Anàlisi de l’expressió gènica en la trombocitèmia essencial. Relació amb la policitèmia vera

La trombocitèmia essencial (TE) és una neoplasia mieloproliferativa que es caracteritza per una hiperplàsia megacariocítica medul·lar, un increment persistent de la xifra de plaquetes circulants i, clínicament, per episodis de trombosi i/o hemorràgia. No presenta un marcador diagnòstic específic ja que només es coneixen les alteracions moleculars causants de la malaltia en un 50% dels pacients, sent la mutació JAK2V617F l’alteració més comú. En aquesta tesi doctoral s’ha analitzat el perfil d’expressió gènica de granulòcits de sang perifèrica de la TE i de pacients amb policitèmia vera (PV) i trombocitosis reactives, utilitzant la tècnica de microarrays d’expressió i de RT-PCR quantitativa a temps real amb la plataforma de Taqman® Low density Arrays (TLDA). S’han inclòs un total de 98 pacients (57 TE i 41 PV), sis trombocitosis reactives i 10 individus sans com a control. L’anàlisi d’expressió en els pacients amb TE ha mostrat un perfil proinflamatori que caracteritza aquesta malaltia. També s’han detectat gens diferencialment expressats entre els pacients JAK2V617Fpositius i JAK2V617F-negatius que han permès identificar vies de senyalització afectades per la mutació JAK2V617F i d’altres independents de la mutació, que podrien estar afectades per alteracions moleculars encara desconegudes. A més, aquest perfil d’expressió s’ha comparat amb el de la PV, neoplàsia mieloproliferativa en la que el 95% dels pacients presenten la mutació JAK2V617F, i amb les trombocitosis reactives. Com a resultat, s’han definit gens l’expressió dels quals podrien tenir una implicació en la patogènesi de la TE, especialment en les TE JAK2V617F-negatives.Essential thrombocythemia (ET) is a myeloproliferative neoplasm characterized by increased bone marrow megakaryocytes, persistent thrombocytosis and an increased risk of thrombohemorragic complications. ET does not have specific biological markers as in only in 50% of patients specific molecular abnormalities have been described, being JAK2V617F mutation the most frequent. In polycythemia vera (PV), another myeloproliferative neoplasm, JAK2V617F mutation is detected in about 95% of patients. In this project we characterized the gene expression profile of peripheral blood granulocytes in ET, in polycythemia vera (PV) and in reactive thrombocytosis, using whole genome oligonucleotide microarray technology and real-time quantitative RT-PCR (using Taqman® Low density Arrays (TLDA)). A total of 98 patients (57 ET and 41 PV), six reactive thrombocytosis and 10 healthy individual used as controls, were included in the study. Gene expression analysis defined a proinflammatory pattern in ET. Moreover, genes differentially expressed between JAK2V617F-negative and JAK2V617F-positive ET patients were detected. Those set of genes identified JAK2V617F dependent and JAK2V617F independent signaling pathways. Those signalling pathways altered in JAK2V617F-negative patients could highlight molecular abnormalities which are still unknown. ET results were compared to PV and secondary thrombocytosis gene expression profiles. As a result, a set of genes that could provide insight into ET pathogenesis, specially in JAK2V617F-negative patients, was detected

Anàlisi de l'expressió gènica en la trombocitèmia essencial : relació amb la policitèmia vera /

La trombocitèmia essencial (TE) és una neoplasia mieloproliferativa que es caracteritza per una hiperplàsia megacariocítica medul·lar, un increment persistent de la xifra de plaquetes circulants i, clínicament, per episodis de trombosi i/o hemorràgia. No presenta un marcador diagnòstic específic ja que només es coneixen les alteracions moleculars causants de la malaltia en un 50% dels pacients, sent la mutació JAK2V617F l'alteració més comú. En aquesta tesi doctoral s'ha analitzat el perfil d'expressió gènica de granulòcits de sang perifèrica de la TE i de pacients amb policitèmia vera (PV) i trombocitosis reactives, utilitzant la tècnica de microarrays d'expressió i de RT-PCR quantitativa a temps real amb la plataforma de Taqman® Low density Arrays (TLDA). S'han inclòs un total de 98 pacients (57 TE i 41 PV), sis trombocitosis reactives i 10 individus sans com a control. L'anàlisi d'expressió en els pacients amb TE ha mostrat un perfil proinflamatori que caracteritza aquesta malaltia. També s'han detectat gens diferencialment expressats entre els pacients JAK2V617Fpositius i JAK2V617F-negatius que han permès identificar vies de senyalització afectades per la mutació JAK2V617F i d'altres independents de la mutació, que podrien estar afectades per alteracions moleculars encara desconegudes. A més, aquest perfil d'expressió s'ha comparat amb el de la PV, neoplàsia mieloproliferativa en la que el 95% dels pacients presenten la mutació JAK2V617F, i amb les trombocitosis reactives. Com a resultat, s'han definit gens l'expressió dels quals podrien tenir una implicació en la patogènesi de la TE, especialment en les TE JAK2V617F-negatives.Essential thrombocythemia (ET) is a myeloproliferative neoplasm characterized by increased bone marrow megakaryocytes, persistent thrombocytosis and an increased risk of thrombohemorragic complications. ET does not have specific biological markers as in only in 50% of patients specific molecular abnormalities have been described, being JAK2V617F mutation the most frequent. In polycythemia vera (PV), another myeloproliferative neoplasm, JAK2V617F mutation is detected in about 95% of patients. In this project we characterized the gene expression profile of peripheral blood granulocytes in ET, in polycythemia vera (PV) and in reactive thrombocytosis, using whole genome oligonucleotide microarray technology and real-time quantitative RT-PCR (using Taqman® Low density Arrays (TLDA)). A total of 98 patients (57 ET and 41 PV), six reactive thrombocytosis and 10 healthy individual used as controls, were included in the study. Gene expression analysis defined a proinflammatory pattern in ET. Moreover, genes differentially expressed between JAK2V617F-negative and JAK2V617F-positive ET patients were detected. Those set of genes identified JAK2V617F dependent and JAK2V617F independent signaling pathways. Those signalling pathways altered in JAK2V617F-negative patients could highlight molecular abnormalities which are still unknown. ET results were compared to PV and secondary thrombocytosis gene expression profiles. As a result, a set of genes that could provide insight into ET pathogenesis, specially in JAK2V617F-negative patients, was detected

Transcriptome analysis of severely active chronic spontaneous urticaria shows an overall immunological skin involvement

BACKGROUND: The knowledge about chronic spontaneous urticaria (CSU) phenotypes is based on its clinical characteristics, associated comorbidities, course of the disease, and its response to the available effective drugs. Genotype expression and its further correlation with CSU phenotypes are still unknown. We describe the cutaneous transcriptome of patients suffering a severely active CSU refractory to antihistamine treatment. METHODS: Through the bioinformatic analysis of the whole Human Genome with Oligo Microarrays and quantitative real-time polymerase chain reaction (qPCR), relevant genes expressed in nonlesional (NLS-CSU) and lesional skin (LS-CSU) and peripheral blood were identified in 20 patients suffering from severely active CSU and 10 healthy controls (HCs). RESULTS: From 39 genes differentially expressed in NLS-CSU when compared with HCs, 31 (79.48%) were confirmed by qPCR corresponding to genes involved in epidermal homeostasis and dermal repair. From the analysis comparing LS-CSU with NLS-CSU, a selection of 142 genes was studied with qPCR, and 103 (72.53%) were confirmed. Differentially expressed genes in the phenomenon of wheal development are involved in a variety of biological functions as, epidermal differentiation, intracellular signal function, transcriptional factors cell cycle differentiation, inflammation, or coagulation. Differentially expressed genes that uniformly increase or decrease along the skin worsening until the wheal appearance is shown. CONCLUSION: The skin of CSU patients with a severely active disease shows an overall immunological skin involvement showing a peculiar gene profile

Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs

MicroRNAs (miRNAs) have emerged as promising biomarkers of disease. Their potential use in clinical practice requires standardized protocols with very low miRNA concentrations, particularly in plasma samples. Here we tested the most appropriate method for miRNA quantification and validated the performance of a hybridization platform using lower amounts of starting RNA. miRNAs isolated from human plasma and from a reference sample were quantified using four platforms and profiled with hybridization arrays and RNA sequencing (RNA-seq). Our results indicate that the Infinite® 200 PRO Nanoquant and Nanodrop 2000 spectrophotometers magnified the miRNA concentration by detecting contaminants, proteins, and other forms of RNA. The Agilent 2100 Bioanalyzer PicoChip and SmallChip gave valuable information on RNA profile but were not a reliable quantification method for plasma samples. The Qubit® 2.0 Fluorometer provided the most accurate quantification of miRNA content, although RNA-seq confirmed that only ~58% of small RNAs in plasma are true miRNAs. On the other hand, reducing the starting RNA to 70% of the recommended amount for miRNA profiling with arrays yielded results comparable to those obtained with the full amount, whereas a 50% reduction did not. These findings provide important clues for miRNA determination in human plasma samples

A 12-gene expression signature is associated with aggressive histological in prostate cancer: SEC14L1 and TCEB1 genes are potential markers of progression. American journal of pathology

The main challenge for clinical management of prostate cancer is to distinguish tumors that will progress faster and will show a higher tendency to recur from the more indolent ones. We have compared expression profiles of 18 prostate cancer samples (seven with a Gleason score of 6, eight with a Gleason score of 7, and three with a Gleason score of ≥8) and five nonneoplastic prostate samples, using the Affymetrix Human Array GeneChip Exon 1.0 ST. Microarray analysis revealed 99 genes showing statistically significant differences among tumors with Gleason scores of 6, 7, and ≥8. In addition, mRNA expression of 29 selected genes was analyzed by real-time quantitative RT-PCR with microfluidic cards in an extended series of 30 prostate tumors. Of the 29 genes, 18 (62%) were independently confirmed in the extended series by quantitative RT-PCR: 14 were up-regulated and 4 were down-regulated in tumors with a higher Gleason score. Twelve of these genes were differentially expressed in tumors with a Gleason score of 6 to 7 versus ≥8. Finally, IHC validation of the protein levels of two genes from the 12-gene signature (SEC14L1 and TCEB1) showed strong protein expression levels of both genes, which were statistically associated with a high combined Gleason score, advanced stage, and prostate-specific antigen progression. This set of genes may contribute to a better understanding of the molecular basis of prostate cancer. TCEB1 and SELC14L1 are good candidate markers for predicting prognosis and progression of prostate cancer

A 12-gene expression signature is associated with aggressive histological in prostate cancer: SEC14L1 and TCEB1 genes are potential markers of progression. American journal of pathology

The main challenge for clinical management of prostate cancer is to distinguish tumors that will progress faster and will show a higher tendency to recur from the more indolent ones. We have compared expression profiles of 18 prostate cancer samples (seven with a Gleason score of 6, eight with a Gleason score of 7, and three with a Gleason score of ≥8) and five nonneoplastic prostate samples, using the Affymetrix Human Array GeneChip Exon 1.0 ST. Microarray analysis revealed 99 genes showing statistically significant differences among tumors with Gleason scores of 6, 7, and ≥8. In addition, mRNA expression of 29 selected genes was analyzed by real-time quantitative RT-PCR with microfluidic cards in an extended series of 30 prostate tumors. Of the 29 genes, 18 (62%) were independently confirmed in the extended series by quantitative RT-PCR: 14 were up-regulated and 4 were down-regulated in tumors with a higher Gleason score. Twelve of these genes were differentially expressed in tumors with a Gleason score of 6 to 7 versus ≥8. Finally, IHC validation of the protein levels of two genes from the 12-gene signature (SEC14L1 and TCEB1) showed strong protein expression levels of both genes, which were statistically associated with a high combined Gleason score, advanced stage, and prostate-specific antigen progression. This set of genes may contribute to a better understanding of the molecular basis of prostate cancer. TCEB1 and SELC14L1 are good candidate markers for predicting prognosis and progression of prostate cancer

Dose and time effects of solar-simulated ultraviolet radiation on the in vivo human skin transcriptome

BACKGROUND: Terrestrial ultraviolet (UV) radiation causes erythema, oxidative stress, DNA mutations and skin cancer. Skin can adapt to these adverse effects by DNA repair, apoptosis, keratinization and tanning. OBJECTIVES: To investigate the transcriptional response to fluorescent solar-simulated radiation (FSSR) in sun-sensitive human skin in vivo. METHODS: Seven healthy male volunteers were exposed to 0, 3 and 6 standard erythemal doses (SED). Skin biopsies were taken at 6 h and 24 h after exposure. Gene and microRNA expression were quantified with next generation sequencing. A set of candidate genes was validated by quantitative polymerase chain reaction (qPCR); and wavelength dependence was examined in other volunteers through microarrays. RESULTS: The number of differentially expressed genes increased with FSSR dose and decreased between 6 and 24 h. Six hours after 6 SED, 4071 genes were differentially expressed, but only 16 genes were affected at 24 h after 3 SED. Genes for apoptosis and keratinization were prominent at 6 h, whereas inflammation and immunoregulation genes were predominant at 24 h. Validation by qPCR confirmed the altered expression of nine genes detected under all conditions; genes related to DNA repair and apoptosis; immunity and inflammation; pigmentation; and vitamin D synthesis. In general, candidate genes also responded to UVA1 (340-400 nm) and/or UVB (300 nm), but with variations in wavelength dependence and peak expression time. Only four microRNAs were differentially expressed by FSSR. CONCLUSIONS: The UV radiation doses of this acute study are readily achieved daily during holidays in the sun, suggesting that the skin transcriptional profile of 'typical' holiday makers is markedly deregulated. What's already known about this topic? The skin's transcriptional profile underpins its adverse (i.e. inflammation) and adaptive molecular, cellular and clinical responses (i.e. tanning, hyperkeratosis) to solar ultraviolet radiation. Few studies have assessed microRNA and gene expression in vivo in humans, and there is a lack of information on dose, time and waveband effects. What does this study add? Acute doses of fluorescent solar-simulated radiation (FSSR), of similar magnitude to those received daily in holiday situations, markedly altered the skin's transcriptional profiles. The number of differentially expressed genes was FSSR-dose-dependent, reached a peak at 6 h and returned to baseline at 24 h. The initial transcriptional response involved apoptosis and keratinization, followed by inflammation and immune modulation. In these conditions, microRNA expression was less affected than gene expression.This study was supported by CERCA Programme/Generalitat de Catalunya and it was funded by the AGAUR with the support of Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement de la Generalitat de Catalunya (2017 SGR 919), the Instituto de Salud Carlos III (PI10/02235 and PI17/01225, the European Union (FEDER), “Una manera de hacer Europa”), the Spanish Ministry of Economy and Competitiveness (MTM2015‐68140‐R), the European Commission, under the Framework 7 Programme Environment Theme [Contract No. 227020: The Impact of Climate and Environmental Factors on Personal Ultraviolet Radiation Exposure and Human Health (ICEPURE)] and the U.K. National Institute for Health Research (NIHR) Biomedical Research Centre based at Guy's and St Thomas’ NHS Foundation Trust and King's College London, London, U.K. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the U.K. Department of Health. W.K. and M.R.F. acknowledge funding from the Strategic Research Area programme of the Swedish Research Council through Stockholm University. La Roche‐Posay provided funding for the microarray processing that was done by Milteyni Biotec GmbH (Bergisch Gladbach, Germany). AGAUR (2017 SGR 919)

Chronic lymphocytic leukemia-like monoclonal B-cell lymphocytosis exhibits an increased inflammatory signature that is reduced in early-stage chronic lymphocytic leukemia

Several studies in chronic lymphocytic leukemia (CLL) patients have reported impaired immune cell functions, which contribute to tumor evasion and disease progression. However, studies on CLL-like monoclonal B-cell lymphocytosis (MBL) are scarce. In the study described here, we characterized the immune environment in 62 individuals with clinical MBL, 56 patients with early-stage CLL, and 31 healthy controls. Gene expression arrays and quantitative reverse transcription polymerase chain reaction were performed on RNA from CD4+ peripheral blood cells; serum cytokines were measured with immunoassays; and HLA-DR expression on circulating monocytes, as well as the percentages of Th1, cytotoxic, exhausted, and effector CD4+ T cells, were evaluated by flow cytometry. In addition, cell cultures of clonal B cells and CD14-enriched or -depleted cell fractions were performed. Strikingly, MBL and early-stage CLL differed in pro-inflammatory signatures. An increased inflammatory drive orchestrated mainly by monocytes was identified in MBL, which exhibited enhanced phagocytosis, pattern recognition receptors, interleukin-8 (IL8), HMGB1, and acute response signaling pathways and increased pro-inflammatory cytokines (in particular IL8, interferon γ [IFNγ], and tumor necrosis factor α). This inflammatory signature was diminished in early-stage CLL (reduced IL8 and IFNγ levels, IL8 signaling pathway, and monocytic HLA-DR expression compared with MBL), especially in those patients with mutations in IGHV genes. Additionally, CD4+ T cells of MBL and early-stage CLL exhibited a similar upregulation of Th1 and cytotoxic genes and expanded CXCR3+ and perforin+ CD4+ T cells, as well as PD1+ CD4+ T cells, compared with controls. Cell culture assays disclosed tumor-supporting effects of monocytes similarly observed in MBL and early-stage CLL. These novel findings reveal differences in the inflammatory environment between MBL and CLL, highlighting an active role for antigen stimulation in the very early stages of the disease, potentially related to malignant B-cell transformation

Reduced expansion of CD94/NKG2C + NK cells in chronic lymphocytic leukemia and CLL-like monoclonal B-cell lymphocytosis is not related to increased human cytomegalovirus seronegativity or NKG2C deletions

Data de publicació electrònica: 22-02-2021Introduction: Dysregulated NK cell-mediated immune responses contribute to tumor evasion in chronic lymphocytic leukemia (CLL), although the NK cell compartment in CLL-like monoclonal B-cell lymphocytosis (MBL) is poorly understood. In healthy individuals, human cytomegalovirus (HCMV) induces the expansion of NK cells expressing high levels of CD94/NKG2C NK cell receptor (NKR) specific for HLA-E. Methods: We analyzed the expression of NKG2A, NKG2C, ILT2, KIR, CD161, and CD57 in 24 MBL and 37 CLL. NKG2C was genotyped in these patients and in 81 additional MBL/CLL, while NKG2C gene expression was assessed in 26 cases. In 8 CLL patients with increased lymphocytosis (≥20 × 109 /L), tumor HLA-E and HLA-G expression was evaluated. Results: NKR distribution did not significantly differ between MBL and CLL patients, although they exhibited reduced NKG2C+ NK cells compared with a non-CLL group (4.6% vs 12.2%, P = .012). HCMV+ patients showed increased percentages of NKG2C+ NK cells compared with HCMV- (7.3% vs 2.9%, P = .176). Frequencies of NKG2C deletions in MBL/CLL were similar to those of the general population. Low/undetectable NKG2C expression was found among NKG2C+/- (45%) and NKG2C+/+ (12%) patients. CLL cases with increased lymphocytosis displayed especially reduced NKG2C expression (1.8% vs 8.1%, P = .029) and tumor cells with high HLA-E (>98%) and variable HLA-G expression (12.4%, range: 0.5-56.4). CLL patients with low NKG2C expression (<7%) showed shorter time to first treatment (P = .037). Conclusion: Reduced percentages of CD94/NKG2C+ NK cells were observed in CLL and MBL patients independently of HCMV serostatus and NKG2C zygosity, particularly in CLL patients with increased lymphocytosis, which could potentially be related to the exposure to tumor cells