Learning Tumour Immunology from COVID-19
Recent years have seen an explosive growth in the applications of cancer immunotherapeutic modalities designed to either boost T cells in situ, for example via checkpoint blockade, or to provide activated T cells, as in CAR-T therapy. Initially focussed on αβ T cells, those approaches have now been extended to γδ T cells in respect of their widespread implication in cancer immunesurveillance. Nonetheless, tumours are commonly highly immunosuppressive and the success rates of T cell therapies vary greatly according to indication, as do the adverse events. One challenge in overcoming this has been our scant understanding of how T cell responses develop and progress over time in the face of “real-life” human disease settings. COVID-19 offered the chance to redress this issue, providing evidence of severe yet selective T cell dysregulation that was rapidly induced in a pro-inflammatory context. Likewise, evolving γδ T cell responses and dysregulation could be actively monitored. In this way, these studies have provided biomarkers of immune dysregulation that may be helpful in tracking natural and engineered T cell responses in cancer patients, and in other settings. On an optimistic note, most COVID-19 patients, including those with Stage IV advanced malignancies, successfully navigated the milieu of T cell pathology, developing virus-specific responses and recovering from disease. Hence, studies of COVID-19 offer insight into how patient-beneficial immune responses may be developed and sustained even within highly adverse pathologic settings.

Trained in biochemistry and with a PhD in molecular virology, Adrian Hayday took up immunology at MIT where, in 1985, he and his colleagues described the entirely unanticipated T cell receptor γ-chain genes. Since then he has shown γδ T cell biology to be overtly distinct from conventional T cell biology, and provided the first evidence that γδ T cells naturally protect against carcinogenesis. Since then he has identified molecular mechanisms by which γδ T cells discriminate tumours from normal tissue, and is committed to the cells’ clinical application.
He is first or corresponding author on more than 120 out of a total of 230 publications of which over 150 describe original research. He has co-authored many patents. His awards include the William Clyde deVane Medal, Yale College’s highest honour for scholarship; the UK Business of Science Award, 2017; and election as Fellow of the Royal Society, and of the Academy of Medical Sciences. He was elected to lead the British Society of Immunology (2005-09) and has co-organized major meetings including the 2014 Gordon Conference in Immunochemistry and Immunobiology, the scientific programme for the 2012 European Congress of Immunology, the 2016 international γδ T cell forum, and the first 2021 Cold Spring Harbor COVID-19 meeting.
He has chaired Wellcome Trust, CRUK, and American Cancer Society funding committees, and has served on many advisory boards, including the Pasteur Institute, Paris, the Max Planck Society, and the University of Kyoto. In the private sector he was on the SAB of MedImmune and has co-founded three biotech start-up companies.

Immunity to TB: Balancing protection with pathology
Mycobacterium tuberculosis is a master manipulator of the human immune system. There is a strong commitment to driving antigen-specific immune responses but thius is countered by strong inflammatory signals that create environments that can limit the expression of immunity. This works for the host as for most events where bacteria are deposited in tissue (either lung or through dissemination other tissues) then immunity is strong and effective and no disease occurs. It also works for the some lung lesions where inflammation inhibits expression of immunity and disease can progress can occur in an otherwise healthy host and therefore transmission can occur. To combat TB we have to learn how to make T cells that can cope with those inflammatory environments that limit T cell survival and function. In this talk some intrinsic and extrinsic factors that modulate T cell behaviour within the inflammatory environment will be discussed.

Andrea Cooper received her undergraduate degree from University College, London and Doctoral degree from The London School of Hygiene and Tropical Medicine UK, where she investigated the interaction between macrophages and protozoan parasites of the genus Leishmania.
Moving to the National Institutes of Health in Bethesda, Maryland, USA, she expanded her investigation of leishmaniasis to include the T cell response of patients suffering from cutaneous, mucocutaneous and visceral forms of this disease. Andrea then moved to the Mycobacterial Research Labs at Colorado State University and began studying the protective immune response to Mycobacterium tuberculosis.
Prior to her move to the University of Leicester, she was at the Trudeau Institute, Inc. for 12 years, where she held the E.L. Trudeau Chair which allowed her to study the cellular immune response to Mycobacterium tuberculosis.

Nutrients and metabolites in the control of lymphocyte responses
Our immune system is important for our health protecting us from infection/cancer, but inappropriate immune responses cause us harm. Diverse diseases could be treated through therapeutic manipulation of our immune systems. My research group wants to understand how to control immune cells and is now revealing the importance of cellular metabolism. Our research shows that the cellular fuels available to immune cells and the ways that these fuels are used have a big impact on their function. We are revealing novel strategies to modulate immune cell function through targeting cellular metabolism and new therapeutic opportunities are being explored. Specifically, our data show that the metabolic regulators mTORC1, cMyc and Srebp are key regulators of immune cell metabolism and function in Natural Killer (NK) cells. In contrast to lymphocytes, mTORC1 and glycolytic metabolism inhibits the function of Dendritic Cells (DC); starving DC of glucose results in increased proinflammatory outputs and enhanced DC-induced T cell responses. Our work is further characterising the molecular links between cellular metabolism and immune cell function.

David Finlay is Associate Professor in Immunometabolism in the Schools of Biochemistry and Immunology, and Pharmacy and Pharmaceutical Science at Trinity College Dublin. He was awarded a B.A. (Mod) in Biochemistry in 2001. He completed his PhD (2006) and postdoctoral training at the University of Dundee in Scotland and was elected to fellowship of Trinity College Dublin in 2018. He has been a principal investigator in the Trinity Biomedical Sciences Institute since 2011. His research expertise lies at the interface of immunology and cellular metabolism with a focus on Natural Killer cells and Dendritic cells. His team is revealing novel strategies to modulate immune cell function through targeting metabolism and metabolic signalling pathways. Dr Finlay’s research has been supported by awards including a Science Foundation Ireland Career Development Award in 2014 and a European Research Council Consolidator Award in 2017.

Macrophage Transitions during Tuberculosis
The central pathogen-immune interface in tuberculosis is the granuloma, a complex host immune structure that dictates infection trajectory and physiology. Granuloma macrophages undergo a dramatic transition in which entire epithelial modules are induced and define granuloma architecture. Using the zebrafish-Mycobacterium marinum model, we identified a basis for granuloma macrophage transformation. Single-cell RNA-sequencing analysis of zebrafish granulomas and analysis of Mycobacterium tuberculosis-infected macaques reveal that, even in the presence of robust type 1 immune responses, countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling, mediated via stat6, is absolutely required for epithelialization and granuloma formation. In mixed chimeras, stat6 acts cell autonomously within macrophages, where it is required for epithelioid transformation and incorporation into necrotic granulomas. These findings establish the signaling pathway that produces the hallmark structure of mycobacterial infection.

David M. Tobin is an Associate Professor and Director of Graduate Studies at the Duke University School of Medicine. He received his PhD. in Genetics Microbiology from the University of California at San Francisco, in 2001. From 2004 until 2010, he was a Senior Fellow in the laboratory of Dr. Lalita Ramakrishnan, at the Departments of Microbiology, Medicine and Immunology, in the University of Washington. David is a member of the Editorial Board of Infection and Immunity and PLOS One. His laboratory combines zebrafish models with human clinical data and analyses to understand the host immune response during bacterial and fungal infections. We have developed new methods and approaches in the zebrafish to understand host genetic susceptibility to mycobacterial infection and have translated these findings into human cohorts.

Dissecting immunity against SARS-CoV-2: cell by cell, patient by patient, cohort by cohort.
The molecular and functional understanding of human immune responses against pathogens and in context of major non-communicable diseases is currently accelerated by the introduction of large scale single cell technologies. Within the first year of the pandemic, we saw numerous single cell studies addressing different aspects of the immune response towards SARS-CoV-2. I will try to provide an overview of the immunology that was revealed by these studies, highlight some important findings, challenge the way many studies were done and conclude with a suggestion for the future. Moreover, I try to develop a model, how these technologies can be integrated into clinical immunology in the years to come, since it is entirely clear that the current development in the single cell omics field will greatly shape how human immunology will be carried out in the years to come.

Joachim L. Schultze is Director of Systems Medicine at the German Center for Neurodegenerative Diseases (DZNE) and Founding Director of the PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn. He went to Medical School at the University of Tübingen, spent almost 10 years at Dana-Farber Cancer Institute, Harvard Medical School, in Boston before he returned to Germany with a Sofia Kovalevskaya Award of the Humboldt Foundation. He is the coordinator of the German DFG-funded NGS competence centers in Germany, and one of the speakers of the West German Genome Center. He contributes his expertise to several EU consortia, amongst them ImmunoSep, DiscovAIR or SYSCID. He is an expert in macrophage biology and works at the interphase between immunology, genomics and the computational sciences. With his team he was the first to apply memory driven computing and Swarm Learning to medical research. With his own research group and the PRECISE platform, his goal is to bring single cell technologies and machine learning approaches to the clinical arena. He is leading several programs on applying single cell technologies, memory driven computing and Swarm Learning to patients with Alzheimer’s disease, chronic obstructive pulmonary disease, lung cancer or HIV. He has established research collaborations with HPE, AstraZeneca, Boehringer Ingelheim, Becton Dickinson and other companies.

Regulatory T cells in hematopoietic stem cell transplantation
Allogeneic hematopoietic stem cell transplantation is an essential therapeutic tool for patients with hematologic malignancies and other diseases with impaired hematopoiesis. Donor immunity emerging post-transplant plays a pivotal role in the protection against infections, such as CMV and EBV, as well as in the development of graft versus host disease (GVHD) and graft versus leukemia (GVL) effect. All these variables impact in patient survival. Regulatory T cells (Treg) are a naturally immunosuppressive T-cell population that plays an important role in the establishment of immune tolerance post-transplant. Since patients with chronic GVHD have impaired Treg reconstitution post-transplant, several strategies have been developed in order to increase the Treg pool, such as the administration of low-dose IL-2 and infusions of fresh donor Treg, such as the clinical trials we are conducting (www.tregeneration.eu). At the same time, we are developing in vitro systems to grow different Treg populations with the aim of bringing to the clinic a Treg pool that may be more specific in its antigen recognition and suppressive function. These therapies may have an impact in the prevention and/or treatment of GVHD, balancing the control of GVHD versus the beneficial GVL effect.

João F. Lacerda, MD PhD obtained his Medical Degree at the University of Lisbon in 1988. Completed in 1995 the Hematology and Bone Marrow Transplant Fellowship at the University of Lisbon Hospital de Santa Maria and at Memorial Sloan-Kettering Cancer Center in New York. Attending Hematologist at Hospital de Santa Maria since 1996. PhD and habilitation (Agregação) at the University of Lisbon in 1998 and 2007, respectively. Currently holds the following positions: Senior Attending Physician at the Hematology and Bone Marrow Transplant Service, Hospital de Santa Maria, Professor of Hematology and Head of the International Office, Faculty of Medicine of the University of Lisbon, Group Leader of the Hematology and Transplant Immunology Group at Instituto de Medicina Molecular João Lobo Antunes. President of the Ethics Committee and Vice-President of the Clinical Research Center, Lisbon Academic Medical Center.

Diving into the dark side of IL-7 and IL-7R and their contribution to lymphoid leukemia development
Interleukin (IL)-7 and its receptor (IL-7R) are critical for T- and, in the mouse, B-cell development, as well as differentiation and survival of naïve T-cells, and generation and maintenance of memory T-cells. In line with this, the IL-7-IL-7R axis can play an important role in anti-tumoral immunity. However, IL-7 and IL-7R can also have a ‘dark side’ as promoters of cancer development. We have shown that IL-7 accelerates acute lymphoblastic leukemia (ALL) development in vivo and that around 10% of T-cell ALL patients display IL7R gain-of-function mutations. IL7R mutations also occur in a small fraction of high risk B- cell ALL patients. Although IL7R mutational activation is a driver of leukemia, it is not known whether it is sufficient to initiate leukemogenesis. I will present our studies, using conditional knock-in mutant Il7r mice, demonstrating that IL-7R can initiate T-cell ALL, as well as B-cell ALL with features of Ph-like and PAX5 P80R human B-cell ALL, which can be targeted with inhibitors of PI3K signaling or of sphingosine kinases. I will discuss also other IL-7R-related vulnerabilities that we have identified, which can be exploited therapeutically to treat ALL.

João T. Barata is Lab Head at Instituto de Medicina Molecular, and Associate Professor at the Faculty of Medicine of Lisbon University, Portugal, where he is co-chair of Oncobiology for medical students and coordinator of the Masters in Oncobiology. He is a current recipient of an ERC Consolidator Grant (2015-2021) to study the mechanisms of IL-7R signaling in cancer and of an ERC Proof-of-concept grant to explore targeted therapies against IL-7R in cancer. He graduated in Biology in 1996 from the University of Coimbra, Portugal. In 2003, completed his Ph.D. in Biomedical Sciences, at the University of Porto, Portugal, as one of the first students of the GABBA program, after conducting research work at Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA for several years. From 2003 until 2006, he was a Post-doctoral Fellow at Instituto de Medicina Molecular. During that period his work developed also at Pasteur Institute, Paris, France; and Utrecht University Medical Center, The Netherlands. In 2006 he established his independent lab.
João is Editorial Board Member of Cells and Cellular Signalling, ad hoc Section Editor for Leukemia, and reviewer for a number of international journals (including Nature Medicine, Nature Communications, EMBO Molecular Medicine, Science Translational Medicine, Journal of Clinical Investigation, Blood, Leukemia, Oncogene, amongst many others), and expert reviewer of grant applications for several science funding agencies including ERC and EHA; FWO and VLK (Belgium); Wellcome Trust/DBT India Alliance (India); CARIPARO, AIRC and ANVUR (Italy); Health Research Board (Ireland); Dutch Arthritis Association and Dutch Cancer Society (The Netherlands); Worldwide Cancer Research (UK) – of which he is currently part of the Scientific Advisory Committee; and FCT (Portugal). In 2007, he created, together with Dr. Peter Jordan, the annual meetings SINAL (on signal transduction) and has been teaching oncobiology-related topics in postgraduate courses at different Portuguese Universities.
João’s lab focuses on studying the signal transduction pathways that are deregulated in cancer by cell-autonomous lesions and microenvironmental cues. His work, focused on signal transduction and the characterization of novel mechanisms driving tumor development, has identified important genetic and posttranslational alterations promoting lymphoid leukemia. He has published in journals such as the Journal of Clinical Investigation, Journal of Experimental Medicine, Science Signaling, Nature Genetics, Nature Immunology, Blood, Leukemia, Cancer Research or Oncogene. He has been distinguished with three Pfizer Awards (2008, 2011 and 2014), one Pulido Valente Science Prize (2009), one SPI Best Immunology Paper Award (2012), amongst others; one vote of congratulations from the Portuguese Parliament to the quality of scientific research in Portugal recognizing the work conducted by his research team (2011) and one Medal for Distinct Services from the Portuguese Health Ministry (2013).

The choreography of T cell development by thymic epithelial cells
The development of vaccines for the treatment of infectious diseases, cancer and autoimmunity depends on our knowledge of T-cell differentiation. My presentation is focused on the thymus, the organ responsible for the generation of T cells that are responsive against pathogen-derived antigens, and yet tolerant to self. Within the thymus, thymic epithelial cells (TECs) provide key inductive microenvironments for the development and selection of T cells that arise from hematopoietic progenitors. As a result, defects in TEC differentiation cause syndromes that range from immunodeficiency to autoimmunity, which makes the study of TECs of fundamental, and clinical, importance to understand immunity and tolerance induction. TECs are divided into two functionally distinct cortical (cTECs) and medullary (mTECs) subtypes, which derive from common bipotent TEC progenitors (TEPs). Whereas cTECs mediate early stages of T cell development, as lineage commitment and positive selection, mTECs control later steps of T cell differentiation, including negative selection and T cell regulatory differentiation. Still, we know little about the molecular principles that control de differentiation and function of TECs.
To identify novel genes involved in the specialized antigen-processing capacities of TECs, we obtained the genome- wide transcriptional profile of embryonic and adult TEC subsets. We identified Lamp2 as a gene highly expressed in cTECs and selected it as a target for further functional studies. The lysosomal associated membrane protein-2 (Lamp2) is a component of the lysosomal membrane, with a crucial role in lysosome maturation and autophagy. I will present experimental evidence that point for a critical contribution of Lamp2 in TECs in regulating their role during CD4/CD8 T cell selection. I will discuss the implication of these results for our understanding CD4 TCR repertoire formation.

Nuno L. Alves is a group leader at “Instituto de Investigação e Inovação em Saúde” (i3S) in Porto. He graduated in Biology from the University of Porto in 2000 and completed his a Ph.D. in Immunology at the University of Amsterdam in 2007 with the support of a GABBA/FCT PhD fellowship. Next, he obtained a long-term EMBO fellowship to develop his post-doctoral research at the Institut Pasteur in Paris. In 2010, he returned to Portugal under the Ciência2008 program and started his independent research team at Instituto de Biologia Molecular e Celular (IBMC) in Porto. In 2014, he established his research group at i3S/IBMC. Currently, he holds the position of Principal Investigator under the umbrella of the FCT scientific employment program.
The studies in his laboratory are focused on the differentiation of thymic epithelial cells (TECs), which play a prominent role in T-cell development and in the establishment of immunological tolerance. His group made key contributions to the understanding of the mechanism that regulate TEC differentiation and thymus and T cell biology (Blood 2017, 2003, JI 2018, 2013, 2010, 2007, 2005; EJI 2020, 2017, 2014, PNAS 2009, Immunity 2007). His findings have represented new advances in the areas of haematology, immune development and senescence and autoimmunity. Nuno L. Alves has authored 35 articles in prominent journals in the field of Immunology, coordinated as PI several international (ERC starting grant, ERA Chair H2020-WIDESPREAD) and national (4 FCT projects) research grants and supervised several PhD student and postdoctoral fellows (ORCID: 0000-0002-1567-8389).

Regulation of tolerance and inflammation by human antigen-specific CD4+ T cells
Humans are continuously exposed to harmless environmental substances, e.g. via the breathing air. Harmless airborne antigens are normally tolerated by the healthy immune system but dysregulated immune responses result in allergic diseases and inflammation. Such pathologic responses are orchestrated by CD4+ effector T cells, which are tightly controlled by Foxp3 regulatory T cells (Treg). The intestinal microbiota has been suggested to modulate pulmonary inflammation although the contribution of individual microbes and the mechanisms of action of this gut-lung axis remain elusive. In humans both, the mediators of tolerance, as well as of immune pathology have so far been poorly characterized on the antigen-specific level.
Analysis of human T cell responses against ubiquitous environmental antigens surprisingly identified two members of the mycobiome as major targets of prototypic human T cell responses involved in these processes. The ubiquitous airborne fungus Aspergillus fumigatus, is a main inducer of antigen-specific Tregs, which mainly seem to prevent allergies. Surprisingly, we found no evidence of functional impairment of Treg responses in allergic donors. Rather, major allergenic proteins, known to rapidly dissociate from inhaled allergenic particles, escape the Treg induction process. Thus, our data highlight the importance of Treg antigen-specificity for tolerance in humans and identify antigen-specific escape from Treg control as a new mechanism enabling antigen-specific loss of tolerance in human allergy.
In contrast, the intestinal commensal Candida albicans is a major inducer of human Th17 responses. Surprisingly, Th17 cells directed against other fungi rely on cross-reactivity to C. albicans. Intestinal inflammation expands total C. albicans- and cross-reactive Th17 cells. Strikingly, Th17 cells cross-reactive to the airborne fungus A. fumigatus are selectively activated and expanded in patients with airway inflammation, such as asthma, COPD and cystic fibrosis and especially during acute allergic bronchopulmonary aspergillosis, suggesting their specific contribution to lung pathology. This indicates a direct link between protective intestinal Th17 responses against C. albicans and lung inflammation caused by airborne fungi. Our data identify the mycobiome as major modulator of the human T cell repertoire. We further identify heterologous immunity to a single, ubiquitous member of the mycobiota as a central mechanism for systemic induction of human anti-fungal Th17 responses and as a risk factor for pulmonary inflammatory diseases.

Petra Bacher holds a junior professorship for Immunology and Immunogenetics, and is group leader of the Intestinal Immunoregulation Group at Kiel University (CAU). She received her PhD in Cellular Immunology from the Charité, Berlin, in 2014. The Bacher group aims at understanding the malfunction of tolerance mechanisms in the human immune system during chronic inflammatory diseases, including the interaction of environmental factors with microbial and inflammatory processes. Therein, the group specifically investigates the role of T cells in immune-regulated diseases by means of novel direct analyses of antigen-specific T cells.