Probabilistic analysis of gene expression measurements from heterogeneous tissues

Motivation: Tissue heterogeneity, arising from multiple cell types, is a major confounding factor in experiments that focus on studying cell types, e.g. their expression profiles, in isolation. Although sample heterogeneity can be addressed by manual microdissection, prior to conducting experiments, computational treatment on heterogeneous measurements have become a reliable alternative to perform this microdissection in silico. Favoring computation over manual purification has its advantages, such as time consumption, measuring responses of multiple cell types simultaneously, keeping samples intact of external perturbations and unaltered yield of molecular content

Somatic mutations in lymphocytes in patients with immune-mediated aplastic anemia

The prevalence and functional impact of somatic mutations in nonleukemic T cells is not well characterized, although clonal T-cell expansions are common. In immune-mediated aplastic anemia (AA), cytotoxic T-cell expansions are shown to participate in disease pathogenesis. We investigated the mutation profiles of T cells in AA by a custom panel of 2533 genes. We sequenced CD4+ and CD8+ T cells of 24 AA patients and compared the results to 20 healthy controls and whole-exome sequencing of 37 patients with AA. Somatic variants were common both in patients and healthy controls but enriched to AA patients' CD8+ T cells, which accumulated most mutations on JAK-STAT and MAPK pathways. Mutation burden was associated with CD8+ T-cell clonality, assessed by T-cell receptor beta sequencing. To understand the effect of mutations, we performed single-cell sequencing of AA patients carrying STAT3 or other mutations in CD8+ T cells. STAT3 mutated clone was cytotoxic, clearly distinguishable from other CD8+ T cells, and attenuated by successful immunosuppressive treatment. Our results suggest that somatic mutations in T cells are common, associate with clonality, and can alter T-cell phenotype, warranting further investigation of their role in the pathogenesis of AA.Peer reviewe

Adult-Onset Anti-Citrullinated Peptide Antibody-Negative Destructive Rheumatoid Arthritis Is Characterized by a Disease-Specific CD8+T Lymphocyte Signature

Rheumatoid arthritis (RA) is a complex autoimmune disease targeting synovial joints. Traditionally, RA is divided into seropositive (SP) and seronegative (SN) disease forms, the latter consisting of an array of unrelated diseases with joint involvement. Recently, we described a severe form of SN-RA that associates with characteristic joint destruction. Here, we sought biological characteristics to differentiate this rare but aggressive anti-citrullinated peptide antibody-negative destructive RA (CND-RA) from early seropositive (SP-RA) and seronegative rheumatoid arthritis (SN-RA). We also aimed to study cytotoxic CD8+ lymphocytes in autoimmune arthritis. CND-RA, SP-RA and SN-RA were compared to healthy controls to reveal differences in T-cell receptor beta (TCR beta) repertoire, cytokine levels and autoantibody repertoires. Whole-exome sequencing (WES) followed by single-cell RNA-sequencing (sc-RNA-seq) was performed to study somatic mutations in a clonally expanded CD8+ lymphocyte population in an index patient. A unique TCR beta signature was detected in CND-RA patients. In addition, CND-RA patients expressed higher levels of the bone destruction-associated TNFSF14 cytokine. Blood IgG repertoire from CND-RA patients recognized fewer endogenous proteins than SP-RA patients' repertoires. Using WES, we detected a stable mutation profile in the clonally expanded CD8+ T-cell population characterized by cytotoxic gene expression signature discovered by sc-RNA-sequencing. Our results identify CND-RA as an independent RA subset and reveal a CND-RA specific TCR signature in the CD8+ lymphocytes. Improved classification of seronegative RA patients underlines the heterogeneity of RA and also, facilitates development of improved therapeutic options for the treatment resistant patients

Reconstruction and Validation of RefRec: A Global Model for the Yeast Molecular Interaction Network

Molecular interaction networks establish all cell biological processes. The networks are under intensive research that is facilitated by new high-throughput measurement techniques for the detection, quantification, and characterization of molecules and their physical interactions. For the common model organism yeast Saccharomyces cerevisiae, public databases store a significant part of the accumulated information and, on the way to better understanding of the cellular processes, there is a need to integrate this information into a consistent reconstruction of the molecular interaction network. This work presents and validates RefRec, the most comprehensive molecular interaction network reconstruction currently available for yeast. The reconstruction integrates protein synthesis pathways, a metabolic network, and a protein-protein interaction network from major biological databases. The core of the reconstruction is based on a reference object approach in which genes, transcripts, and proteins are identified using their primary sequences. This enables their unambiguous identification and non-redundant integration. The obtained total number of different molecular species and their connecting interactions is ∼67,000. In order to demonstrate the capacity of RefRec for functional predictions, it was used for simulating the gene knockout damage propagation in the molecular interaction network in ∼590,000 experimentally validated mutant strains. Based on the simulation results, a statistical classifier was subsequently able to correctly predict the viability of most of the strains. The results also showed that the usage of different types of molecular species in the reconstruction is important for accurate phenotype prediction. In general, the findings demonstrate the benefits of global reconstructions of molecular interaction networks. With all the molecular species and their physical interactions explicitly modeled, our reconstruction is able to serve as a valuable resource in additional analyses involving objects from multiple molecular -omes. For that purpose, RefRec is freely available in the Systems Biology Markup Language format

Rullakuljetinlinjan peruskunnostus

M-real Oyj:n Äänekosken paperitehdas päätti investoida paperitehtaan arkittamoon ostamalla kaksi uutta arkkileikkuria. Koska rullien koot (leveys ja paino) kasvavat huomattavasti, oli rullakuljetinjärjestelmää kunnostettava. Kunnostus on tehty Metson kuntotarkastusraportin pohjalta. Tässä opinnäytetyössä keskityttiin niihin laitteisiin, jotka uusien arkkileikkureiden tultua jäävät vielä käyttöön. Tarkemmin työn tavoitteena oli ID-aseman jälkeisen välipysäyttimen modifiointi, pituusleikkuri ykköseltä eteenpäin vievän kuljettimen kunnostus ja raportissa mainittujen työntimien ja vastaanottimien kunnostus. Nämä korjaustyöt on tehty olemassa oleviin laitteisiin, jolloin korjaustyön hinta saatiin pysymään edullisena verrattuna Metson esittämään tarjoukseen. Sekä välipysäyttimen modifiointi että vastaanottimien ja työntimien laakeriholkkien ja akseleiden vaihto onnistui hyvin. Opinnäytetyönä suoritetusta rullakuljetinlaitteiden korjauksesta johtuen kunnostetut laitteet kestävät uusien investoitavien arkkileikkureiden myötä kasvavien paperirullien painon.The M-real Äänekoski Paper decided to invest in the finishing line by purchasing two new sheet cutters. Since the size of the paper rolls will increase substantially, the roll handling line had to be renovated before the investment. This renovation was done according to a report made by Metso. This thesis focused on those devices in the finishing line that will be used after the new sheet cutters are in operation. More specifically, the aim of this thesis was the modification of the stopper located after ID-station and the renovation of the conveyor after the cutter number one. In addition to this, the objective was also the renovation of the pushers and receivers mentioned in the Metso’s report. These repairs were done to the existing devices. Because of this, the costs of the repairs were lower when compared to the offer made by Metso. The modification of the stopper as well as the changes of the bearing bushings and axes succeeded well. As a result, the renovated devices will sustain the increasing weight of the paper rolls