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Current HIV cure trials primarily focus on people living with HIV (PLWH) who started antiretroviral therapy (ART) during the primary infection stage, as they are known to have smaller HIV reservoirs. However, there is a substantial knowledge gap regarding the size of the HIV reservoir in majority of PLWH. Our study aims to address this gap by exploring the size of the HIV reservoir through comprehensive clinical, immunological, and virological assessments, and by developing an algorithm to predict HIV reservoir size.To achieve this, the CHART-C study will include 200 PLWH on long-term successful ART, with a substudy examining the HIV reservoir in the central nervous system of 20 participants. We will use advanced assays such as IPDA, CADseq method, and quantification of HIV-specific humoral/cellular responses. Machine learning techniques will be employed to develop an algorithm to identify individuals with the smallest HIV reservoirs.The outcome of this study will be a clinical algorithm designed to select individuals with the smallest HIV reservoirs, thereby optimizing the inclusion criteria for future HIV cure trials and enhancing the potential for therapeutic success. Additionally, we will prepare for an analytical treatment interruption  HIV cure trial using two long-acting broadly neutralizing antibodies. The CHART-C trial aims to make a significant contribution to global HIV cure strategies and position Swedish HIV research at the forefront of this critical field.

Our goal is: (i) To perform a longitudinal assessment of adaptive immune responses in SARS-CoV-2 mRNA vaccinated immunocompromised patient groups and healthy controls. The rational for the studies is that many of the studied patient groups have an increased risk of developing severe COVID-19 upon SARS-CoV-2 infection. Hence, information on vaccine-induced immune status in real-time in the studied patient groups is important. It serves to provide necessary advice on protective measurements needed to be taken as well as for detemining the need for prophylactic treatment, and upon SARS-CoV-2 infection, need for immediate treatment. (ii) To perform a deep assessment of adaptive immune responses in SARS-CoV-2 mRNA vaccinated immunocompromised patients and healthy controls. The rational for the studies is that it is currently unknown to what extent multiple SARS-CoV-2 mRNA vaccine doses may over time affect qualitative aspects of the adpative immune response generated. The latter informtion may impact future vaccine design and/or vaccination strategies. (iii) To undertake long-term capacity building for very rapidly being able to assess prevailing immunity in SARS-CoV-2 mRNA vaccinated patient groups and healthy controls in the event of an emerging new SARS-CoV-2 variant-of-concern outbreak. The rational being that new emerging variants may escape parts of current vaccine-induced immunity. This may be particular harmful for several of the presently studied patient groups.

CD8+ T cells are critical to generate immunity to most viral infections. Studies of human blood have been instrumental to advance our understanding of how CD8+ T cells function and can control different viruses. However, most of CD8+ T cells are not found in the blood, but mainly in tissues. This fact, together with the notion that humans respond very differently to the same virus, force a re-evaluation of how different factors, such as genetics and localization, affect antiviral CD8+ T cell differentiation and functions across tissues and blood. We will first use single-cell techniques on unique organ donor samples to establish a reference map of where virus-specific CD8+ T cell clones are preferentially located in the human body (aim 1). Through innovative live-attenuated yellow fever virus vaccination protocols, we will next track how virus-specific CD8+ T cells develop in draining vs. non-draining lymph nodes compared to the blood (aim 2). Using the same vaccine platform, we will finally assess the impact of genetics on circulating memory CD8+ T cell differentiation through studies on monozygotic twins (aim 3). This ambitious, but technically feasible project, will establish a framework for many future immunological studies in the field of antiviral immunity and inform the development of more effective vaccine platforms and immune therapies against future viral threats.

CD8+ T cells are critical to generate immunity to most viral infections. Studies of human blood have been instrumental to advance our understanding of how CD8+ T cells function and can control different viruses. However, most of CD8+ T cells are not found in the blood, but mainly in tissues. This fact, together with the notion that humans respond very differently to viral infections, force a re-evaluation of how different factors, such as genetics and localization, affect antiviral CD8+ T cell differentiation and functions across tissues and blood. We will first use single-cell techniques on unique organ donor samples to establish a reference map of where virus-specific CD8+ T cell clones are preferentially located in the human body (aim 1). Through innovative live-attenuated yellow fever virus vaccination protocols, we will next track how virus-specific CD8+ T cells develop in draining vs. non-draining lymph nodes compared to the blood (aim 2). Using the same vaccine platform, we will finally assess the impact of genetics on circulating memory CD8+ T cell differentiation through studies on monozygotic twins (aim 3). This ambitious, but technically feasible project, will establish a framework for many future immunological studies in the field of antiviral immunity and inform the development of more effective vaccine platforms and immune therapies against future viral threats.

The covid-19 pandemic has created tremendous damage to the world´s economy and society, but it has also highlighted the importance of science and innovations as tools to survive and respond to life treatening challenges. Vaccines based on mRNA technology have been massively manufactured and administered, dissipating any doubg about the feasibility of this approach. This technology has been initially developed to target cancer antigens and had shown promising results in small clinical trials. Vaccination is one of the most succesfull form of immunotherapy and can be directed towards multiple antigens, the challenge in the filed of cancer immunotherapy is to identify the right target to achieve tumor eradication. In 2020 our team started a project focused on the identification of immunogeneic neoantigens in patients affected by HCC. At today we collected and sequenced tumors from 16 individulas and we identified several neoantigens that can raise a T cell response in the patients. With the present project we aim at complementing the screening of T cell immunogeic neoantigens with the design of specifc mRNA vaccines that can elicit immune response as support/integration of adoptive cell therapy.

Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults in Sweden. Over the past decade, more targeted therapies that inhibit tumor growth have improved the prognosis of patients with the disease. However, CLL remains incurable, with many patients eventually developing treatment resistance. Many patients also suffer from other complications, such as infectious diseases - this has not least been witnessed in recent years with high mortality in covid-19 in CLL patients. Taken together, this underscores the need to understand why our immune system is unable to eradicate leukemia cells and control various pathogens in patients with CLL. The body's T cells are essential in controlling and eliminating many infections and malignancies. New findings in the CLL field indicate that many T cells put on their 'brakes' by upregulating inhibitory receptors, such as PD-1, and consequently become dysfunctional. This process is known as T cell exhaustion and has been described by us and others for T cells in both malignancies and chronic viral infections. The underlying causes of increased T-cell exhaustion in CLL are currently unknown, but could probably be a contributing factor to T-cells being unable to knock out leukemia cells or potentially control various pathogens. Through a collaboration with leading researchers and clinicians in oncology, hematology and immunology, we want to understand how memory T cells recognize pathogens and leukemia cells in CLL patients. We also want to understand if we can reverse this process and generate more effective immunotherapies.

Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease COVID-19. During the two years since the virus and the disease was first discovered, COVID-19 has by mid-March 2022 caused at least 480 million infections and 6.2 million deaths world-wide. The pandemic hit unevenly across the world population, with characteristics such as age, male sex, underlying conditions, and host genetics influencing the risk of developing severe disease. Interestingly, available data suggests that East African countries such as Uganda have been relatively less affected in terms of severe COVID-19 disease and mortality compared to many western countries, despite very limited and delayed vaccine availability. In this proposal, we hypothesize that pre-existing T cell immunity to coronaviruses gained before the pandemic may influence these patterns of susceptibility to severe COVID-19. To address this possibility, we will utilize the Ugandan arm of the RV329 African Cohort Study (AFRICOS), which has a retrospective longitudinal set of cryopreserved samples covering pre-pandemic and pandemic time-points. This cohort will also allow us to address the impact of HIV-1 infection on the characteristics of pre-existing immunity. We anticipate that the proposed experiments, together with the comprehensive clinical data collected in the AFRICOS study, will significantly enhance our understanding of the role of pre-existing T cell immunity to protect from severe COVID-19.

Patients with primary immunodeficiency have been severely affected by the COVID-19 pandemic with an increased risk of infection and severe disease. During the pandemic, we changed our planned research and focused on helping this vulnerable group of patients. We applied our concept with screening, advanced diagnostics and targeted treatment and prevention. This turned out to be very successful with direct benefit for patients but also led to scientific progress at the highest international level. We have been able to identify three completely new immunodeficiency diseases that increase the susceptibility to COVID-19: TLR7 deficiency, IRF7 deficiency and autoantibodies to interferon-alpha. We have also conducted a large clinical study where the effect of COVID-19 vaccine has been evaluated in patients with poor immune system. Now we want to continue to develop the concept of screening inpatients to find additional patients with underlying immunodeficiency, deepen the molecular diagnostics and integrate novel methods in clinical practise, target our treatment and follow up vaccine responses and mechanisms over time. The network that we have built up over the past two years will allow us to develop the clinical and translational research on immunodeficiency in the coming years. We believe the new knowledge can be quickly implemented in clinical care and lead to patient benefit and scientific progress both in the short and long term. (1452 ch)

Long COVID is a largely unexplored disease spectrum of unknown etiology with need to gain rapid insights into the etiology to improve diagnosis and treatment options. Long COVID could result from a number of factors including i) the induction of reactive autoimmune responses as a consequence of cross-reactivity with viral antigens and/or ii) viral persistence and concomitant ongoing immune activation. As such, we here hypothesize that differential clinical syndromes will segregate with distinct immunologic and/or virologic parameters/phenotypes. Longitudinal samples (blood and tissues/fluid) will be collected from both long COVID patients and convalescent controls at the new Karolinska Huddinge postcovid clinic. Our interdisciplinary team of clinicians and researchers will create a biobank and data pool by combining a detailed history and examination of all patients with virological and immunologic analyses, including next-generation measurements of inflammatory cytokines, autoantibodies, immune activation profiles and adaptive immunity to SARS-CoV-2, and direct measurements of viral titers in nasopharyngeal fluid, saliva, stool, BAL and cerebrospinal fluid. Also, prognostic facctors, morbidity and mortality of long Covid in clinical cohorts and national regsiter cohorts will be analyzed. These studies will enable the identification and prospective testing of potential biomarkers, which in turn will inform the development of new diagnostic tests and treatments for long COVID.

'Immune checkpoint blockade' (ICB) of inhibitory receptors (such as PD-1) has revolutionized cancer treatment. These therapies block the brakes of the immune system (inhibitory receptors) and thereby lead to better recognition of tumor cells for killer T cells. In particular, anti-PD-1 therapy can induce long-term remission and even 'cure' metastatic disease for multiple malignancies. However, far from all patients undergoing anti-PD-1 immunotherapy respond to treatment. This emphasizes the importance of understanding the underlying immunological mechanisms in order to improve ICB therapy in future forms of treatment. In this project, we will study the types of killer T cells that respond to anti-PD-1 immunotherapy and where these cells are located. Our preliminary studies suggest that we can identify persistent and functional killer T cells that express PD-1 in lymph nodes. Through mechanistic studies on animal models that can be translated directly to humans after collecting clinical samples from malignant melanoma and liver cancer, we want to understand whether persistent PD-1 + killer-T cells in draining lymph nodes or tumors are the source of an effective response to anti-PD- 1 immunotherapy. The new generation of immunotherapies has changed the landscape for various cancers. However, a sustainable immune response is limited to a small subset of cancer patients. By identifying which killer T cells respond to this new generation of cancer treatments, we will not only identify a reliable predictive biomarker but also gain insight into how such cells can be further used as targets in combination with PD-1 inhibitors, to extend immunotherapy to more tumor types and a larger population of patients.

'Immune checkpoint blockade' (ICB) of inhibitory receptors (such as PD-1) has revolutionized cancer treatment. These therapies block the brakes of the immune system (inhibitory receptors) and thereby lead to better recognition of tumor cells for killer T cells. In particular, anti-PD-1 therapy can induce long-term remission and even 'cure' metastatic disease for multiple malignancies. However, far from all patients undergoing anti-PD-1 immunotherapy respond to treatment. This emphasizes the importance of understanding the underlying immunological mechanisms in order to improve ICB therapy in future forms of treatment. In this project, we will study the types of killer T cells that respond to anti-PD-1 immunotherapy and where these cells are located. Our preliminary studies suggest that we can identify persistent and functional killer T cells that express PD-1 in lymph nodes. Through mechanistic studies on animal models that can be translated directly to humans after collecting clinical samples from malignant melanoma and liver cancer, we want to understand whether persistent PD-1 + killer-T cells in draining lymph nodes or tumors are the source of an effective response to anti-PD- 1 immunotherapy. The new generation of immunotherapies has changed the landscape for various cancers. However, a sustainable immune response is limited to a small subset of cancer patients. By identifying which killer T cells respond to this new generation of cancer treatments, we will not only identify a reliable predictive biomarker but also gain insight into how such cells can be further used as targets in combination with PD-1 inhibitors, to extend immunotherapy to more tumor types and a larger population of patients.