Browsing by Subject "REPERTOIRE"

Sort by: Order: Results:

Now showing items 1-9 of 9
  • Rinne, Maiju; Tanoli, Zia-Ur-Rehman; Khan, Asifullah; Xhaard, Henri (2019)
    We conduct a cartography of rhodopsin-like non-olfactory G protein-coupled receptors in the Ensembl database. The most recent genomic data (releases 90-92, 90 vertebrate genomes) are analyzed through the online interface and receptors mapped on phylogenetic guide trees that were constructed based on a set of similar to 14.000 amino acid sequences. This snapshot of genomic data suggest vertebrate genomes to harbour 142 clades of GPCRs without human orthologues. Among those, 69 have not to our knowledge been mentioned or studied previously in the literature, of which 28 are distant from existing receptors and likely new orphans. These newly identified receptors are candidates for more focused evolutionary studies such as chromosomal mapping as well for in-depth pharmacological characterization. Interestingly, we also show that 37 of the 72 human orphan (or recently deorphanized) receptors included in this study cluster into nineteen closely related groups, which implies that there are less ligands to be identified than previously anticipated. Altogether, this work has significant implications when discussing nomenclature issues for GPCRs.
  • Bhattacharya, Dipabarna; Teramo, Antonella; Gasparini, Vanessa Rebecca; Huuhtanen, Jani; Kim, Daehong; Theodoropoulos, Jason; Schiavoni, Gianluca; Barila, Gregorio; Vicenzetto, Cristina; Calabretto, Giulia; Facco, Monica; Kawakami, Toru; Nakazawa, Hideyuki; Falini, Brunangelo; Tiacci, Enrico; Ishida, Fumihiro; Semenzato, Gianpietro; Kelkka, Tiina; Zambello, Renato; Mustjoki, Satu (2022)
    CD4+ T-cell large granular lymphocyte leukemia (T-LGLL) is a rare subtype of T-LGLL with unknown etiology. In this study, we molecularly characterized a cohort of patients (n = 35) by studying their T-cell receptor (TCR) repertoire and the presence of somatic STAT5B mutations. In addition to the previously described gain-of-function mutations (N642H, Y665F, Q706L, S715F), we discovered six novel STAT5B mutations (Q220H, E433K, T628S, P658R, P702A, and V712E). Multiple STAT5B mutations were present in 22% (5/23) of STAT5B mutated CD4+ T-LGLL cases, either coexisting in one clone or in distinct clones. Patients with STAT5B mutations had increased lymphocyte and LGL counts when compared to STAT5B wild-type patients. TCR beta sequencing showed that, in addition to large LGL expansions, non-leukemic T cell repertoires were more clonal in CD4+ T-LGLL compared to healthy. Interestingly, 25% (15/59) of CD4+ T-LGLL clonotypes were found, albeit in much lower frequencies, in the non-leukemic CD4+ T cell repertoires of the CD4+ T-LGLL patients. Additionally, we further confirmed the previously reported clonal dominance of TRBV6-expressing clones in CD4+ T-LGLL. In conclusion, CD4+ T-LGLL patients have a typical TCR and mutation profile suggestive of aberrant antigen response underlying the disease.
  • Heikkilä, Nelli; Hetemäki, Iivo; Sormunen, Silja; Isoniemi, Helena; Kekäläinen, Eliisa; Saramäki, Jari; Arstila, T. Petteri (2022)
    Long-term T-cell memory is dependent on the maintenance of memory T cells in the lymphoid tissues, and at the surface interfaces that provide entry routes for pathogens. However, much of the current information on human T-cell memory is based on analyzing circulating T cells. Here, we have studied the distribution and age-related changes of memory T-cell subsets in samples from blood, mesenteric LNs, spleen, and ileum, obtained from donors ranging in age from 5 days to 67 years of age. Our data show that the main reservoir of polyclonal naive cells is found in the LNs, and the resting memory subsets capable of self-renewal are also prominent there. In contrast, nondividing but functionally active memory subsets dominate the spleen, and especially the ileum. In general, the replacement of naive cells with memory subsets continues throughout our period of observation, with no apparent plateau. In conclusion, the analysis of lymphoid and nonlymphoid tissues reveals a dynamic pattern of changes distinct to each tissue, and with substantial differences between CD4(+) and CD8(+) compartments.
  • Hämäläinen, Liisa; Mappes, Johanna; Thorogood, Rose; Valkonen, Janne K.; Karttunen, Kaijamari; Salmi, Tuuli; Rowlanda, Hannah M. (2020)
    Many prey species contain defensive chemicals that are described as tasting bitter. Bitter taste perception is, therefore, assumed to be important when predators are learning about prey defenses. However, it is not known how individuals differ in their response to bitter taste, and how this influences their foraging decisions. We conducted taste perception assays in which wild-caught great tits (Parus major) were given water with increasing concentrations of bitter-tasting chloroquine diphosphate until they showed an aversive response to bitter taste. This response threshold was found to vary considerably among individuals, ranging from chloroquine concentrations of 0.01 mmol/L to 8 mmol/L. We next investigated whether the response threshold influenced the consumption of defended prey during avoidance learning by presenting birds with novel palatable and defended prey in a random sequence until they refused to attack defended prey. We predicted that individuals with taste response thresholds at lower concentrations would consume fewer defended prey before rejecting them, but found that the response threshold had no effect on the birds' foraging choices. Instead, willingness to consume defended prey was influenced by the birds' body condition. This effect was age- and sex-dependent, with adult males attacking more of the defended prey when their body condition was poor, whereas body condition did not have an effect on the foraging choices of juveniles and females. Together, our results suggest that even though taste perception might be important for recognizing prey toxicity, other factors, such as predators' energetic state, drive the decisions to consume chemically defended prey. Lay Summary: Individual differences in predators' bitter taste perception do not influence the consumption of chemically defended prey. Many prey species have bitter-tasting defenses that generate aversive responses in predators. We show that great tits vary in their response to bitter taste, but this does not influence the number of novel defended prey they attack during avoidance learning. This suggests that other factors, such as the current physiological state, have a larger impact on predators' foraging decisions.
  • Kim, Daehong; Park, Giljun; Huuhtanen, Jani; Lundgren, Sofie; Khajuria, Rajiv K.; Hurtado, Ana M.; Munoz-Calleja, Cecilia; Cardenoso, Laura; Gomez-Garcia de Soria, Valle; Chen-Liang, Tzu Hua; Eldfors, Samuli; Ellonen, Pekka; Hannula, Sari; Kankainen, Matti; Bruck, Oscar; Kreutzman, Anna; Salmenniemi, Urpu; Lönnberg, Tapio; Jerez, Andres; Itälä-Remes, Maija; Myllymäki, Mikko; Keränen, Mikko A. I.; Mustjoki, Satu (2020)
    Graft versus host disease (GvHD) is the main complication of allogeneic hematopoietic stem cell transplantation (HSCT). Here we report studies of a patient with chronic GvHD (cGvHD) carrying persistent CD4(+) T cell clonal expansion harboring somatic mTOR, NFKB2, and TLR2 mutations. In the screening cohort (n=134), we detect the mTOR P2229R kinase domain mutation in two additional cGvHD patients, but not in healthy or HSCT patients without cGvHD. Functional analyses of the mTOR mutation indicate a gain-of-function alteration and activation of both mTORC1 and mTORC2 signaling pathways, leading to increased cell proliferation and decreased apoptosis. Single-cell RNA sequencing and real-time impedance measurements support increased cytotoxicity of mutated CD4(+) T cells. High throughput drug-sensitivity testing suggests that mutations induce resistance to mTOR inhibitors, but increase sensitivity for HSP90 inhibitors. Our findings imply that somatic mutations may contribute to aberrant T cell proliferations and persistent immune activation in cGvHD, thereby paving the way for targeted therapies. Chronic graft versus host disease (cGvHD) is a major cause of morbidity and mortality in allogeneic bone marrow transplantation. Here the authors identify a recurrent activating mTOR mutation in expanded donor T-cell clones of 3 cGvHD patients, which suggests somatic mutations may contribute to GvHD pathogenesis and opens avenues to targeted therapies.
  • Vanhanen, Reetta; Heikkila, Nelli; Aggarwal, Kunal; Hamm, David; Tarkkila, Heikki; Pätilä, Tommi; Jokiranta, T. Sakari; Saramaki, Jari; Arstila, T. Petteri (2016)
    A diverse T cell receptor (TCR) repertoire is essential for adaptive immune responses and is generated by somatic recombination of TCR alpha and TCR beta gene segments in the thymus. Previous estimates of the total TCR diversity have studied the circulating mature repertoire, identifying 1 to 3 x 10(6) unique TCR beta and 0.5 x 10(6) TCR alpha sequences. Here we provide the first estimate of the total TCR diversity generated in the human thymus, an organ which in principle can be sampled in its entirety. High-throughput sequencing of samples from four pediatric donors detected up to 10.3 x 10(6) unique TCR beta sequences and 3.7 x 10(6) TCR alpha sequences, the highest directly observed diversity so far for either chain. To obtain an estimate of the total diversity we then used three different estimators, preseq and DivE, which measure the saturation of rarefaction curves, and Chao2, which measures the size of the overlap between samples. Our results provide an estimate of a thymic repertoire consisting of 40 to 70 x 10(6) unique TCR beta sequences and 60 to 100 x 10(6) TCR alpha sequences. The thymic repertoire is thus extremely diverse. Moreover, extrapolation of the data and comparison with earlier estimates of peripheral diversity also suggest that the thymic repertoire is transient, with different clones produced at different times. (C) 2016 Elsevier Ltd. All rights reserved.
  • Rajala, Hanna L. M.; Olson, Thomas; Clemente, Michael J.; Lagstrom, Sonja; Ellonen, Pekka; Lundan, Tuija; Hamm, David E.; Zaman, Syed Arshi Uz; Marti, Jesus M. Lopez; Andersson, Emma I.; Jerez, Andres; Porkka, Kimmo; Maciejewski, Jaroslaw P.; Loughran, Thomas P.; Mustjoki, Satu (2015)
  • Peltonen, Karita; Feola, Sara; Umer, Husen M.; Chiaro, Jacopo; Mermelekas, Georgios; Ylösmaki, Erkko; Pesonen, Sari; Branca, Rui M. M.; Lehtiö, Janne; Cerullo, Vincenzo (2021)
    Simple Summary Immunotherapy has revolutionized cancer treatment, yet many tumors remain resistant to current immuno-oncology therapies. Here we explore a novel, customized oncolytic adenovirus vaccine platform as immunotherapy in a resistant tumor model. We present a workflow for customizing the oncolytic vaccine for improved tumor targeting. This targeting is based on experimentally discovered tumor antigens, which are incorporated as active components of the vaccine formulation. The pipeline may be further applied for designing personalized therapeutic cancer vaccines. Knowledge of clinically targetable tumor antigens is becoming vital for broader design and utility of therapeutic cancer vaccines. This information is obtained reliably by directly interrogating the MHC-I presented peptide ligands, the immunopeptidome, with state-of-the-art mass spectrometry. Our manuscript describes direct identification of novel tumor antigens for an aggressive triple-negative breast cancer model. Immunopeptidome profiling revealed 2481 unique antigens, among them a novel ERV antigen originating from an endogenous retrovirus element. The clinical benefit and tumor control potential of the identified tumor antigens and ERV antigen were studied in a preclinical model using two vaccine platforms and therapeutic settings. Prominent control of established tumors was achieved using an oncolytic adenovirus platform designed for flexible and specific tumor targeting, namely PeptiCRAd. Our study presents a pipeline integrating immunopeptidome analysis-driven antigen discovery with a therapeutic cancer vaccine platform for improved personalized oncolytic immunotherapy.