Biology subjects

Saavalainen, P.

Publications and source records attributed to Saavalainen, P..

6 recordsLinked to original sources

bioRxiv2026

Celiac disease patient derived iPSC small intestinal epithelial cells are more persistent under cytokine stimuli than healthy control cells

Background & AimsCeliac disease is a wheat-induced immune-mediated enteropathy. Intestinal organoid models for adult stem cell-based celiac disease exist, but planar intestinal models derived from celiac disease patients that would allow direct assessment from both sides of the epithelium have been lacking. We aimed to bridge this gap by setting up a two-dimensional in vitro model based on small intestinal epithelial cells (SIECs) derived from induced pluripotent stem cells (iPSC) from celiac disease patients. MethodsIPSCs from celiac disease and control patients were sequentially differentiated towards SIECs. The models applicability was tested under cytokine stimuli. ResultsCeliac disease and control patient iPSCs matured similarly towards SIECs. However, they had inherent gene expression differences in inflammation- and immune-related genes, such as IRF1 and HLA-DRB1. Both iPSC-SIECs responded in a SIEC-specific manner to the cytokine stimulation. The response in celiac disease iPSC-SIECs was attenuated compared with that of control iPSC-SIECs. ConclusionsThe data confirm that iPSC-derived SIECs represent an appropriate platform for studying inflammation-associated enteropathies, such as celiac disease, but also suggest that there might be inherent patient-specific or cell type-specific differences in the responses.

cell biology↗

bioRxiv2023

Respiratory Complex I Regulates Dendritic Cell Maturation in Explant Model of Human Tumor Immune Microenvironment

Combining cytotoxic chemotherapy or novel anticancer drugs with T-cell modulators holds great promise in treating advanced cancers. However, the response varies depending on the tumor immune microenvironment (TIME). Therefore, there is a clear need for pharmacologically tractable models of the TIME to dissect its influence on mono- and combination treatment response at the individual level. Here we establish a Patient-Derived Explant Culture (PDEC) model of breast cancer, which retains the immune contexture of the primary tumor, recapitulating cytokine profiles and CD8+ T cell cytotoxic activity. We explored the immunomodulatory action of a synthetic lethal BCL2 inhibitor venetoclax + metformin drug combination ex vivo, discovering metformin cannot overcome the lymphocyte-depleting action of venetoclax. Instead, metformin promotes dendritic cell maturation through inhibition of mitochondrial complex I, increasing their capacity to co-stimulate CD4+ T cells and thus facilitating anti-tumor immunity. Our results establish PDECs as a feasible model to identify immunomodulatory functions of anticancer drugs in the context of patient-specific TIME.

cancer biology↗

bioRxiv2023

Repurposing host-guest chemistry to sequester virulence and eradicate biofilms in multidrug resistant Pseudomonas aeruginosa and Acinetobacter baumannii

The limited diversity in targets of available antibiotic therapies has put tremendous pressure on the treatment of bacterial pathogens, where numerous resistance mechanisms that counteract their function are becoming increasingly prevalent. Here, we utilize an unconventional anti-virulence screen of host-guest interacting macrocycles, and identify a water-soluble synthetic macrocycle, Pillar[5]arene, that is non-bactericidal/bacteriostatic and has a mechanism of action that involves binding to both homoserine lactones and lipopolysaccharides, key virulence factors in Gram-negative pathogens. Pillar[5]arene is active against Top Priority carbapenem- and third/fourth-generation cephalosporin-resistant Pseudomonas aeruginosa and Acinetobacter baumannii, suppressing toxins and biofilms and increasing the penetration and efficacy of standard-of-care antibiotics in combined administrations. The binding of homoserine lactones and lipopolysaccharides also sequesters their direct effects as toxins on eukatryotic membranes, neutralizing key tools that promote bacterial colonization and impede immune defenses, both in vitro and in vivo. Pillar[5]arene evades both existing antibiotic resistance mechanisms, as well as the build-up of rapid tolerance/resistance. The versatility of macrocyclic host-guest chemistry provides ample strategies for tailored targeting of virulence in a wide range of Gram-negative infectious diseases.

biochemistry↗

bioRxiv2018

Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences

MotivationDeep immune receptor sequencing, Repseq, provides unprecedented opportunities to identify condition-associated T-cell clones, represented by T-cell receptor (TCR) CDR3 sequences. TCR profiling has potential value for increasing immunopathological understanding of various diseases, and holds considerable clinical relevance. However, due to the immense diversity of the immune repertoire, identification of condition relevant TCR CDR3s from total repertoires has so far been limited either to mostly \"public\" CDR3 sequences, which are shared across unrelated individuals, or to comparisons of CDR3 frequencies from multiple samples from the same individual. A methodology for the identification of condition-associated TCR CDR3s by population level comparison of groups of Repseq samples is currently lacking.\n\nResultsWe implemented a computational pipeline that allows population level comparison of Repseq sample groups at the level of the immune repertoire sub-units that are shared across individuals. These sub-units (or sub-repertoires) represent shared immuno-genomic features across individuals that potentially encode common signatures in the immune response to antigens. The method first performs unsupervised clustering of CDR3 sequences within each sample based on their similarity in nucleotide or amino acid subsequence frequency. Next, it finds matching clusters across samples, the immune sub-repertoires, and performs statistical differential abundance testing at the level of the identified sub-repertoires. We applied the method on total TCR CDR3{beta} Repseq datasets of celiac disease patients in gluten exposed and unexposed conditions, as well as on public dataset of yellow fever vaccination volunteers before and after immunization. The method successfully identified condition-associated CDR3{beta} sequences, as evidenced by considerable agreement of TRBV-gene and positional amino acid usage patterns in the detected CDR3{beta} sequences with previously known CDR3{beta} species relevant to celiac disease. The method also recovered significantly high numbers of previously known CDR3{beta} sequences, relevant to each condition than would be expected by chance. We conclude that immune sub-repertoires of similar immuno-genomic features, shared across unrelated individuals, encode common immunological information. Moreover, they can serve as viable units of population level immune repertoire comparison, serving as proxy for identification of condition-associated CDR3 sequences.

bioinformatics↗

bioRxiv2018

HLA RNAseq reveals high allele-specific variability in mRNA expression

The HLA gene complex is the most important, single genetic factor in susceptibility to most diseases with autoimmune or autoinflammatory origin and in transplantation matching. The majority of the studies have focused on the huge allelic variation in these genes; only a few studies have explored differences in expression levels of HLA alleles. To study the expression levels of HLA alleles more systematically we utilised two different RNA sequencing methods. Illumina RNAseq has a high sequencing accuracy and depth but is limited by the short read length, whereas Oxford Nanopores technology can sequence long templates, but has a poor accuracy. We studied allelic mRNA levels of HLA class I and II alleles from peripheral blood samples of 50 healthy individuals. The results demonstrate large differences in mRNA expression levels between HLA alleles. The method can be applied to quantitate the expression differences of HLA alleles in various tissues and to evaluate the role of this type of variation in transplantation matching and susceptibility to autoimmune diseases.\n\nAuthor SummaryEven though HLA is widely studied less is known of its allele-specific expression. Due to the pivotal role of HLA in infection response, autoimmunity, and transplantation biology its expression surely must play a part as well. In hematopoietic stem cell transplantation the challenge often is to find a suitable HLA-matched donor due to the high allelic variation. Classical HLA typing methods do not take into account HLA allele-specific expression. However, differential allelic expression levels could be crucial in finding permissive mismatches in order to save a patients life. Additionally, differential HLA expression levels can lead into beneficial impact in viral clearance but also undesirable effects in autoimmune diseases. To study HLA expression we developed a novel RNAseq-based method to systematically characterize allele-specific expression levels of classical HLA genes. We tested our method in a set of 50 healthy individuals and found differential expression levels between HLA alleles as well as interindividual variability at the gene level. Since NGS is already well adopted in HLA research the next step could be to determine HLA allele-specific expression in addition to HLA allelic variation and HLA-disease association studies in various cells, tissues, and diseases.

immunology↗

bioRxiv2017

Genetics of vaccination-related narcolepsy

Narcolepsy type 1 is a severe hypersomnia affecting 1/3000 individuals. It is caused by a loss of neurons producing hypocretin/orexin in the hypothalamus. In 2009/2010, an immunization campaign directed towards the new pandemic H1N1 Influenza-A strain was launched and increased risk of narcolepsy reported in Northern European countries following vaccination with Pandemrix(R), an adjuvanted H1N1 vaccine resulting in ~250 vaccination-related cases in Finland alone. Using whole genome sequencing data of 2000 controls, exome sequencing data of 5000 controls and HumanCoreExome chip genotypes of 81 cases with vaccination-related narcolepsy and 2796 controls, we, built a multilocus genetic risk score with established narcolepsy risk variants. We also analyzed, whether novel risk variants would explain vaccine-related narcolepsy. We found that previously discovered risk variants had strong predictive power (accuracy of 73% and P<2.2*10-16; and ROC curve AUC 0.88) in vaccine-related narcolepsy cases with only 4.9% of cases being assigned to the low risk category. Our findings indicate genetic predisposition to vaccine-triggered narcolepsy, with the possibility of identifying 95% of people at risk.

genetics↗