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  • 1
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 379, No. 6633 ( 2023-02-17)
    Abstract: Immune checkpoint blockade (ICB) therapy that blocks inhibitory T cell checkpoint molecules such as programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte–associated protein 4 (CTLA-4) has revolutionized cancer treatments. Despite its efficacy, half of the treated patients respond poorly and experience disease progression after therapy. To further improve immunotherapy outcome, a better understanding of the immune landscape and the tumor microenvironment (TME) is needed. In this context, dendritic cells (DCs), a functionally diverse system of antigen-presenting cells, play an instrumental role in eliciting antitumor responses during ICB therapy by inducing de novo CD8 + cytotoxic and CD4 + helper T cells against cancer-specific antigens. However, the specific DC features that are critical for driving effective T cell immunity and how subset composition in the tissue affects responsiveness to therapy remain unresolved. RATIONALE CD5, which is a transmembrane glycoprotein expressed on the surfaces of conventional T cells and some B cells, was recently recognized as a marker of a subset of DCs in both mice and humans. CD5 plays an important role in fine-tuning T cell receptor signaling during development and in their effector function in the periphery. However, the physiological roles of CD5 on DCs and the impact of such CD5 + DCs on tumor immunity remain unclear. In our previous work, we showed that migratory CD5 + DCs in the human skin prime helper T cells and multifunctional cytotoxic T cells more effectively than DCs that lack CD5. We hypothesized that the increased frequency of CD5 + DCs in inflammatory settings correlates with their involvement in antitumor responses and responses to ICB therapy. RESULTS We investigated the mechanisms that underlie DC-mediated effector T cell priming, focusing on the role of CD5 expressed by these interacting cells. We analyzed the myeloid compartment of human skin draining lymph nodes and found that the frequency of the CD5 + DC population within the DC2 compartment was reduced in human melanoma-affected lymph nodes compared with the same population in unaffected tissue. Accordingly, CD5 expression as well as a CD5 + DC gene signature correlated with greater survival and relapse-free survival in patients with a variety of cancers, including melanoma. We identified a critical immunostimulatory function for CD5 on DCs that potentiates the priming of tumor-reactive T cell activation, proliferation, effector function, and response to ICB therapy. The expression of CD5 on DCs correlated directly with the extent of effector helper CD4 + and cytotoxic T cell priming in humans. Selective deletion of CD5 expression in DCs prevented an efficient response to ICB therapy in tumor-bearing mice, resulting in defective immune rejection of tumors. This defect correlated with the activation of CD5 lo T cells, including CD5 lo CD4 + T cells and neoantigen-specific CD5 lo CD8 + T cells with poor effector function. In parallel, we examined biopsies of patients with melanoma and found that CD5 hi T cell frequencies aligned with the CD5 + DC density. Similarly, deletion of CD5 expression in T cells negatively affected CD5 + DC-mediated T cell priming, antitumor immunity, and the response to ICB. Moreover, we found increased numbers of CD5 + DCs after ICB in vivo, which corresponded to increased numbers of these cells in a patient with PD-1 deficiency. Furthermore, interleukin-6 (IL-6), which was abundant in the cells of this patient, was also detected at higher levels within tumors after ICB therapy compared with baseline measurements. Correspondingly, we identified IL-6 as an important factor in CD5 + DC differentiation and survival. CONCLUSION Our data provide insight into how immunotherapies like ICB work and identify CD5 on DCs as a new potential target for enhancing response rates among patients undergoing treatments. The role of DC CD5 in engaging effective antitumor immunity provides one explanation for the correlation of human DC2s, the only conventional DC subpopulation in humans that expresses CD5, with effector helper T cell density in tumors and with the patient responsiveness to ICB therapy. Overall, increased CD5 + DCs in human lymphoid tissue aligns with markers of effector T cell quality, as well as with patient overall survival. Thus, harnessing CD5 on DCs may be a promising avenue for enhancing the efficacy of immunotherapy against multiple tumors. DC CD5 directs the response to immunotherapy. CD5 + DC frequency was reduced in tumor-affected lymph nodes, and their presence correlated with greater patient survival in multiple tumors. CD5 +  DC numbers increased during ICB therapy, and low IL-6 concentrations promoted their de novo differentiation. The requirement for CD5 on DCs was linked to the priming of effector CD5 hi T cells and optimal ICB therapy. [Figure created with Biorender.com ]
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2023
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  • 2
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 381, No. 6658 ( 2023-08-11)
    Abstract: Comparative epigenomics is an emerging field that combines epigenetic signatures with phylogenetic relationships to elucidate species characteristics such as maximum life span. For this study, we generated cytosine DNA methylation (DNAm) profiles ( n = 15,456) from 348 mammalian species using a methylation array platform that targets highly conserved cytosines. RATIONALE Nature has evolved mammalian species of greatly differing life spans. To resolve the relationship of DNAm with maximum life span and phylogeny, we performed a large-scale cross-species unsupervised analysis. Comparative studies in many species enables the identification of epigenetic correlates of maximum life span and other traits. RESULTS We first tested whether DNAm levels in highly conserved cytosines captured phylogenetic relationships among species. We constructed phyloepigenetic trees that paralleled the traditional phylogeny. To avoid potential confounding by different tissue types, we generated tissue-specific phyloepigenetic trees. The high phyloepigenetic-phylogenetic congruence is due to differences in methylation levels and is not confounded by sequence conservation. We then interrogated the extent to which DNA methylation associates with specific biological traits. We used an unsupervised weighted correlation network analysis (WGCNA) to identify clusters of highly correlated CpGs (comethylation modules). WGCNA identified 55 distinct comethylation modules, of which 30 were significantly associated with traits including maximum life span, adult weight, age, sex, human mortality risk, or perturbations that modulate murine life span. Both the epigenome-wide association analysis (EWAS) and eigengene-based analysis identified methylation signatures of maximum life span, and most of these were independent of aging, presumably set at birth, and could be stable predictors of life span at any point in life. Several CpGs that are more highly methylated in long-lived species are located near HOXL subclass homeoboxes and other genes that play a role in morphogenesis and development. Some of these life span–related CpGs are located next to genes that are also implicated in our analysis of upstream regulators (e.g., ASCL1 and SMAD6 ). CpGs with methylation levels that are inversely related to life span are enriched in transcriptional start site (TSS1) and promoter flanking (PromF4, PromF5) associated chromatin states. Genes located in chromatin state TSS1 are constitutively active and enriched for nucleic acid metabolic processes. This suggests that long-living species evolved mechanisms that maintain low methylation levels in these chromatin states that would favor higher expression levels of genes essential for an organism’s survival. The upstream regulator analysis of the EWAS of life span identified the pluripotency transcription factors OCT4 , SOX2 , and NANOG. Other factors, such as POLII , CTCF , RAD21 , YY1 , and TAF1 , showed the strongest enrichment for negatively life span–related CpGs. CONCLUSION The phyloepigenetic trees indicate that divergence of DNA methylation profiles closely parallels that of genetics through evolution. Our results demonstrate that DNA methylation is subjected to evolutionary pressures and selection. The publicly available data from our Mammalian Methylation Consortium are a rich source of information for different fields such as evolutionary biology, developmental biology, and aging. DNAm network relates to mammalian phylogeny and traits. ( A ) Phyloepigenetic tree from the DNAm data generated from blood samples. ( B ) Unsupervised WGCNA networks identified 55 comethylation modules. ( C ) EWAS of log-transformed maximum life span. Each dot corresponds to the methylation levels of a highly conserved CpG. Shown is the log (base 10)–transformed P value ( y axis) versus the human genome coordinate Hg19 ( x axis). ( D ) Comethylation module correlated with maximum life span of mammals. Eigengene (first principal component of scaled CpGs in the midnightblue module) versus log (base e) transformed maximum life span. Each dot corresponds to a different species.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2023
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  • 3
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2023
    In:  Morphology Vol. 33, No. 3 ( 2023-09), p. 361-395
    In: Morphology, Springer Science and Business Media LLC, Vol. 33, No. 3 ( 2023-09), p. 361-395
    Abstract: This paper provides an in-depth investigation of the possibility of systematically using flexemes – i.e., lexical units characterized in terms of form, as opposed to lexemes, characterized in terms of meaning – to model overabundance – i.e., the availability of more than one form in the same paradigm cell. The starting point is a preliminary evaluation of the advantages and disadvantages of using flexemes to account for different overabundance phenomena, showing that flexemes are a good way to capture the systematicity of overabundance, either across lexemes or across cells. Consequently, it is suggested that flexemes can be an interesting technical solution for the creation of a lexicon of Latin verbs that not only documents all the competing wordforms available as principal parts, but also captures the systematic relationship that sometimes holds between variants filling different cells. A principled method to identify such systematicity is then described in detail. It is argued that a constructive approach based on the identity of stems and/or inflection class is not fully adequate for the data at hand. Therefore, the proposed procedure adopts an abstractive, word-based perspective that only relies on alternation patterns between unsegmented wordforms. Practical and theoretical implications of the work are finally discussed, particularly regarding the usefulness of a formal approach to the identification of lexical units and paradigm cells.
    Type of Medium: Online Resource
    ISSN: 1871-5621 , 1871-5656
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
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  • 4
    Online Resource
    Online Resource
    John Benjamins Publishing Company ; 2022
    In:  Studies in Language Vol. 46, No. 4 ( 2022-10-27), p. 753-792
    In: Studies in Language, John Benjamins Publishing Company, Vol. 46, No. 4 ( 2022-10-27), p. 753-792
    Abstract: In this paper, we investigate the value of derivational information in predicting the inflectional behavior of lexemes. We focus on Latin, for which large-scale data on both inflection and derivation are easily available. We train boosting tree classifiers to predict the inflection class of verbs and nouns with and without different pieces of derivational information. For verbs, we also model inflectional behavior in a word-based fashion, training the same type of classifier to predict wordforms given knowledge of other wordforms of the same lexemes. We find that derivational information is indeed helpful, and document an asymmetry between the beginning and the end of words, in that the final element in a word is highly predictive, while prefixes prove to be uninformative. The results obtained with the word-based methodology also allow for a finer-grained description of the behavior of different pairs of cells.
    Type of Medium: Online Resource
    ISSN: 0378-4177 , 1569-9978
    URL: Issue
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    Language: English
    Publisher: John Benjamins Publishing Company
    Publication Date: 2022
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  • 5
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 118, No. 6 ( 2021-02-09)
    Abstract: An important question is what genes govern the differentiation of plant embryos into suspensor and embryo proper regions following fertilization and division of the zygote. We compared embryo proper and suspensor transcriptomes of four plants that vary in embryo morphology within the suspensor region. We determined that genes encoding enzymes in several metabolic pathways leading to the formation of hormones, such as gibberellic acid, and other metabolites are up-regulated in giant scarlet runner bean and common bean suspensors. Genes involved in transport and Golgi body organization are up-regulated within the suspensors of these plants as well, strengthening the view that giant specialized suspensors serve as a hormone factory and a conduit for transferring substances to the developing embryo proper. By contrast, genes controlling transcriptional regulation, development, and cell division are up-regulated primarily within the embryo proper. Transcriptomes from less specialized soybean and Arabidopsis suspensors demonstrated that fewer genes encoding metabolic enzymes and hormones are up-regulated. Genes active in the embryo proper, however, are functionally similar to those active in scarlet runner bean and common bean embryo proper regions. We uncovered a set of suspensor- and embryo proper–specific transcription factors (TFs) that are shared by all embryos irrespective of morphology, suggesting that they are involved in early differentiation processes common to all plants. Chromatin immunoprecipitation sequencing (ChIP-Seq) experiments with scarlet runner bean and soybean WOX9, an up-regulated suspensor TF, gained entry into a regulatory network important for suspensor development irrespective of morphology.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2021
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  • 6
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 114, No. 45 ( 2017-11-07)
    Abstract: We profiled soybean and Arabidopsis methylomes from the globular stage through dormancy and germination to understand the role of methylation in seed formation. CHH methylation increases significantly during development throughout the entire seed, targets primarily transposable elements (TEs), is maintained during endoreduplication, and drops precipitously within the germinating seedling. By contrast, no significant global changes in CG- and CHG-context methylation occur during the same developmental period. An Arabidopsis ddcc mutant lacking CHH and CHG methylation does not affect seed development, germination, or major patterns of gene expression, implying that CHH and CHG methylation does not play a significant role in seed development or in regulating seed gene activity. By contrast, over 100 TEs are transcriptionally de-repressed in ddcc seeds, suggesting that the increase in CHH-context methylation may be a failsafe mechanism to reinforce transposon silencing. Many genes encoding important classes of seed proteins, such as storage proteins, oil biosynthesis enzymes, and transcription factors, reside in genomic regions devoid of methylation at any stage of seed development. Many other genes in these classes have similar methylation patterns, whether the genes are active or repressed. Our results suggest that methylation does not play a significant role in regulating large numbers of genes important for programming seed development in both soybean and Arabidopsis. We conclude that understanding the mechanisms controlling seed development will require determining how cis -regulatory elements and their cognate transcription factors are organized in genetic regulatory networks.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2017
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  • 7
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2008
    In:  Proceedings of the National Academy of Sciences Vol. 105, No. 12 ( 2008-03-25), p. 4709-4714
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 105, No. 12 ( 2008-03-25), p. 4709-4714
    Abstract: X chromosome inactivation (XCI) is an essential mechanism for dosage compensation of X-linked genes in female cells. We report that subcultures from lines of female human embryonic stem cells (hESCs) exhibit variation (0–100%) for XCI markers, including XIST RNA expression and enrichment of histone H3 lysine 27 trimethylation (H3K27me3) on the inactive X chromosome (Xi). Surprisingly, regardless of the presence or absence of XCI markers in different cultures, all female hESCs we examined (H7, H9, and HSF6 cells) exhibit a monoallelic expression pattern for a majority of X-linked genes. Our results suggest that these established female hESCs have already completed XCI during the process of derivation and/or propagation, and the XCI pattern of lines we investigated is already not random. Moreover, XIST gene expression in subsets of cultured female hESCs is unstable and subject to stable epigenetic silencing by DNA methylation. In the absence of XIST expression, ≈12% of X-linked promoter CpG islands become hypomethylated and a portion of X-linked alleles on the Xi are reactivated. Because alterations in dosage compensation of X-linked genes could impair somatic cell function, we propose that XCI status should be routinely checked in subcultures of female hESCs, with cultures displaying XCI markers better suited for use in regenerative medicine.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2008
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  • 8
    Online Resource
    Online Resource
    Charles University in Prague, Karolinum Press ; 2022
    In:  Prague Bulletin of Mathematical Linguistics Vol. 119, No. 1 ( 2022-10), p. 67-92
    In: Prague Bulletin of Mathematical Linguistics, Charles University in Prague, Karolinum Press, Vol. 119, No. 1 ( 2022-10), p. 67-92
    Type of Medium: Online Resource
    ISSN: 1804-0462 , 0032-6585
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    Language: English
    Publisher: Charles University in Prague, Karolinum Press
    Publication Date: 2022
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  • 9
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 328, No. 5976 ( 2010-04-16), p. 351-354
    Abstract: Although dimorphic sexes have evolved repeatedly in multicellular eukaryotes, their origins are unknown. The mating locus ( MT ) of the sexually dimorphic multicellular green alga Volvox carteri specifies the production of eggs and sperm and has undergone a remarkable expansion and divergence relative to MT from Chlamydomonas reinhardtii , which is a closely related unicellular species that has equal-sized gametes. Transcriptome analysis revealed a rewired gametic expression program for Volvox MT genes relative to Chlamydomonas and identified multiple gender-specific and sex-regulated transcripts. The retinoblastoma tumor suppressor homolog MAT3 is a Volvox MT gene that displays sexually regulated alternative splicing and evidence of gender-specific selection, both of which are indicative of cooption into the sexual cycle. Thus, sex-determining loci affect the evolution of both sex-related and non–sex-related genes.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2010
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  • 10
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2013
    In:  Proceedings of the National Academy of Sciences Vol. 110, No. 9 ( 2013-02-26), p. 3621-3626
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 110, No. 9 ( 2013-02-26), p. 3621-3626
    Abstract: The maintenance of functional chloroplasts in photosynthetic eukaryotes requires real-time coordination of the nuclear and plastid genomes. Tetrapyrroles play a significant role in plastid-to-nucleus retrograde signaling in plants to ensure that nuclear gene expression is attuned to the needs of the chloroplast. Well-known sites of synthesis of chlorophyll for photosynthesis, plant chloroplasts also export heme and heme-derived linear tetrapyrroles (bilins), two critical metabolites respectively required for essential cellular activities and for light sensing by phytochromes. Here we establish that Chlamydomonas reinhardtii, one of many chlorophyte species that lack phytochromes, can synthesize bilins in both plastid and cytosol compartments. Genetic analyses show that both pathways contribute to iron acquisition from extracellular heme, whereas the plastid-localized pathway is essential for light-dependent greening and phototrophic growth. Our discovery of a bilin-dependent nuclear gene network implicates a widespread use of bilins as retrograde signals in oxygenic photosynthetic species. Our studies also suggest that bilins trigger critical metabolic pathways to detoxify molecular oxygen produced by photosynthesis, thereby permitting survival and phototrophic growth during the light period.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2013
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