IsomiRs and tRNA-derived fragments are associated with metastasis and patient survival in uveal melanoma.

Abstract:

:Uveal melanoma (UVM) is the most common primary intraocular malignancy in adults. With over 50% of patients developing metastatic disease, there is an unmet need for improved diagnostic and therapeutic options. Efforts to understand the molecular biology of the disease have revealed several markers that correlate with patient prognosis, including the copy number of chromosome 3, genetic alterations in the BAP1, EIF1AX and SF3B1 genes, and other transcriptional features. Here, we expand upon previous reports by comprehensively characterizing the short RNA-ome in 80 primary UVM tumor samples. In particular, we describe a previously unseen complex network involving numerous regulatory molecules that comprise microRNA (miRNAs), novel UVM-specific miRNA loci, miRNA isoforms (isomiRs), and tRNA-derived fragments (tRFs). Importantly, we show that the abundance profiles of isomiRs and tRFs associate with various molecular phenotypes, metastatic disease, and patient survival. Our findings suggest deep involvement of isomiRs and tRFs in the disease etiology of UVM. We posit that further study and characterization of these novel molecules will improve understanding of the mechanisms underlying UVM, and lead to the development of new diagnostic and therapeutic approaches.

authors

Londin E,Magee R,Shields CL,Lally SE,Sato T,Rigoutsos I

doi

10.1111/pcmr.12810

subject

Has Abstract

pub_date

2020-01-01 00:00:00

pages

52-62

issue

1

eissn

1755-1471

issn

1755-148X

journal_volume

33

pub_type

杂志文章
  • Keratinocytes in culture accumulate phagocytosed melanosomes in the perinuclear area.

    abstract::There are many techniques for evaluating melanosome transfer to keratinocytes but the spectrophotometric quantification of melanosomes incorporated by keratinocyte phagocytosis has not been previously reported. Here we describe a new method that allows the spectrophotometric visualization of melanosome uptake by norma...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/j.1755-148X.2009.00640.x

    authors: Ando H,Niki Y,Yoshida M,Ito M,Akiyama K,Kim JH,Yoon TJ,Lee JH,Matsui MS,Ichihashi M

    更新日期:2010-02-01 00:00:00

  • Meeting report: fourth international congress of the Society for Melanoma Research.

    abstract::The 4th international melanoma congress of the Society for Melanoma Research (SMR), organized by Marianne Berwick (University of New Mexico), Paul Chapman (Memorial Sloan-Kettering Cancer Center), Rene Gonzalez (University of Colorado) and Ze'ev Ronai (Burnham Institute), was held at the Marriott Hotel in downtown New...

    journal_title:Pigment cell & melanoma research

    pub_type:

    doi:10.1111/j.1755-148X.2007.00437.x

    authors: Fisher DE,Medrano EE,McMahon M,Soengas MS,Schuchter L,Wolchok JD,Merlino G

    更新日期:2008-02-01 00:00:00

  • BRAF mutations in cutaneous melanoma are independently associated with age, anatomic site of the primary tumor, and the degree of solar elastosis at the primary tumor site.

    abstract::Oncogenic BRAF mutations are more frequent in cutaneous melanoma occurring at sites with little or moderate sun-induced damage than at sites with severe cumulative solar ultraviolet (UV) damage. We studied cutaneous melanomas from geographic regions with different levels of ambient UV radiation to delineate the relati...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/j.1755-148X.2011.00837.x

    authors: Bauer J,Büttner P,Murali R,Okamoto I,Kolaitis NA,Landi MT,Scolyer RA,Bastian BC

    更新日期:2011-04-01 00:00:00

  • Genetic modulation of the iris transillumination defect: a systems genetics analysis using the expanded family of BXD glaucoma strains.

    abstract::We investigated the contributions of Tyrp1 and Gpnmb to the iris transillumination defect (TID) in five age cohorts of BXD mice. Using systems genetics, we also evaluated the role of other known pigmentation genes (PGs). Mapping studies indicate that Tyrp1 contributes to the phenotype at all ages, yet the TID maps to ...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12106

    authors: Swaminathan S,Lu H,Williams RW,Lu L,Jablonski MM

    更新日期:2013-07-01 00:00:00

  • NRASQ61K melanoma tumor formation is reduced by p38-MAPK14 activation in zebrafish models and NRAS-mutated human melanoma cells.

    abstract::Oncogenic BRAF and NRAS mutations drive human melanoma initiation. We used transgenic zebrafish to model NRAS-mutant melanoma, and the rapid tumor onset allowed us to study candidate tumor suppressors. We identified P38α-MAPK14 as a potential tumor suppressor in The Cancer Genome Atlas melanoma cohort of NRAS-mutant m...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12925

    authors: Banik I,Cheng PF,Dooley CM,Travnickova J,Merteroglu M,Dummer R,Patton EE,Busch-Nentwich EM,Levesque MP

    更新日期:2020-09-10 00:00:00

  • T-type calcium channel blockers inhibit autophagy and promote apoptosis of malignant melanoma cells.

    abstract::We have recently reported that human melanoma cells express a variety of voltage-gated calcium (Ca(2+) ) channel types, including low-voltage-activated T-type channels that play a significant role in melanoma cell cycle progression. Here, we challenged melanoma metastatic cells with T-type channel blockers of clinical...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12155

    authors: Das A,Pushparaj C,Herreros J,Nager M,Vilella R,Portero M,Pamplona R,Matias-Guiu X,Martí RM,Cantí C

    更新日期:2013-11-01 00:00:00

  • Raman spectroscopy as a non-invasive technique for the quantification of melanins in feathers and hairs.

    abstract::The quantification of melanins is a complex task due to the chemical heterogeneity of the pigments and the difficulty of their isolation. The best accepted procedure currently consists in the chemical cleavage of melanins and the subsequent detection of degradation products by HPLC, which implies the destruction of sa...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12140

    authors: Galván I,Jorge A,Ito K,Tabuchi K,Solano F,Wakamatsu K

    更新日期:2013-11-01 00:00:00

  • Re-evaluation of insect melanogenesis research: Views from the dark side.

    abstract::Melanins (eumelanin and pheomelanin) are synthesized in insects for several purposes including cuticle sclerotization and color patterning, clot formation, organogenesis, and innate immunity. Traditional views of insect immunity detail the storage of pro-phenoloxidases inside specialized blood cells (hemocytes) and th...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章,评审

    doi:10.1111/pcmr.12590

    authors: Whitten MMA,Coates CJ

    更新日期:2017-07-01 00:00:00

  • Osteoblasts contribute to a protective niche that supports melanoma cell proliferation and survival.

    abstract::Melanoma is the deadliest form of skin cancer; a primary driver of this high level of morbidity is the propensity of melanoma cells to metastasize. When malignant tumours develop distant metastatic lesions the new local tissue niche is known to impact on the biology of the cancer cells. However, little is known about ...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12812

    authors: Ferguson J,Wilcock DJ,McEntegart S,Badrock AP,Levesque M,Dummer R,Wellbrock C,Smith MP

    更新日期:2020-01-01 00:00:00

  • Postnatal lineage mapping of follicular melanocytes with the Tyr::CreER(T) (2) transgene.

    abstract::One of the main advantages of using inducible and conditional transgenes to study pigment cell biology is that they allow for genetic manipulation within melanocytes after roles in general neural crest or melanoblast development have been fulfilled. Specifically, we focus here on the ability of the Tyr::CreER(T) ...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12048

    authors: Harris ML,Pavan WJ

    更新日期:2013-03-01 00:00:00

  • Pigmentation PAX-ways: the role of Pax3 in melanogenesis, melanocyte stem cell maintenance, and disease.

    abstract::Transcription factors initiate programs of gene expression and are catalysts in downstream molecular cascades that modulate a variety of cellular processes. Pax3 is a transcription factor that is important in the melanocyte and influences melanocytic proliferation, resistance to apoptosis, migration, lineage specifici...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章,评审

    doi:10.1111/j.1755-148X.2008.00514.x

    authors: Kubic JD,Young KP,Plummer RS,Ludvik AE,Lang D

    更新日期:2008-12-01 00:00:00

  • Silencing and re-expression of retinoic acid receptor beta2 in human melanoma.

    abstract::Many melanoma cells are resistant to the anti-proliferative effect of all trans retinoic acid (ATRA). Retinoic Acid Receptor-beta2 (RAR-beta2) mediates the ATRA growth inhibition. We found a correlation between the anti-proliferative activity of ATRA and expression of RAR-beta2. There was not a strict correlation betw...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/j.1755-148X.2010.00702.x

    authors: Fan J,Eastham L,Varney ME,Hall A,Adkins NL,Chetel L,Sollars VE,Georgel P,Niles RM

    更新日期:2010-06-01 00:00:00

  • Insights into genetic alterations of liver metastases from uveal melanoma.

    abstract::The liver is the organ usually affected by metastatic uveal melanoma (MUM). Current treatments are almost always ineffective and mortality remains high. In this study, copy number variations (CNVs) were identified in 12 metastatic and five matched primary UMs (PUMs). Our data revealed a wide spectrum of genetic altera...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12433

    authors: McCarthy C,Kalirai H,Lake SL,Dodson A,Damato BE,Coupland SE

    更新日期:2016-01-01 00:00:00

  • Increasing the complexity: new genes and new types of albinism.

    abstract::Albinism is a rare genetic condition globally characterized by a number of specific deficits in the visual system, resulting in poor vision, in association with a variable hypopigmentation phenotype. This lack or reduction in pigment might affect the eyes, skin, and hair (oculocutaneous albinism, OCA), or only the eye...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章,评审

    doi:10.1111/pcmr.12167

    authors: Montoliu L,Grønskov K,Wei AH,Martínez-García M,Fernández A,Arveiler B,Morice-Picard F,Riazuddin S,Suzuki T,Ahmed ZM,Rosenberg T,Li W

    更新日期:2014-01-01 00:00:00

  • Premature senescence in human melanocytes after exposure to solar UVR: An exosome and UV-miRNA connection.

    abstract::Ultraviolet radiation (UVR) can play two roles: induce cellular senescence and convert skin melanocytes into melanoma. To assess whether this conversion might rely on melanocytes having to first acquire a senescent phenotype, we studied the effects of physiological doses of UVR (UVA + UVB) on quiescent melanocytes in ...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12888

    authors: Sha J,Arbesman J,Harter ML

    更新日期:2020-09-01 00:00:00

  • The interaction between vitamin D receptor polymorphisms and sun exposure around time of diagnosis influences melanoma survival.

    abstract::Evidence on the relationship between the vitamin D pathway and outcomes in melanoma is growing, although it is not always clear. We investigated the impact of measured levels of sun exposure at diagnosis on associations of vitamin D receptor gene (VDR) polymorphisms and melanoma death in 3336 incident primary melanoma...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12653

    authors: Orlow I,Shi Y,Kanetsky PA,Thomas NE,Luo L,Corrales-Guerrero S,Cust AE,Sacchetto L,Zanetti R,Rosso S,Armstrong BK,Dwyer T,Venn A,Gallagher RP,Gruber SB,Marrett LD,Anton-Culver H,Busam K,Begg CB,Berwick M,GEM Study

    更新日期:2018-03-01 00:00:00

  • MicroRNA-125a promotes resistance to BRAF inhibitors through suppression of the intrinsic apoptotic pathway.

    abstract::Melanoma patients with BRAFV600E -mutant tumors display striking responses to BRAF inhibitors (BRAFi); however, almost all invariably relapse with drug-resistant disease. Here, we report that microRNA-125a (miR-125a) expression is upregulated in human melanoma cells and patient tissues upon acquisition of BRAFi resist...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12578

    authors: Koetz-Ploch L,Hanniford D,Dolgalev I,Sokolova E,Zhong J,Díaz-Martínez M,Bernstein E,Darvishian F,Flaherty KT,Chapman PB,Tawbi H,Hernando E

    更新日期:2017-05-01 00:00:00

  • Advances in melanoma senescence and potential clinical application.

    abstract::Normal cells possess a limited proliferative life span, after which they enter a state of irreversible growth arrest, called replicative senescence, which acts as a potent barrier against transformation. Transformed cells have escaped the process of replicative senescence and theoretically can not re-enter senescence....

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章,评审

    doi:10.1111/j.1755-148X.2010.00820.x

    authors: Giuliano S,Ohanna M,Ballotti R,Bertolotto C

    更新日期:2011-04-01 00:00:00

  • Genetic variation in IRF4 expression modulates growth characteristics, tyrosinase expression and interferon-gamma response in melanocytic cells.

    abstract::A SNP within intron4 of the interferon regulatory factor4 (IRF4) gene, rs12203592*C/T, has been independently associated with pigmentation and age-specific effects on naevus count in European-derived populations. We have characterized the cis-regulatory activity of this intronic region and using human foreskin-derived...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12620

    authors: Chhabra Y,Yong HXL,Fane ME,Soogrim A,Lim W,Mahiuddin DN,Kim RSQ,Ashcroft M,Beatson SA,Ainger SA,Smit DJ,Jagirdar K,Walker GJ,Sturm RA,Smith AG

    更新日期:2018-01-01 00:00:00

  • Two light-activated neuroendocrine circuits arising in the eye trigger physiological and morphological pigmentation.

    abstract::Two biological processes regulate light-induced skin colour change. A fast 'physiological pigmentation change' (i.e. circadian variations or camouflage) involves alterations in the distribution of pigment containing granules in the cytoplasm of chromatophores, while a slower 'morphological pigmentation change' (i.e. s...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12531

    authors: Bertolesi GE,Hehr CL,Munn H,McFarlane S

    更新日期:2016-11-01 00:00:00

  • NGS-based 100-gene panel of hypopigmentation identifies mutations in Chinese Hermansky-Pudlak syndrome patients.

    abstract::Hermansky-Pudlak syndrome (HPS) is a rare recessive disorder characterized by hypopigmentation, bleeding diathesis, and other symptoms due to multiple defects in lysosome-related organelles. Ten HPS subtypes have been identified with mutations in HPS1 to HPS10. Only four patients with HPS-1 have been reported in Chine...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12534

    authors: Wei A,Yuan Y,Bai D,Ma J,Hao Z,Zhang Y,Yu J,Zhou Z,Yang L,Yang X,Li L,Li W

    更新日期:2016-11-01 00:00:00

  • Integrins: versatile receptors controlling melanocyte adhesion, migration and proliferation.

    abstract::From the onset of melanocyte specification from the neural crest, throughout their migration during embryogenesis and until they reside in their niche in the basal keratinocyte layer, melanocytes interact in dynamic ways with the extracellular environment of the growing embryo. To recognize and to adhere to their envi...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章,评审

    doi:10.1111/j.1755-148X.2010.00806.x

    authors: Pinon P,Wehrle-Haller B

    更新日期:2011-04-01 00:00:00

  • The Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10.

    abstract::The Dark brown (DB) mutation in chickens reduces expression of black eumelanin and enhances expression of red pheomelanin, but only in certain parts of the plumage. Here, we present genetic evidence that an 8.3-kb deletion upstream of the SOX10 transcription start site is the causal mutation underlying the DB phenotyp...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/j.1755-148X.2011.00825.x

    authors: Gunnarsson U,Kerje S,Bed'hom B,Sahlqvist AS,Ekwall O,Tixier-Boichard M,Kämpe O,Andersson L

    更新日期:2011-04-01 00:00:00

  • PLX3397 inhibits the accumulation of intra-tumoral macrophages and improves bromodomain and extra-terminal inhibitor efficacy in melanoma.

    abstract::Bromodomain and extra-terminal inhibitors (BETi) delay tumor growth, in part, through tumor cell intrinsic alterations and initiation of anti-tumor CD8+ T-cell responses. By contrast, BETi effects on pro-tumoral immune responses remain unclear. Here, we show that the next-generation BETi, PLX51107, delayed tumor growt...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12845

    authors: Erkes DA,Rosenbaum SR,Field CO,Chervoneva I,Villanueva J,Aplin AE

    更新日期:2020-03-01 00:00:00

  • The avidity of tumor-specific T cells amplified by a plasmacytoid dendritic cell-based assay can predict the clinical evolution of melanoma patients.

    abstract::The advent of immune checkpoint blockers and targeted therapies has changed the outcome of melanoma. However, many patients experience relapses, emphasizing the need for predictive and prognostic biomarkers. We developed a strategy based on plasmacytoid dendritic cells (pDCs) loaded with melanoma tumor antigens that a...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12618

    authors: Charles J,Chaperot L,Revol B,Baudin M,Mouret S,Hamon A,Leccia MT,Plumas J,Aspord C

    更新日期:2018-01-01 00:00:00

  • D-tyrosine negatively regulates melanin synthesis by competitively inhibiting tyrosinase activity.

    abstract::Although L-tyrosine is well known for its melanogenic effect, the contribution of D-tyrosine to melanin synthesis was previously unexplored. Here, we reveal that, unlike L-tyrosine, D-tyrosine dose-dependently reduced the melanin contents of human MNT-1 melanoma cells and primary human melanocytes. In addition, 500 μM...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12668

    authors: Park J,Jung H,Kim K,Lim KM,Kim JY,Jho EH,Oh ES

    更新日期:2018-05-01 00:00:00

  • Reverse TCA cycle flux through isocitrate dehydrogenases 1 and 2 is required for lipogenesis in hypoxic melanoma cells.

    abstract::The tricarboxylic acid (TCA) cycle is the central hub of oxidative metabolism, running in the classic forward direction to provide carbon for biosynthesis and reducing agents for generation of ATP. Our metabolic tracer studies in melanoma cells showed that in hypoxic conditions the TCA cycle is largely disconnected fr...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/j.1755-148X.2012.00989.x

    authors: Filipp FV,Scott DA,Ronai ZA,Osterman AL,Smith JW

    更新日期:2012-05-01 00:00:00

  • High frequency of PTEN mutations in nevi and melanomas from xeroderma pigmentosum patients.

    abstract::We examined nevi and melanomas in 10 xeroderma pigmentosum (XP) patients with defective DNA repair. The lesions had a lentiginous appearance with markedly increased numbers of melanocytes. Using laser capture microdissection, we performed DNA sequencing of 18 benign and atypical nevi and 75 melanomas (melanoma in situ...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12226

    authors: Masaki T,Wang Y,DiGiovanna JJ,Khan SG,Raffeld M,Beltaifa S,Hornyak TJ,Darling TN,Lee CC,Kraemer KH

    更新日期:2014-05-01 00:00:00

  • Pathogenesis of a variant in the 5' untranslated region of ADAR1 in dyschromatosis symmetrica hereditaria.

    abstract::Dyschromatosis symmetrica hereditaria (DSH) is a pigmentary genodermatosis caused by mutations in ADAR1. In this study, we performed mutation analysis on a family that included typical DSH patients. No mutations were found in any coding regions or exon-intron boundary regions of ADAR1, but a previously unreported non-...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章

    doi:10.1111/pcmr.12863

    authors: Suganuma M,Kono M,Yamanaka M,Akiyama M

    更新日期:2020-07-01 00:00:00

  • Lighting a path to pigmentation: mechanisms of MITF induction by UV.

    abstract::While sunlight is important for life, ultraviolet radiation (UVR) can have harmful and mutagenic effects. This duality is particularly relevant to human skin, in which UVR both participates in evolutionarily important photochemical reactions yet may act as a potential carcinogen. UVR can upregulate production of melan...

    journal_title:Pigment cell & melanoma research

    pub_type: 杂志文章,评审

    doi:10.1111/j.1755-148X.2010.00775.x

    authors: Liu JJ,Fisher DE

    更新日期:2010-12-01 00:00:00