji, Yun; Gautam, Sanjivan; Suriano, Chiara; Martín-Santos, Azucena; Schelker, Roland C; Patel, Nisha; Mann, Jennifer; Goff, Stephanie; Mikkilineni, Lekha; Yang, James C; Kwong, Mei Li M; Patel, Rashmika; Rehli, Michael; Highfill, Steven L; Stroncek, David F; Rosenberg, Steven A; Biasco, Luca; Lugli, Enrico; Brudno, Jennifer N; Kochenderfer, James N
Distinct in vivo dynamics of donor-derived stem cell memory CAR T cells post-allogeneic HSCT relapse Journal Article
In: Cell, vol. 189, no. 12, pp. 3686–3700.e10, 2026, ISSN: 1097-4172.
@article{pmid42066750,
title = {Distinct in vivo dynamics of donor-derived stem cell memory CAR T cells post-allogeneic HSCT relapse},
author = {Luca Gattinoni and Gabriele Inchingolo and Dennis C Harrer and Alberto Susana and Simone Puccio and Dragana Slavkovic-Lukic and Danielle A Natrakul and Nicholas Strieder and Christoph Heuser-Loy and Jeremy G Baldwin and Jessica Fioravanti and Yun Ji and Sanjivan Gautam and Chiara Suriano and Azucena Martín-Santos and Roland C Schelker and Nisha Patel and Jennifer Mann and Stephanie Goff and Lekha Mikkilineni and James C Yang and Mei Li M Kwong and Rashmika Patel and Michael Rehli and Steven L Highfill and David F Stroncek and Steven A Rosenberg and Luca Biasco and Enrico Lugli and Jennifer N Brudno and James N Kochenderfer},
doi = {10.1016/j.cell.2026.03.047},
issn = {1097-4172},
year = {2026},
date = {2026-06-01},
journal = {Cell},
volume = {189},
number = {12},
pages = {3686--3700.e10},
abstract = {Donor-derived CD19-CAR T cells offer a therapeutic option for B cell malignancies relapsing after allogeneic hematopoietic stem cell transplantation but are often constrained by poor engraftment, expansion, and persistence. In a first-in-human study (NCT01087294), we found that CAR-modified stem-cell memory T (T) cells exhibited greater expansion and persistence than standard CAR T cells, enabling complete responses at low doses in the absence of lymphodepletion. CAR T cells induced mild cytokine-release syndrome, dominated by IFN-γ. Both products differentiated into effectors; however, only CAR T cells robustly reconstituted the stem-like compartment over time. CAR T cells were sustained through clonal succession, whereas persisting standard CAR T cells resulted from maintenance or contraction of early-expanded clones. While poor expansion limited standard CAR T cell activity, resistance to CAR T cells was driven primarily by tumor- and host-related factors. These findings establish CAR T cells as a promising platform for next-generation CAR T cell therapies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Donor-derived CD19-CAR T cells offer a therapeutic option for B cell malignancies relapsing after allogeneic hematopoietic stem cell transplantation but are often constrained by poor engraftment, expansion, and persistence. In a first-in-human study (NCT01087294), we found that CAR-modified stem-cell memory T (T) cells exhibited greater expansion and persistence than standard CAR T cells, enabling complete responses at low doses in the absence of lymphodepletion. CAR T cells induced mild cytokine-release syndrome, dominated by IFN-γ. Both products differentiated into effectors; however, only CAR T cells robustly reconstituted the stem-like compartment over time. CAR T cells were sustained through clonal succession, whereas persisting standard CAR T cells resulted from maintenance or contraction of early-expanded clones. While poor expansion limited standard CAR T cell activity, resistance to CAR T cells was driven primarily by tumor- and host-related factors. These findings establish CAR T cells as a promising platform for next-generation CAR T cell therapies.
2025
Marelli, Giulia; Morina, Nicolò; Puccio, Simone; Iovino, Marta; Pandini, Marta; Portale, Federica; Carvetta, Mattia; Mishra, Divya; Diana, Elisabetta; Meregalli, Greta; Paraboschi, Elvezia; Cibella, Javier; Peano, Clelia; Basso, Gianluca; Simone, Gabriele De; Camisaschi, Chiara; Magrini, Elena; Sartori, Giulio; Karimi, Elham; Colombo, Piergiuseppe; Lazzeri, Massimo; Casale, Paolo; Morosi, Lavinia; Martano, Giuseppe; Asselta, Rosanna; Bonavita, Eduardo; Matsunami, Hiro; Bertoni, Francesco; Walsh, Logan; Lugli, Enrico; Mitri, Diletta Di
Chemosensor receptors are lipid-detecting regulators of macrophage function in cancer Journal Article
In: Nat Immunol, vol. 26, no. 7, pp. 1182–1197, 2025, ISSN: 1529-2916.
@article{pmid40588561,
title = {Chemosensor receptors are lipid-detecting regulators of macrophage function in cancer},
author = {Giulia Marelli and Nicolò Morina and Simone Puccio and Marta Iovino and Marta Pandini and Federica Portale and Mattia Carvetta and Divya Mishra and Elisabetta Diana and Greta Meregalli and Elvezia Paraboschi and Javier Cibella and Clelia Peano and Gianluca Basso and Gabriele De Simone and Chiara Camisaschi and Elena Magrini and Giulio Sartori and Elham Karimi and Piergiuseppe Colombo and Massimo Lazzeri and Paolo Casale and Lavinia Morosi and Giuseppe Martano and Rosanna Asselta and Eduardo Bonavita and Hiro Matsunami and Francesco Bertoni and Logan Walsh and Enrico Lugli and Diletta Di Mitri},
doi = {10.1038/s41590-025-02191-x},
issn = {1529-2916},
year = {2025},
date = {2025-07-01},
journal = {Nat Immunol},
volume = {26},
number = {7},
pages = {1182--1197},
abstract = {Infiltration of macrophages into tumors is a hallmark of cancer progression, and re-educating tumor-associated macrophages (TAMs) toward an antitumor status is a promising immunotherapy strategy. However, the mechanisms through which cancer cells affect macrophage education are unclear, limiting the therapeutic potential of this approach. Here we conducted an unbiased genome-wide CRISPR screen of primary macrophages. Our study confirms the function of known regulators in TAM responses and reveals new insights into the behavior of these cells. We identify olfactory and vomeronasal receptors, or chemosensors, as important drivers of a tumor-supportive macrophage phenotype across multiple cancers. In vivo deletion of selected chemosensors in TAMs resulted in cancer regression and increased infiltration of tumor-reactive CD8 T cells. In human prostate cancer tissues, palmitic acid bound to olfactory receptor 51E2 (OR51E2) expressed by TAMs, enhancing their protumor phenotype. Spatial lipidomics analysis further confirmed the presence of palmitic acid in close proximity to TAMs in prostate cancer, supporting the function of this lipid mediator in the tumor microenvironment. Overall, these data implicate chemosensors in macrophage sensing of the lipid-enriched milieu and highlight these receptors as possible therapeutic targets for enhancing antitumor immunity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Infiltration of macrophages into tumors is a hallmark of cancer progression, and re-educating tumor-associated macrophages (TAMs) toward an antitumor status is a promising immunotherapy strategy. However, the mechanisms through which cancer cells affect macrophage education are unclear, limiting the therapeutic potential of this approach. Here we conducted an unbiased genome-wide CRISPR screen of primary macrophages. Our study confirms the function of known regulators in TAM responses and reveals new insights into the behavior of these cells. We identify olfactory and vomeronasal receptors, or chemosensors, as important drivers of a tumor-supportive macrophage phenotype across multiple cancers. In vivo deletion of selected chemosensors in TAMs resulted in cancer regression and increased infiltration of tumor-reactive CD8 T cells. In human prostate cancer tissues, palmitic acid bound to olfactory receptor 51E2 (OR51E2) expressed by TAMs, enhancing their protumor phenotype. Spatial lipidomics analysis further confirmed the presence of palmitic acid in close proximity to TAMs in prostate cancer, supporting the function of this lipid mediator in the tumor microenvironment. Overall, these data implicate chemosensors in macrophage sensing of the lipid-enriched milieu and highlight these receptors as possible therapeutic targets for enhancing antitumor immunity.
Yang, Jie; Yamashita-Kanemaru, Yumi; Morris, Benjamin I; Contursi, Annalisa; Trajkovski, Daniel; Xu, Jingru; Patrascan, Ilinca; Benson, Jayme; Evans, Alexander C; Conti, Alberto G; Al-Deka, Aws; Dahmani, Layla; Avdic-Belltheus, Adnan; Zhang, Baojie; Okkenhaug, Hanneke; Whiteside, Sarah K; Imianowski, Charlotte J; Wesolowski, Alexander J; Webb, Louise V; Puccio, Simone; Tacconelli, Stefania; Bruno, Annalisa; Berardino, Sara Di; Michele, Alessandra De; Welch, Heidi C E; Yu, I-Shing; Lin, Shu-Wha; Mitra, Suman; Lugli, Enrico; van der Weyden, Louise; Okkenhaug, Klaus; Saeb-Parsy, Kourosh; Patrignani, Paola; Adams, David J; Roychoudhuri, Rahul
Aspirin prevents metastasis by limiting platelet TXA suppression of T cell immunity Journal Article
In: Nature, vol. 640, no. 8060, pp. 1052–1061, 2025, ISSN: 1476-4687.
@article{pmid40044852,
title = {Aspirin prevents metastasis by limiting platelet TXA suppression of T cell immunity},
author = {Jie Yang and Yumi Yamashita-Kanemaru and Benjamin I Morris and Annalisa Contursi and Daniel Trajkovski and Jingru Xu and Ilinca Patrascan and Jayme Benson and Alexander C Evans and Alberto G Conti and Aws Al-Deka and Layla Dahmani and Adnan Avdic-Belltheus and Baojie Zhang and Hanneke Okkenhaug and Sarah K Whiteside and Charlotte J Imianowski and Alexander J Wesolowski and Louise V Webb and Simone Puccio and Stefania Tacconelli and Annalisa Bruno and Sara Di Berardino and Alessandra De Michele and Heidi C E Welch and I-Shing Yu and Shu-Wha Lin and Suman Mitra and Enrico Lugli and Louise van der Weyden and Klaus Okkenhaug and Kourosh Saeb-Parsy and Paola Patrignani and David J Adams and Rahul Roychoudhuri},
doi = {10.1038/s41586-025-08626-7},
issn = {1476-4687},
year = {2025},
date = {2025-04-01},
journal = {Nature},
volume = {640},
number = {8060},
pages = {1052--1061},
abstract = {Metastasis is the spread of cancer cells from primary tumours to distant organs and is the cause of 90% of cancer deaths globally. Metastasizing cancer cells are uniquely vulnerable to immune attack, as they are initially deprived of the immunosuppressive microenvironment found within established tumours. There is interest in therapeutically exploiting this immune vulnerability to prevent recurrence in patients with early cancer at risk of metastasis. Here we show that inhibitors of cyclooxygenase 1 (COX-1), including aspirin, enhance immunity to cancer metastasis by releasing T cells from suppression by platelet-derived thromboxane A (TXA). TXA acts on T cells to trigger an immunosuppressive pathway that is dependent on the guanine exchange factor ARHGEF1, suppressing T cell receptor-driven kinase signalling, proliferation and effector functions. T cell-specific conditional deletion of Arhgef1 in mice increases T cell activation at the metastatic site, provoking immune-mediated rejection of lung and liver metastases. Consequently, restricting the availability of TXA using aspirin, selective COX-1 inhibitors or platelet-specific deletion of COX-1 reduces the rate of metastasis in a manner that is dependent on T cell-intrinsic expression of ARHGEF1 and signalling by TXA in vivo. These findings reveal a novel immunosuppressive pathway that limits T cell immunity to cancer metastasis, providing mechanistic insights into the anti-metastatic activity of aspirin and paving the way for more effective anti-metastatic immunotherapies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Metastasis is the spread of cancer cells from primary tumours to distant organs and is the cause of 90% of cancer deaths globally. Metastasizing cancer cells are uniquely vulnerable to immune attack, as they are initially deprived of the immunosuppressive microenvironment found within established tumours. There is interest in therapeutically exploiting this immune vulnerability to prevent recurrence in patients with early cancer at risk of metastasis. Here we show that inhibitors of cyclooxygenase 1 (COX-1), including aspirin, enhance immunity to cancer metastasis by releasing T cells from suppression by platelet-derived thromboxane A (TXA). TXA acts on T cells to trigger an immunosuppressive pathway that is dependent on the guanine exchange factor ARHGEF1, suppressing T cell receptor-driven kinase signalling, proliferation and effector functions. T cell-specific conditional deletion of Arhgef1 in mice increases T cell activation at the metastatic site, provoking immune-mediated rejection of lung and liver metastases. Consequently, restricting the availability of TXA using aspirin, selective COX-1 inhibitors or platelet-specific deletion of COX-1 reduces the rate of metastasis in a manner that is dependent on T cell-intrinsic expression of ARHGEF1 and signalling by TXA in vivo. These findings reveal a novel immunosuppressive pathway that limits T cell immunity to cancer metastasis, providing mechanistic insights into the anti-metastatic activity of aspirin and paving the way for more effective anti-metastatic immunotherapies.
Martini, Elisa; Cremonesi, Marco; Felicetta, Arianna; Serio, Simone; Puccio, Simone; Pelamatti, Erica; van Beek, Jasper J P; Papadopoulou, Vasiliki; Catalano, Chiara; Fanuele, Francesca; Giuliano, Desirée; Basso, Gianluca; Bonfiglio, Cecilia Assunta; Panico, Cristina; Vacchiano, Marco; Carullo, Pierluigi; Papa, Laura; D'Andrea, Carla; Tuzger, Naz; Marchini, Sergio; Magistroni, Paola; Deaglio, Silvia; Amoroso, Antonio; Lugli, Enrico; Condorelli, Gianluigi; Kallikourdis, Marinos
Autoimmune-Like Mechanism in Heart Failure Enables Preventive Vaccine Therapy Journal Article
In: Circ Res, vol. 136, no. 1, pp. 4–25, 2025, ISSN: 1524-4571.
@article{pmid39629560,
title = {Autoimmune-Like Mechanism in Heart Failure Enables Preventive Vaccine Therapy},
author = {Elisa Martini and Marco Cremonesi and Arianna Felicetta and Simone Serio and Simone Puccio and Erica Pelamatti and Jasper J P van Beek and Vasiliki Papadopoulou and Chiara Catalano and Francesca Fanuele and Desirée Giuliano and Gianluca Basso and Cecilia Assunta Bonfiglio and Cristina Panico and Marco Vacchiano and Pierluigi Carullo and Laura Papa and Carla D'Andrea and Naz Tuzger and Sergio Marchini and Paola Magistroni and Silvia Deaglio and Antonio Amoroso and Enrico Lugli and Gianluigi Condorelli and Marinos Kallikourdis},
doi = {10.1161/CIRCRESAHA.124.324999},
issn = {1524-4571},
year = {2025},
date = {2025-01-01},
journal = {Circ Res},
volume = {136},
number = {1},
pages = {4--25},
abstract = {BACKGROUND: Heart failure (HF) is strongly associated with inflammation. In pressure overload (PO)-induced HF, cardiac stress triggers adaptive immunity, ablation or inhibition of which blocks disease progression. We hypothesized that PO-HF might fulfill the often-used criteria of autoimmunity: if so, the associated adaptive immune response would be not only necessary but also sufficient to induce HF; it should also be possible to identify self-antigens driving the autoimmune response. Finally, we hypothesized that such an antigen-specific response can be manipulated to preventively reduce the severity of PO-HF in a tolerizing vaccine.nnMETHODS: We used the transfer of lymphocytes or serum from PO-HF mice into healthy recipients to assess whether the adaptive response is sufficient to induce disease. We devised a novel pipeline to identify self-antigens driving the response. We immunized healthy mice with novel antigens to assess whether they induce disease. To determine whether these antigens could be present in human patients, we sought to detect existing responses against these antigens in patients with HF. Finally, we used the antigens in an oral tolerance protocol to preventively protect mice from subsequently induced PO-HF, analyzing the results with next-generation sequencing.nnRESULTS: We found that PO-HF fulfills the criteria of an autoimmune disease, albeit partially, and identified novel cardiac self-antigens, capable of inducing cardiac dysfunction. The novel antigens in a tolerizing vaccine formulation preemptively reduced the severity of disease triggered by subsequent application of PO, via induction of effector regulatory T cells, enabling a potent reduction of PO-driven loss of systolic function, cardiac inflammation, and proinflammatory CD4 T-cell clonal expansion.nnCONCLUSIONS: We demonstrate that PO-HF is triggered by hemodynamic stress and then sets off an autoimmune-like response against cardiac self-antigens. The antigens can be used to reduce the severity of future-onset disease, via oral tolerization, effectively acting as a protective vaccine.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: Heart failure (HF) is strongly associated with inflammation. In pressure overload (PO)-induced HF, cardiac stress triggers adaptive immunity, ablation or inhibition of which blocks disease progression. We hypothesized that PO-HF might fulfill the often-used criteria of autoimmunity: if so, the associated adaptive immune response would be not only necessary but also sufficient to induce HF; it should also be possible to identify self-antigens driving the autoimmune response. Finally, we hypothesized that such an antigen-specific response can be manipulated to preventively reduce the severity of PO-HF in a tolerizing vaccine.nnMETHODS: We used the transfer of lymphocytes or serum from PO-HF mice into healthy recipients to assess whether the adaptive response is sufficient to induce disease. We devised a novel pipeline to identify self-antigens driving the response. We immunized healthy mice with novel antigens to assess whether they induce disease. To determine whether these antigens could be present in human patients, we sought to detect existing responses against these antigens in patients with HF. Finally, we used the antigens in an oral tolerance protocol to preventively protect mice from subsequently induced PO-HF, analyzing the results with next-generation sequencing.nnRESULTS: We found that PO-HF fulfills the criteria of an autoimmune disease, albeit partially, and identified novel cardiac self-antigens, capable of inducing cardiac dysfunction. The novel antigens in a tolerizing vaccine formulation preemptively reduced the severity of disease triggered by subsequent application of PO, via induction of effector regulatory T cells, enabling a potent reduction of PO-driven loss of systolic function, cardiac inflammation, and proinflammatory CD4 T-cell clonal expansion.nnCONCLUSIONS: We demonstrate that PO-HF is triggered by hemodynamic stress and then sets off an autoimmune-like response against cardiac self-antigens. The antigens can be used to reduce the severity of future-onset disease, via oral tolerization, effectively acting as a protective vaccine.
2023
Puccio, Simone; Grillo, Giorgio; Alvisi, Giorgia; Scirgolea, Caterina; Galletti, Giovanni; Mazza, Emilia Maria Cristina; Consiglio, Arianna; Simone, Gabriele De; Licciulli, Flavio; Lugli, Enrico
CRUSTY: a versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data Journal Article
In: Nat Commun, vol. 14, no. 1, pp. 5102, 2023, ISSN: 2041-1723.
@article{pmid37666818,
title = {CRUSTY: a versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data},
author = {Simone Puccio and Giorgio Grillo and Giorgia Alvisi and Caterina Scirgolea and Giovanni Galletti and Emilia Maria Cristina Mazza and Arianna Consiglio and Gabriele De Simone and Flavio Licciulli and Enrico Lugli},
doi = {10.1038/s41467-023-40790-0},
issn = {2041-1723},
year = {2023},
date = {2023-09-01},
journal = {Nat Commun},
volume = {14},
number = {1},
pages = {5102},
abstract = {Flow cytometry (FCM) can investigate dozens of parameters from millions of cells and hundreds of specimens in a short time and at a reasonable cost, but the amount of data that is generated is considerable. Computational approaches are useful to identify novel subpopulations and molecular biomarkers, but generally require deep expertize in bioinformatics and the use of different platforms. To overcome these limitations, we introduce CRUSTY, an interactive, user-friendly webtool incorporating the most popular algorithms for FCM data analysis, and capable of visualizing graphical and tabular results and automatically generating publication-quality figures within minutes. CRUSTY also hosts an interactive interface for the exploration of results in real time. Thus, CRUSTY enables a large number of users to mine complex datasets and reduce the time required for data exploration and interpretation. CRUSTY is accessible at https://crusty.humanitas.it/ .},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Flow cytometry (FCM) can investigate dozens of parameters from millions of cells and hundreds of specimens in a short time and at a reasonable cost, but the amount of data that is generated is considerable. Computational approaches are useful to identify novel subpopulations and molecular biomarkers, but generally require deep expertize in bioinformatics and the use of different platforms. To overcome these limitations, we introduce CRUSTY, an interactive, user-friendly webtool incorporating the most popular algorithms for FCM data analysis, and capable of visualizing graphical and tabular results and automatically generating publication-quality figures within minutes. CRUSTY also hosts an interactive interface for the exploration of results in real time. Thus, CRUSTY enables a large number of users to mine complex datasets and reduce the time required for data exploration and interpretation. CRUSTY is accessible at https://crusty.humanitas.it/ .
van Beek, Jasper J P; Puccio, Simone; Vito, Clara Di; Paoli, Federica De; Zaghi, Elisa; Calvi, Michela; Scarpa, Alice; Peano, Clelia; Basso, Gianluca; Cibella, Javier; Philippis, Chiara De; Sarina, Barbara; Timofeeva, Inna; Capizzuto, Rossana; Mannina, Daniele; Mineri, Rossana; Mariotti, Jacopo; Crocchiolo, Roberto; Santoro, Armando; Castagna, Luca; Bramanti, Stefania; Mavilio, Domenico; Lugli, Enrico
Selected memory T cells infused post-haploidentical hematopoietic stem cell transplantation persist and hyperexpand Journal Article
In: Blood Adv, vol. 7, no. 14, pp. 3458–3468, 2023, ISSN: 2473-9537.
@article{pmid36469095,
title = {Selected memory T cells infused post-haploidentical hematopoietic stem cell transplantation persist and hyperexpand},
author = {Jasper J P van Beek and Simone Puccio and Clara Di Vito and Federica De Paoli and Elisa Zaghi and Michela Calvi and Alice Scarpa and Clelia Peano and Gianluca Basso and Javier Cibella and Chiara De Philippis and Barbara Sarina and Inna Timofeeva and Rossana Capizzuto and Daniele Mannina and Rossana Mineri and Jacopo Mariotti and Roberto Crocchiolo and Armando Santoro and Luca Castagna and Stefania Bramanti and Domenico Mavilio and Enrico Lugli},
doi = {10.1182/bloodadvances.2022007735},
issn = {2473-9537},
year = {2023},
date = {2023-07-01},
journal = {Blood Adv},
volume = {7},
number = {14},
pages = {3458--3468},
abstract = {Haploidentical hematopoietic stem cell transplantation (haplo-HSCT) with post-transplant cyclophosphamide is a curative treatment for many hematological malignancies, yet a majority of patients still suffers from recurrent infections. Post-transplant infusion of memory T-cells could potentially enhance immunological protection without increasing the risk of eliciting acute graft-versus-host disease, which is mainly induced by naïve T-cells. Here, we performed longitudinal analysis of the lymphocyte compartment in 19 patients who underwent haplo-HSCT previously enrolled in a phase II prospective clinical trial (www.clinicaltrials.gov as #NCT04687982), in which they received post-transplant CD45RA-depleted donor lymphocyte infusions (DLI). T-cell receptor sequencing analysis showed that, surprisingly, CD45RA-depleted DLI do not increase T-cell clonal diversity, but lead to prominent expansion of a selected number of infused memory T-cell clones, suggesting recruitment of these cells in the immune response. Pathogen-specific memory T-cells, including cytomegalovirus (CMV)-specific cells, were engrafted and were able to persist for at least 1 month. Deep immunophenotyping revealed strong polyfunctional effector CMV-specific T-cell responses in the majority of patients, with their expansion correlating with the frequency of CMV-specific cells in the donor. These findings provide a rationale behind the suggested improved protection against viral infections in patients receiving CD45RA-depleted DLI.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Haploidentical hematopoietic stem cell transplantation (haplo-HSCT) with post-transplant cyclophosphamide is a curative treatment for many hematological malignancies, yet a majority of patients still suffers from recurrent infections. Post-transplant infusion of memory T-cells could potentially enhance immunological protection without increasing the risk of eliciting acute graft-versus-host disease, which is mainly induced by naïve T-cells. Here, we performed longitudinal analysis of the lymphocyte compartment in 19 patients who underwent haplo-HSCT previously enrolled in a phase II prospective clinical trial (www.clinicaltrials.gov as #NCT04687982), in which they received post-transplant CD45RA-depleted donor lymphocyte infusions (DLI). T-cell receptor sequencing analysis showed that, surprisingly, CD45RA-depleted DLI do not increase T-cell clonal diversity, but lead to prominent expansion of a selected number of infused memory T-cell clones, suggesting recruitment of these cells in the immune response. Pathogen-specific memory T-cells, including cytomegalovirus (CMV)-specific cells, were engrafted and were able to persist for at least 1 month. Deep immunophenotyping revealed strong polyfunctional effector CMV-specific T-cell responses in the majority of patients, with their expansion correlating with the frequency of CMV-specific cells in the donor. These findings provide a rationale behind the suggested improved protection against viral infections in patients receiving CD45RA-depleted DLI.
2021
Beek, Jasper J P Van; Puccio, Simone; Roberto, Alessandra; Paoli, Federica De; Graziano, Giulia; Salviato, Elisa; Alvisi, Giorgia; Zanon, Veronica; Scarpa, Alice; Zaghi, Elisa; Calvi, Michela; Vito, Clara Di; Mineri, Rossana; Sarina, Barbara; Philippis, Chiara De; Santoro, Armando; Mariotti, Jacopo; Bramanti, Stefania; Ferrari, Francesco; Castagna, Luca; Mavilio, Domenico; Lugli, Enrico
2021, ISSN: 1592-8721.
@misc{pmid34233445,
title = {Single-cell profiling reveals the dynamics of cytomegalovirus-specific T cells in haploidentical hematopoietic stem cell transplantation},
author = {Jasper J P Van Beek and Simone Puccio and Alessandra Roberto and Federica De Paoli and Giulia Graziano and Elisa Salviato and Giorgia Alvisi and Veronica Zanon and Alice Scarpa and Elisa Zaghi and Michela Calvi and Clara Di Vito and Rossana Mineri and Barbara Sarina and Chiara De Philippis and Armando Santoro and Jacopo Mariotti and Stefania Bramanti and Francesco Ferrari and Luca Castagna and Domenico Mavilio and Enrico Lugli},
doi = {10.3324/haematol.2020.276352},
issn = {1592-8721},
year = {2021},
date = {2021-10-01},
journal = {Haematologica},
volume = {106},
number = {10},
pages = {2768--2773},
keywords = {},
pubstate = {published},
tppubtype = {misc}
}
Bella, Chiara Della; Soluri, Maria Felicia; Puccio, Simone; Benagiano, Marisa; Grassi, Alessia; Bitetti, Jacopo; Cianchi, Fabio; Sblattero, Daniele; Peano, Clelia; D'Elios, Mario Milco
The CagY Protein Drives Gastric Th1 and Th17 Inflammation and B Cell Proliferation in Gastric MALT Lymphoma Journal Article
In: Int J Mol Sci, vol. 22, no. 17, 2021, ISSN: 1422-0067.
@article{pmid34502367,
title = {The CagY Protein Drives Gastric Th1 and Th17 Inflammation and B Cell Proliferation in Gastric MALT Lymphoma},
author = {Chiara Della Bella and Maria Felicia Soluri and Simone Puccio and Marisa Benagiano and Alessia Grassi and Jacopo Bitetti and Fabio Cianchi and Daniele Sblattero and Clelia Peano and Mario Milco D'Elios},
doi = {10.3390/ijms22179459},
issn = {1422-0067},
year = {2021},
date = {2021-08-01},
journal = {Int J Mol Sci},
volume = {22},
number = {17},
abstract = {BACKGROUND: the neoplastic B cells of the -related low-grade gastric mucosa-associated lymphoid tissue (MALT) lymphoma proliferate in response to , however, the nature of the antigen responsible for proliferation is still unknown. The purpose of the study was to dissect whether CagY might be the antigen able to drive B cell proliferation.nnMETHODS: the B cells and the clonal progeny of T cells from the gastric mucosa of five patients with MALT lymphoma were compared with those of T cell clones obtained from five -infected patients with chronic gastritis. The T cell clones were assessed for their specificity to CagY, cytokine profile and helper function for B cell proliferation.nnRESULTS: 22 of 158 CD4 (13.9%) gastric clones from MALT lymphoma and three of 179 CD4 (1.7%) clones from chronic gastritis recognized CagY. CagY predominantly drives Interferon-gamma (IFN-γ) and Interleukin-17 (IL-17) secretion by gastric CD4 T cells from -infected patients with low-grade gastric MALT lymphoma. All MALT lymphoma-derived clones dose dependently increased their B cell help, whereas clones from chronic gastritis lost helper activity at T-to-B-cell ratios greater than 1.nnCONCLUSION: the results obtained indicate that CagY drives both B cell proliferation and T cell activation in gastric MALT lymphomas.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: the neoplastic B cells of the -related low-grade gastric mucosa-associated lymphoid tissue (MALT) lymphoma proliferate in response to , however, the nature of the antigen responsible for proliferation is still unknown. The purpose of the study was to dissect whether CagY might be the antigen able to drive B cell proliferation.nnMETHODS: the B cells and the clonal progeny of T cells from the gastric mucosa of five patients with MALT lymphoma were compared with those of T cell clones obtained from five -infected patients with chronic gastritis. The T cell clones were assessed for their specificity to CagY, cytokine profile and helper function for B cell proliferation.nnRESULTS: 22 of 158 CD4 (13.9%) gastric clones from MALT lymphoma and three of 179 CD4 (1.7%) clones from chronic gastritis recognized CagY. CagY predominantly drives Interferon-gamma (IFN-γ) and Interleukin-17 (IL-17) secretion by gastric CD4 T cells from -infected patients with low-grade gastric MALT lymphoma. All MALT lymphoma-derived clones dose dependently increased their B cell help, whereas clones from chronic gastritis lost helper activity at T-to-B-cell ratios greater than 1.nnCONCLUSION: the results obtained indicate that CagY drives both B cell proliferation and T cell activation in gastric MALT lymphomas.
2020
Galletti, Giovanni; Simone, Gabriele De; Mazza, Emilia M C; Puccio, Simone; Mezzanotte, Claudia; Bi, Timothy M; Davydov, Alexey N; Metsger, Maria; Scamardella, Eloise; Alvisi, Giorgia; Paoli, Federica De; Zanon, Veronica; Scarpa, Alice; Camisa, Barbara; Colombo, Federico S; Anselmo, Achille; Peano, Clelia; Polletti, Sara; Mavilio, Domenico; Gattinoni, Luca; Boi, Shannon K; Youngblood, Benjamin A; Jones, Rhiannon E; Baird, Duncan M; Gostick, Emma; Llewellyn-Lacey, Sian; Ladell, Kristin; Price, David A; Chudakov, Dmitriy M; Newell, Evan W; Casucci, Monica; Lugli, Enrico
Two subsets of stem-like CD8 memory T cell progenitors with distinct fate commitments in humans Journal Article
In: Nat Immunol, vol. 21, no. 12, pp. 1552–1562, 2020, ISSN: 1529-2916.
@article{pmid33046887b,
title = {Two subsets of stem-like CD8 memory T cell progenitors with distinct fate commitments in humans},
author = {Giovanni Galletti and Gabriele De Simone and Emilia M C Mazza and Simone Puccio and Claudia Mezzanotte and Timothy M Bi and Alexey N Davydov and Maria Metsger and Eloise Scamardella and Giorgia Alvisi and Federica De Paoli and Veronica Zanon and Alice Scarpa and Barbara Camisa and Federico S Colombo and Achille Anselmo and Clelia Peano and Sara Polletti and Domenico Mavilio and Luca Gattinoni and Shannon K Boi and Benjamin A Youngblood and Rhiannon E Jones and Duncan M Baird and Emma Gostick and Sian Llewellyn-Lacey and Kristin Ladell and David A Price and Dmitriy M Chudakov and Evan W Newell and Monica Casucci and Enrico Lugli},
doi = {10.1038/s41590-020-0791-5},
issn = {1529-2916},
year = {2020},
date = {2020-12-01},
journal = {Nat Immunol},
volume = {21},
number = {12},
pages = {1552--1562},
abstract = {T cell memory relies on the generation of antigen-specific progenitors with stem-like properties. However, the identity of these progenitors has remained unclear, precluding a full understanding of the differentiation trajectories that underpin the heterogeneity of antigen-experienced T cells. We used a systematic approach guided by single-cell RNA-sequencing data to map the organizational structure of the human CD8 memory T cell pool under physiological conditions. We identified two previously unrecognized subsets of clonally, epigenetically, functionally, phenotypically and transcriptionally distinct stem-like CD8 memory T cells. Progenitors lacking the inhibitory receptors programmed death-1 (PD-1) and T cell immunoreceptor with Ig and ITIM domains (TIGIT) were committed to a functional lineage, whereas progenitors expressing PD-1 and TIGIT were committed to a dysfunctional, exhausted-like lineage. Collectively, these data reveal the existence of parallel differentiation programs in the human CD8 memory T cell pool, with potentially broad implications for the development of immunotherapies and vaccines.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
T cell memory relies on the generation of antigen-specific progenitors with stem-like properties. However, the identity of these progenitors has remained unclear, precluding a full understanding of the differentiation trajectories that underpin the heterogeneity of antigen-experienced T cells. We used a systematic approach guided by single-cell RNA-sequencing data to map the organizational structure of the human CD8 memory T cell pool under physiological conditions. We identified two previously unrecognized subsets of clonally, epigenetically, functionally, phenotypically and transcriptionally distinct stem-like CD8 memory T cells. Progenitors lacking the inhibitory receptors programmed death-1 (PD-1) and T cell immunoreceptor with Ig and ITIM domains (TIGIT) were committed to a functional lineage, whereas progenitors expressing PD-1 and TIGIT were committed to a dysfunctional, exhausted-like lineage. Collectively, these data reveal the existence of parallel differentiation programs in the human CD8 memory T cell pool, with potentially broad implications for the development of immunotherapies and vaccines.
Puccio, Simone; Grillo, Giorgio; Consiglio, Arianna; Soluri, Maria Felicia; Sblattero, Daniele; Cotella, Diego; Santoro, Claudio; Liuni, Sabino; Bellis, Gianluca De; Lugli, Enrico; Peano, Clelia; Licciulli, Flavio
InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data Journal Article
In: Nucleic Acids Res, vol. 48, no. W1, pp. W200–W207, 2020, ISSN: 1362-4962.
@article{pmid32402076b,
title = {InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data},
author = {Simone Puccio and Giorgio Grillo and Arianna Consiglio and Maria Felicia Soluri and Daniele Sblattero and Diego Cotella and Claudio Santoro and Sabino Liuni and Gianluca De Bellis and Enrico Lugli and Clelia Peano and Flavio Licciulli},
doi = {10.1093/nar/gkaa363},
issn = {1362-4962},
year = {2020},
date = {2020-07-01},
journal = {Nucleic Acids Res},
volume = {48},
number = {W1},
pages = {W200--W207},
abstract = {High-Throughput Sequencing technologies are transforming many research fields, including the analysis of phage display libraries. The phage display technology coupled with deep sequencing was introduced more than a decade ago and holds the potential to circumvent the traditional laborious picking and testing of individual phage rescued clones. However, from a bioinformatics point of view, the analysis of this kind of data was always performed by adapting tools designed for other purposes, thus not considering the noise background typical of the 'interactome sequencing' approach and the heterogeneity of the data. InteractomeSeq is a web server allowing data analysis of protein domains ('domainome') or epitopes ('epitome') from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following an Interactome sequencing approach. InteractomeSeq allows users to upload raw sequencing data and to obtain an accurate characterization of domainome/epitome profiles after setting the parameters required to tune the analysis. The release of this tool is relevant for the scientific and clinical community, because InteractomeSeq will fill an existing gap in the field of large-scale biomarkers profiling, reverse vaccinology, and structural/functional studies, thus contributing essential information for gene annotation or antigen identification. InteractomeSeq is freely available at https://InteractomeSeq.ba.itb.cnr.it/.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
High-Throughput Sequencing technologies are transforming many research fields, including the analysis of phage display libraries. The phage display technology coupled with deep sequencing was introduced more than a decade ago and holds the potential to circumvent the traditional laborious picking and testing of individual phage rescued clones. However, from a bioinformatics point of view, the analysis of this kind of data was always performed by adapting tools designed for other purposes, thus not considering the noise background typical of the 'interactome sequencing' approach and the heterogeneity of the data. InteractomeSeq is a web server allowing data analysis of protein domains ('domainome') or epitopes ('epitome') from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following an Interactome sequencing approach. InteractomeSeq allows users to upload raw sequencing data and to obtain an accurate characterization of domainome/epitome profiles after setting the parameters required to tune the analysis. The release of this tool is relevant for the scientific and clinical community, because InteractomeSeq will fill an existing gap in the field of large-scale biomarkers profiling, reverse vaccinology, and structural/functional studies, thus contributing essential information for gene annotation or antigen identification. InteractomeSeq is freely available at https://InteractomeSeq.ba.itb.cnr.it/.
Alvisi, Giorgia; Brummelman, Jolanda; Puccio, Simone; Mazza, Emilia Mc; Tomada, Elisa Paoluzzi; Losurdo, Agnese; Zanon, Veronica; Peano, Clelia; Colombo, Federico S; Scarpa, Alice; Alloisio, Marco; Vasanthakumar, Ajithkumar; Roychoudhuri, Rahul; Kallikourdis, Marinos; Pagani, Massimiliano; Lopci, Egesta; Novellis, Pierluigi; Blume, Jonas; Kallies, Axel; Veronesi, Giulia; Lugli, Enrico
IRF4 instructs effector Treg differentiation and immune suppression in human cancer Journal Article
In: J Clin Invest, vol. 130, no. 6, pp. 3137–3150, 2020, ISSN: 1558-8238.
@article{pmid32125291b,
title = {IRF4 instructs effector Treg differentiation and immune suppression in human cancer},
author = {Giorgia Alvisi and Jolanda Brummelman and Simone Puccio and Emilia Mc Mazza and Elisa Paoluzzi Tomada and Agnese Losurdo and Veronica Zanon and Clelia Peano and Federico S Colombo and Alice Scarpa and Marco Alloisio and Ajithkumar Vasanthakumar and Rahul Roychoudhuri and Marinos Kallikourdis and Massimiliano Pagani and Egesta Lopci and Pierluigi Novellis and Jonas Blume and Axel Kallies and Giulia Veronesi and Enrico Lugli},
doi = {10.1172/JCI130426},
issn = {1558-8238},
year = {2020},
date = {2020-06-01},
journal = {J Clin Invest},
volume = {130},
number = {6},
pages = {3137--3150},
abstract = {The molecular mechanisms responsible for the high immunosuppressive capacity of CD4+ Tregs in tumors are not well known. High-dimensional single-cell profiling of T cells from chemotherapy-naive individuals with non-small-cell lung cancer identified the transcription factor IRF4 as specifically expressed by a subset of intratumoral CD4+ effector Tregs with superior suppressive activity. In contrast to the IRF4- counterparts, IRF4+ Tregs expressed a vast array of suppressive molecules, and their presence correlated with multiple exhausted subpopulations of T cells. Integration of transcriptomic and epigenomic data revealed that IRF4, either alone or in combination with its partner BATF, directly controlled a molecular program responsible for immunosuppression in tumors. Accordingly, deletion of Irf4 exclusively in Tregs resulted in delayed tumor growth in mice while the abundance of IRF4+ Tregs correlated with poor prognosis in patients with multiple human cancers. Thus, a common mechanism underlies immunosuppression in the tumor microenvironment irrespective of the tumor type.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The molecular mechanisms responsible for the high immunosuppressive capacity of CD4+ Tregs in tumors are not well known. High-dimensional single-cell profiling of T cells from chemotherapy-naive individuals with non-small-cell lung cancer identified the transcription factor IRF4 as specifically expressed by a subset of intratumoral CD4+ effector Tregs with superior suppressive activity. In contrast to the IRF4- counterparts, IRF4+ Tregs expressed a vast array of suppressive molecules, and their presence correlated with multiple exhausted subpopulations of T cells. Integration of transcriptomic and epigenomic data revealed that IRF4, either alone or in combination with its partner BATF, directly controlled a molecular program responsible for immunosuppression in tumors. Accordingly, deletion of Irf4 exclusively in Tregs resulted in delayed tumor growth in mice while the abundance of IRF4+ Tregs correlated with poor prognosis in patients with multiple human cancers. Thus, a common mechanism underlies immunosuppression in the tumor microenvironment irrespective of the tumor type.
2019
Salvo, Marco Di; Puccio, Simone; Peano, Clelia; Lacour, Stephan; Alifano, Pietro
In: BMC Bioinformatics, vol. 20, no. 1, pp. 117, 2019, ISSN: 1471-2105.
@article{pmid30845912,
title = {RhoTermPredict: an algorithm for predicting Rho-dependent transcription terminators based on Escherichia coli, Bacillus subtilis and Salmonella enterica databases},
author = {Marco Di Salvo and Simone Puccio and Clelia Peano and Stephan Lacour and Pietro Alifano},
doi = {10.1186/s12859-019-2704-x},
issn = {1471-2105},
year = {2019},
date = {2019-03-01},
journal = {BMC Bioinformatics},
volume = {20},
number = {1},
pages = {117},
abstract = {BACKGROUND: In bacterial genomes, there are two mechanisms to terminate the DNA transcription: the "intrinsic" or Rho-independent termination and the Rho-dependent termination. Intrinsic terminators are characterized by a RNA hairpin followed by a run of 6-8 U residues relatively easy to identify using one of the numerous available prediction programs. In contrast, Rho-dependent termination is mediated by the Rho protein factor that, firstly, binds to ribosome-free mRNA in a site characterized by a C > G content and then reaches the RNA polymerase to induce its release. Conversely on intrinsic terminators, the computational prediction of Rho-dependent terminators in prokaryotes is a very difficult problem because the sequence features required for the function of Rho are complex and poorly defined. This is the reason why it still does not exist an exhaustive Rho-dependent terminators prediction program.nnRESULTS: In this study we introduce RhoTermPredict, the first published algorithm for an exhaustive Rho-dependent terminators prediction in bacterial genomes. RhoTermPredict identifies these elements based on a previously proposed consensus motif common to all Rho-dependent transcription terminators. It essentially searches for a 78 nt long RUT site characterized by a C > G content and with regularly spaced C residues, followed by a putative pause site for the RNA polymerase. We tested RhoTermPredict performances by using available genomic and transcriptomic data of the microorganism Escherichia coli K-12, both in limited-length sequences and in the whole-genome, and available genomic sequences from Bacillus subtilis 168 and Salmonella enterica LT2 genomes. We also estimated the overlap between the predictions of RhoTermPredict and those obtained by the predictor of intrinsic terminators ARNold webtool. Our results demonstrated that RhoTermPredict is a very performing algorithm both for limited-length sequences (F-score obtained about 0.7) and for a genome-wide analysis. Furthermore the degree of overlap with ARNold predictions was very low.nnCONCLUSIONS: Our analysis shows that RhoTermPredict is a powerful tool for Rho-dependent terminators search in the three analyzed genomes and could fill this gap in computational genomics. We conclude that RhoTermPredict could be used in combination with an intrinsic terminators predictor in order to predict all the transcription terminators in bacterial genomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: In bacterial genomes, there are two mechanisms to terminate the DNA transcription: the "intrinsic" or Rho-independent termination and the Rho-dependent termination. Intrinsic terminators are characterized by a RNA hairpin followed by a run of 6-8 U residues relatively easy to identify using one of the numerous available prediction programs. In contrast, Rho-dependent termination is mediated by the Rho protein factor that, firstly, binds to ribosome-free mRNA in a site characterized by a C > G content and then reaches the RNA polymerase to induce its release. Conversely on intrinsic terminators, the computational prediction of Rho-dependent terminators in prokaryotes is a very difficult problem because the sequence features required for the function of Rho are complex and poorly defined. This is the reason why it still does not exist an exhaustive Rho-dependent terminators prediction program.nnRESULTS: In this study we introduce RhoTermPredict, the first published algorithm for an exhaustive Rho-dependent terminators prediction in bacterial genomes. RhoTermPredict identifies these elements based on a previously proposed consensus motif common to all Rho-dependent transcription terminators. It essentially searches for a 78 nt long RUT site characterized by a C > G content and with regularly spaced C residues, followed by a putative pause site for the RNA polymerase. We tested RhoTermPredict performances by using available genomic and transcriptomic data of the microorganism Escherichia coli K-12, both in limited-length sequences and in the whole-genome, and available genomic sequences from Bacillus subtilis 168 and Salmonella enterica LT2 genomes. We also estimated the overlap between the predictions of RhoTermPredict and those obtained by the predictor of intrinsic terminators ARNold webtool. Our results demonstrated that RhoTermPredict is a very performing algorithm both for limited-length sequences (F-score obtained about 0.7) and for a genome-wide analysis. Furthermore the degree of overlap with ARNold predictions was very low.nnCONCLUSIONS: Our analysis shows that RhoTermPredict is a powerful tool for Rho-dependent terminators search in the three analyzed genomes and could fill this gap in computational genomics. We conclude that RhoTermPredict could be used in combination with an intrinsic terminators predictor in order to predict all the transcription terminators in bacterial genomes.
2018
Soluri, Maria Felicia; Puccio, Simone; Caredda, Giada; Grillo, Giorgio; Licciulli, Vito Flavio; Consiglio, Arianna; Edomi, Paolo; Santoro, Claudio; Sblattero, Daniele; Peano, Clelia
Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing Journal Article
In: J Vis Exp, no. 140, 2018, ISSN: 1940-087X.
@article{pmid30346377,
title = {Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing},
author = {Maria Felicia Soluri and Simone Puccio and Giada Caredda and Giorgio Grillo and Vito Flavio Licciulli and Arianna Consiglio and Paolo Edomi and Claudio Santoro and Daniele Sblattero and Clelia Peano},
doi = {10.3791/56981},
issn = {1940-087X},
year = {2018},
date = {2018-10-01},
journal = {J Vis Exp},
number = {140},
abstract = {Folding reporters are proteins with easily identifiable phenotypes, such as antibiotic resistance, whose folding and function is compromised when fused to poorly folding proteins or random open reading frames. We have developed a strategy where, by using TEM-1 β-lactamase (the enzyme conferring ampicillin resistance) on a genomic scale, we can select collections of correctly folded protein domains from the coding portion of the DNA of any intronless genome. The protein fragments obtained by this approach, the so called "domainome", will be well expressed and soluble, making them suitable for structural/functional studies. By cloning and displaying the "domainome" directly in a phage display system, we have showed that it is possible to select specific protein domains with the desired binding properties (e.g., to other proteins or to antibodies), thus providing essential experimental information for gene annotation or antigen identification. The identification of the most enriched clones in a selected polyclonal population can be achieved by using novel next-generation sequencing technologies (NGS). For these reasons, we introduce deep sequencing analysis of the library itself and the selection outputs to provide complete information on diversity, abundance and precise mapping of each of the selected fragment. The protocols presented here show the key steps for library construction, characterization, and validation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Folding reporters are proteins with easily identifiable phenotypes, such as antibiotic resistance, whose folding and function is compromised when fused to poorly folding proteins or random open reading frames. We have developed a strategy where, by using TEM-1 β-lactamase (the enzyme conferring ampicillin resistance) on a genomic scale, we can select collections of correctly folded protein domains from the coding portion of the DNA of any intronless genome. The protein fragments obtained by this approach, the so called "domainome", will be well expressed and soluble, making them suitable for structural/functional studies. By cloning and displaying the "domainome" directly in a phage display system, we have showed that it is possible to select specific protein domains with the desired binding properties (e.g., to other proteins or to antibodies), thus providing essential experimental information for gene annotation or antigen identification. The identification of the most enriched clones in a selected polyclonal population can be achieved by using novel next-generation sequencing technologies (NGS). For these reasons, we introduce deep sequencing analysis of the library itself and the selection outputs to provide complete information on diversity, abundance and precise mapping of each of the selected fragment. The protocols presented here show the key steps for library construction, characterization, and validation.
Pilipow, Karolina; Scamardella, Eloise; Puccio, Simone; Gautam, Sanjivan; Paoli, Federica De; Mazza, Emilia Mc; Simone, Gabriele De; Polletti, Sara; Buccilli, Marta; Zanon, Veronica; Lucia, Pietro Di; Iannacone, Matteo; Gattinoni, Luca; Lugli, Enrico
Antioxidant metabolism regulates CD8+ T memory stem cell formation and antitumor immunity Journal Article
In: JCI Insight, vol. 3, no. 18, 2018, ISSN: 2379-3708.
@article{pmid30232291,
title = {Antioxidant metabolism regulates CD8+ T memory stem cell formation and antitumor immunity},
author = {Karolina Pilipow and Eloise Scamardella and Simone Puccio and Sanjivan Gautam and Federica De Paoli and Emilia Mc Mazza and Gabriele De Simone and Sara Polletti and Marta Buccilli and Veronica Zanon and Pietro Di Lucia and Matteo Iannacone and Luca Gattinoni and Enrico Lugli},
doi = {10.1172/jci.insight.122299},
issn = {2379-3708},
year = {2018},
date = {2018-09-01},
journal = {JCI Insight},
volume = {3},
number = {18},
abstract = {Adoptive T cell transfer (ACT) immunotherapy benefits from early differentiated stem cell memory T (Tscm) cells capable of persisting in the long term and generating potent antitumor effectors. Due to their paucity ex vivo, Tscm cells can be derived from naive precursors, but the molecular signals at the basis of Tscm cell generation are ill-defined. We found that less differentiated human circulating CD8+ T cells display substantial antioxidant capacity ex vivo compared with more differentiated central and effector memory T cells. Limiting ROS metabolism with antioxidants during naive T cell activation hindered terminal differentiation, while allowing expansion and generation of Tscm cells. N-acetylcysteine (NAC), the most effective molecule in this regard, induced transcriptional and metabolic programs characteristic of self-renewing memory T cells. Upon ACT, NAC-generated Tscm cells established long-term memory in vivo and exerted more potent antitumor immunity in a xenogeneic model when redirected with CD19-specific CAR, highlighting the translational relevance of NAC as a simple and inexpensive method to improve ACT.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Adoptive T cell transfer (ACT) immunotherapy benefits from early differentiated stem cell memory T (Tscm) cells capable of persisting in the long term and generating potent antitumor effectors. Due to their paucity ex vivo, Tscm cells can be derived from naive precursors, but the molecular signals at the basis of Tscm cell generation are ill-defined. We found that less differentiated human circulating CD8+ T cells display substantial antioxidant capacity ex vivo compared with more differentiated central and effector memory T cells. Limiting ROS metabolism with antioxidants during naive T cell activation hindered terminal differentiation, while allowing expansion and generation of Tscm cells. N-acetylcysteine (NAC), the most effective molecule in this regard, induced transcriptional and metabolic programs characteristic of self-renewing memory T cells. Upon ACT, NAC-generated Tscm cells established long-term memory in vivo and exerted more potent antitumor immunity in a xenogeneic model when redirected with CD19-specific CAR, highlighting the translational relevance of NAC as a simple and inexpensive method to improve ACT.
Via Rita Levi Montalcini 2, Campus Building F, 20090, Pieve Emanuele (Milan), Italy – c/o Humanitas Research Hospital
simone.puccio@cnr.it
+39 02 82245279