Open Access

Purpose: While more advanced COVID-19 necessitates medical interventions and hospitalization, patients with mild COVID-19 do not require this. Identifying patients at risk of progressing to advanced COVID-19 might guide treatment decisions, particularly for better prioritizing patients in need for hospitalization. Methods: We developed a machine learning-based predictor for deriving a clinical score identifying patients with asymptomatic/mild COVID-19 at risk of progressing to advanced COVID-19. Clinical data from SARS-CoV-2 positive patients from the multicenter Lean European Open Survey on SARS-CoV-2 Infected Patients (LEOSS) were used for discovery (2020-03-16 to 2020-07-14) and validation (data from 2020-07-15 to 2021-02-16). Results: The LEOSS dataset contains 473 baseline patient parameters measured at the first patient contact. After training the predictor model on a training dataset comprising 1233 patients, 20 of the 473 parameters were selected for the predictor model. From the predictor model, we delineated a composite predictive score (SACOV-19, Score for the prediction of an Advanced stage of COVID-19) with eleven variables. In the validation cohort (n = 2264 patients), we observed good prediction performance with an area under the curve (AUC) of 0.73 ± 0.01. Besides temperature, age, body mass index and smoking habit, variables indicating pulmonary involvement (respiration rate, oxygen saturation, dyspnea), inflammation (CRP, LDH, lymphocyte counts), and acute kidney injury at diagnosis were identified. For better interpretability, the predictor was translated into a web interface. Conclusion: We present a machine learning-based predictor model and a clinical score for identifying patients at risk of developing advanced COVID-19.

Crohn´s disease (CD) and Ulcerative colitis (UC) are idiopathic inflammatory disorders. Environmental factors, infectious microbes, ethnic origin, genetic susceptibility, and a dysregulated immune system can result in mucosal inflammation. However, the etiology of both CD and UC still remains largely unclear. Inflammatory bowel diseaserelated animal models suggest that a combination of genetic susceptibility factors and altered immune response driven by microbial factors in the enteric environment may contribute to the initiation and chronification of the disease. The intestinal immune system represents a complex network of different lymphoid and non-lymphoid cell populations as well as humoral factors. In inflammatory bowel disease, the controlled balance of the intestinal immune system is disturbed at all levels. In CD, naïve T cells preferably differentiate into Th1 or Th17 producing cells, while in UC, these cells differentiate into aberrant Th2 cells. Overall, in active inflammatory bowel disease effector T cell activity (Th1, Th17, Th2) predominates over regulatory T cells. Animal models of intestinal inflammation are indispensable for our understanding of the pathogenesis of CD and UC. When chosen appropriately, these models proved to be a helpful tool to investigate pathophysiological mechanisms, as well as to test emerging therapeutic options in the preclinical phase. 2,4,6-Trinitrobenzene sulfonic acid (TNBS) and oxazolone are the two major chemicals applied to induce Th1- and Th2-skewed intestinal inflammation, respectively. Colitis can be induced in susceptible strains of mice by intrarectal instillation of the haptenating substances TNBS or oxazolone in ethanol, which is necessary for an initial desintegration of the epithelial barrier. TNBS or oxazolone are believed to haptenize colonic autologous or microbiotic proteins rendering them immunogenic to the host immune system. While TNBS administration in the presence of ethanol results in a transmural infiltrative disease in the entire colon based on an IL-12/IL-23 driven, Th1-or Th17 mediated response, oxazolone instillation finally leads to a colitis caused by a polarized Th2 IL-13-dominated lymphocyte response. Rectal oxazolone instillation in ethanol produces a more superficial inflammation that affects the distal half of the colon rather than the whole colon. Therapeutic modulation of the disturbed immune response in patients with inflammatory bowel disease still represents a complex challenge in the clinic. Currently, none of the therapeutic measure are disease specific and they generally target the pathophysiology downstream of the driving immunpathology. So, there is still the need to develop a tailored approach to prevention of the initiation and perpetuation of the inflammatory cascade before tissue injury occurs. One important aspect of this approach might involve the induction or re-establishment of immunological tolerance. FTY720 following rapid phosphorylation to FTY-P by endogenous sphingosine kinases acts as a sphingosine-1-phosphate (S1P) receptor agonist and represents the prototype of a new generation of S1P receptor modulators. While changing currently its proposed mode of action still focus on the fact, that FTY720 effectively inhibits the egress of T-cells from lymph nodes, thereby reducing the number of antigen-primed/restimulated cells that re-circulate to peripheral inflammatory tissues. However, recent studies indicate, that its immunomodulatory properties might be more complex and exerted not only via interactions with other S1P receptor subtypes but also via a direct modulation of the inflammatory capacity of dendritic cells (DC) resulting in a modified regulation of T cell effector functions as well as in an induction of regulatory T cells and function. 1,25(OH)2D3, the active form of vitamin D, is a secosteroid hormone that has in addition to its central function in calcium and bone metabolism pronounced immune regulatory properties. The biological effects of calcitriol are mediated by the vitamin D receptor (VDR), a member of the superfamily of nuclear hormone receptors. A number of studies identified calcitriol/VDR as prominent negative regulators of Th1-type immune responses, whereas Th2 responses are not affected or even augmented. These effects have been mainly explained by direct activities on lymphocytes, subsequent studies clearly supported a role of calcitriol in modulating monocyte differentiation or DC maturation. However, to translate the immunosuppressive capacities of calcitriol into an effective immunointervention, a great challenge was the design of structural analogs of calcitriol that are devoid of adverse effects related to hypercalcemic activity. The intense study of the 25-oxa series generated a large number of calcitriol analogs exhibiting substantial dissociation between possible immunomodulatory capacities and undesired hypercalcemia. Especially, the combination of the 22-ene modification with the 25-oxa element as realized in ZK156979 yielded a very promising set of new analogs for further characterization in animal models resembling human autoimmune diseases. So, the overall aim of the studies presented here was to evaluate strategies of enhancing regulatory immunity in mouse models of Th1- and Th2-mediated colitis as a new therapeutic approach. To this end we used FTY720, 22-ene-25-oxa vitamin D (ZK156979), as well as the combination of calcitriol and dexamethasone to evaluate the respective pro-tolerogenic potential in intestinal inflammation models in mice. First, to induce Th1-mediated colitis a rectal enema of TNBS was given to Balb/c mice. FTY720 was administered i.p. from day 0-3 or 3-5. FTY720 substantially reduced all clinical, histopathologic, macroscopic, and microscopic parameters of colitis analyzed. The therapeutic effects of FTY720 were associated with a down-regulation of IL-12p70 and subsequent Th1 cytokines. Importantly, FTY720 treatment resulted in a prominent up-regulation of FoxP3, IL-10, TGFβ and CTLA4. Moreover, we observed a significant increase of CD25 and FoxP3 expression in isolated lamina propria CD4+ T cells of FTY720-treated mice. The impact of FTY720 on regulatory T cell induction was further confirmed by concomitant in vivo blockade of CTLA4 or IL-10R which significantly abrogated its therapeutic activity. Thus, our data provide new and strong evidence that besides its well-established migratory properties FTY720 down-regulates proinflammatory signals while simultaneously inducing the functional activity of CD4+CD25+ regulatory T cells. In a second approach, the rectal instillation of oxazolone yielded a Th2-mediated colitis. Treatment with FTY720 prominently reduced the clinical and histopathologic severity of oxazolone-induced colitis, abrogating body weight loss, diarrhea, and macroscopic and microscopic intestinal inflammation. The therapeutic effects of FTY720 were associated with a prominent reduction of the key Th2 effector cytokines IL-13, IL-4 and IL-5. Moreover, FTY720 inhibited GATA3 and T1/ST2 expression, which represent distinct markers for Th2 differentiation and Th2 effector function. Thus, our data are supportive for the view that FTY720 exhibits beneficial prophylactic as well as therapeutic effects in Th2-mediated experimental colitis by directly affecting Th2 cytokine profiles, probably by reducing GATA3 and T1/ST2. Recently, we described 22-ene-25-oxa-vitamin D (ZK156979) as a representative of a novel class of low calcemic vitamin D analogs showing prominent immunomodulative capacities. Here, we used the Th1-mediated TNBS colitis to test its anti-inflammatory properties in vivo. We found that treatment with ZK156979 clearly inhibited the severity of TNBS-induced colitis without exhibiting calcemic effects. Both early and late treatment abrogated all the clinical macroscopic and microscopic parameters of colitis severity; in addition we observed a clear down-regulation of the relevant Th1 cytokine pattern including the T-box transcription factor, T-bet. On the other hand, application of ZK156979 increased local tissue IL-10 and IL-4. Finally, as a new approach we evaluated the pro-tolerogenic potential of calcitriol and dexamethasone in acute Th1-mediated colitis. Calcitriol and/or dexamethasone were administered i.p. from day 0-3 or from day 3-5 following the instillation of the haptenating agent. The combination of these steroids most effectively reduced the clinical and histopathologic severity of TNBS colitis. Th1-related parameters were down- while Th2 markers like IL-4 and GATA3 were up-regulated. Clearly distinguishable from known steroid effects calcitriol in particular promoted regulatory T cell profiles as indicated by a marked increase of IL-10, TGFß, FoxP3 and CTLA4. Furthermore, analysis of DC mediators responsible for a pro-inflammatory differentiation of T cells revealed a clear reduction of IL-12p70, and IL23p19 as well as IL-6 and IL-17. Thus, our data suggest the concept of a steroid-sparing application of calcitriol derivatives in inflammatory bowel disease. Furthermore, the data presented suggest that early markers of inflammatory DC and Th17 differentiation might qualify as new target molecules for both calcitriol as well as for selective immune modulating vitamin D analogs. In conclusion the data of these published investigations added to the substantial progress in understanding the biology of tolerogenic DC and regulatory T cells with respect to their roles in health and disease achieved in the past years. This has led to an increasing interest in the possibility of using DC and regulatory T cells as biological therapeutics to preserve and restore tolerance to self antigens and alloantigens. Especially DC may be helpful to exert their important roles in directing tolerance and immunity by modulation of subpopulations of effector T cells and regulatory T cells. The data demonstrated in the present studies may assist to define the divergent implications of new therapeutic concepts for the treatment of inflammatory bowel disease, especially with regard to a possible auspicious impact on pro-tolerogenic DC and regulatory T cell functions. However, further studies are needed to fulfil our understanding of the complex immunomodulatory profiles of FTY720 as well as of calcitriol and its low calcemic analog ZK156979, thus accelerating their entry into the clinic as new therapeutic options for the cure of inflammatory bowel disease.

The change in allele frequencies within a population over time represents a fundamental process of evolution. By monitoring allele frequencies, we can analyze the effects of natural selection and genetic drift on populations. To efficiently track time-resolved genetic change, large experimental or wild populations can be sequenced as pools of individuals sampled over time using high-throughput genome sequencing (called the Evolve & Resequence approach, E&R). Here, we present a set of experiments using hundreds of natural genotypes of the model plant Arabidopsis thaliana to showcase the power of this approach to study rapid evolution at large scale. First, we validate that sequencing DNA directly extracted from pools of flowers from multiple plants -- organs that are relatively consistent in size and easy to sample -- produces comparable results to other, more expensive state-of-the-art approaches such as sampling and sequencing of individual leaves. Sequencing pools of flowers from 25-50 individuals at ∼40X coverage recovers genome-wide frequencies in diverse populations with accuracy r > 0.95. Secondly, to enable analyses of evolutionary adaptation using E&R approaches of plants in highly replicated environments, we provide open source tools that streamline sequencing data curation and calculate various population genetic statistics two orders of magnitude faster than current software. To directly demonstrate the usefulness of our method, we conducted a two-year outdoor evolution experiment with A. thaliana to show signals of rapid evolution in multiple genomic regions. We demonstrate how these laboratory and computational Pool-seq-based methods can be scaled to study hundreds of populations across many climates.