Aggressive systemic mastocytosis with the co-occurrence of PRKG2::PDGFRB, KAT6A::NCOA2, and RXRA::NOTCH1 fusion transcripts and a heterozygous RUNX1 frameshift mutation.

Systemic mastocytosis (SM) is a myeloproliferative neoplasm displaying abnormal mast cell proliferation. It is subdivided into different forms, including aggressive systemic mastocytosis (ASM) and systemic mastocytosis with an associated hematologic neoplasm (SM-AHN). Oncogenic genetic alterations include point mutations, mainly the KIT D816V, conferring poor prognosis and therapy resistance, and fusion genes, with those involving PDGFRA/PDGFRB as the most recurrent events. We here describe an ASM case negative to the KIT D816V and JAK2 V617F alterations but showing a RUNX1 frameshift heterozygous mutation and the co-occurrence of three fusion transcripts. The first one, PRKG2::PDGFRB, was generated by a balanced t(4;5)(q24;q32) translocation as the sole abnormality. Other two novel chimeras, KAT6A::NCOA2 and RXRA::NOTCH1, originated from cryptic intra-chromosomal abnormalities. The patient rapidly evolved towards SM-AHN, characterized by the persistence of the PRKG2::PDGFRB chimera, due to the presence of an extra copy of the der(5)t(4;5)(q24;q34) chromosome and an increase in the RUNX1 mutation allelic frequency. The results indicated that the transcriptional landscape and the mutational profile of SM deserve attention to predict the evolution and prognosis of this complex disease, whose classification criteria are still a matter of debate.

Inter- and Intramolecular Interactions in Ether-Functionalized Ionic Liquids.

The intra- and intermolecular interactions in ether-functionalized ionic liquids (ILs) are studied by means of infrared (IR) spectroscopy measurements of N-ethoxyethyl-N-methylpiperidiniumbis(fluorosulfonyl)imide (P1,2O2-FSI) and N-ethoxyethyl-N-methylmorpholiniumbis(fluorosulfonyl)imide (M1,2O2-FSI). The temperature dependence of the spectra in the medium IR range allows the study of the anion conformer distribution and its variation during phase transitions. In particular, it is found that for both ILs the trans conformer of FSI is more stable than the cis conformer, and the enthalpy differences between them are calculated and are found to decrease upon the addition of a Li salt. The results obtained in the far IR range, combined with ab initio calculation of the ionic couple performed using the B3LYP-D functional and considering both empirical dispersion corrections and the presence of a polar solvent, provide evidence for the occurrence of a hydrogen bonding between the O atom of the anion and its closest H atoms directly linked to a C atom of the cation. The comparison with samples having the same cations but with bis(trifluoromethanesulfonyl)imide (TFSI) as an anion, that is, M1,2O2-TFSI and P1,2O2-TFSI, as well as with samples having cations without the ether-functionalization neither in the ring nor in the side chain, such as N-propyl-N-methylpyrrolidinium-FSI (PYR13-FSI) and 1-butyl-1-methylpyrrolidinium-TFSI (PYR14-TFSI), indicates that the occurrence of such highly directional interaction between anion and cation is better observable in the ether-functionalized samples, in particular in those containing FSI as an anion.

New insights into chloromethyl-oxirane and chloromethyl-thiirane in liquid and solid phase from low-temperature infrared spectroscopy and ab initio modeling.

A detailed study of the conformational landscape of chloromethyl-oxirane and chloromethyl-thiirane is here reported. The equilibrium of the three different conformers of the two molecules was assessed, using a joint approach of experimental and theoretical methods. High quality infrared spectroscopy measurements of the liquid and of the crystalline phases were interpreted with the aid of ab initio Molecular Dynamics (AIMD) simulations, anharmonic frequencies and free energy calculations, obtaining a very good reproduction of the experimental data. The modulation of the conformational equilibrium upon the addition of polar and non-polar solvents was computationally evaluated and results found a confirmation in experimental measures.

The infrared spectra of protic ionic liquids: performances of different computational models to predict hydrogen bonds and conformer evolution.

The temperature dependence of the far- and mid-infrared spectrum of two prototypical protic ionic liquids (PILs) sharing a common trialkylammonium cation, but having different anions, is investigated. The exploitation of both the FIR and MIR ranges provides complementary information about the microscopic configurations and the intermolecular interactions, which determine the structure and the properties of ILs. The analysis of the data collected for all the measured frequencies in a wide temperature range reveals several phase transitions and allows the evaluation of the conformer distribution in the different physical states. The difference in the average energy between the H-bonded configurations and the dispersion-governed ones was also determined for the two PILs. Moreover, a computational model for ionic couples based on the ωB97X-D functional and a polar solvent is here successfully exploited for the description of the hydrogen bonding between anion and cation. For the attribution of vibrational lines of the conformers of the cation, the picture based on single ion calculations at the B3LYP level is more valuable and provides better agreement with the experiments.

Concurrent chromothripsis events in a case of TP53 depleted acute myeloid leukemia with myelodysplasia-related changes.

Acute myeloid leukemia with myelodysplasia-related changes (AML-MRC) is a heterogeneous hematological disorder defined by morphological, genetic, and clinical features. Patients with AML-MRC often show cytogenetic changes, which are associated with poor prognosis. Straightforward criteria for AML-MRC diagnosis and a more rigorous characterization of the genetic abnormalities accompanying this disease are needed. Here we describe an informative AML-MRC case, showing two separate, but concurrent, chromothripsis events, occurred at the onset of the tumor, and originating an unbalanced t(5;7) translocation and a derivative chromosome 12 with a highly rearranged short arm. Conversely, despite chromothripsis has been often associated with genomic amplification in cancer, in this case a large marker chromosome harboring amplified sequences from chromosomes 19 and 22 arose from a stepwise mechanism. Notably, the patient also showed a TP53 mutated status, known to be associated with an increased susceptibility towards chromothripsis and a poor prognosis. Our results indicate that multiple chromothripsis events may occur early in neoplastic transformation and act in a synergistic way with progressive chromosomal alterations to determine a dramatic impact on disease outcome, as suggested by the gene expression profile analysis.

Crystallization of mixtures of hydrophilic ionic liquids and water: Evidence of microscopic inhomogeneities.

HYPOTHESIS: We compare the effects of water, either intentionally added or due to absorption from the air, on the phase diagram of the hydrophilic 1-butyl-3-methylimidazolium dicyanamide ionic liquid, extending previous investigations to lower temperatures (down to 140 K), with a special attention to the changes of the environment of water molecules and the interface between water and ionic liquid as a function of temperature. EXPERIMENTS: Combined infrared spectroscopy and ab-initio calculations provide information about the phase transitions and the intermolecular changes occurring in the liquid. FINDINGS: The temperature dependence of the mid-infrared spectrum in the temperature range between 140 and 330 K indicates that in both cases the liquid undergoes a glass transition, but, when the water content is only due to absorption from air, a cold crystallization takes place on heating between ≈240 and ≈265 K, while it is suppressed when water is intentionally added in a greater amount. The analysis of the OH stretching bands indicates the existence of two different "liquid like" water environments. When cold crystallization takes places the water molecules, which seem less coordinated to the other H2O molecules and more related to the anions, appear to be part of the crystallized sample. In both cases, it seems that at microscopic level the sample is not homogeneous, but more likely it is composed of separated clusters or regions of bulk water confined in the ionic liquid.

The effect of ether-functionalisation in ionic liquids analysed by DFT calculation, infrared spectra, and Kamlet-Taft parameters.

The effect of ether-functionalisation on ionic liquids (ILs) is discussed based on Kamlet-Taft parameters and the infrared (IR) spectra of N-ethoxyethyl-N-methylpiperidinium bis(trifluoromethanesulfonyl)imide ([P1,2O2][TFSI]) and N-ethoxyethyl-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide ([M1,2O2][TFSI]). The results are analysed taking into consideration their ion conformers, electronegativity and hardness, and the IR active vibrations obtained by means of DFT calculations. From the evaluation of Kamlet-Taft parameters, the ether-functionalisation in the cationic ring is found to improve the polarity and hydrogen bond acidity of the ILs. This correlates with the computational result which designates that the oxygen atom in the cationic ring increases the electronegativity of the cation. The comparison with the IR spectra, which were obtained experimentally and computationally, revealed that trans-[TFSI] was preferably formed in [M1,2O2][TFSI] compared to [P1,2O2][TFSI]. Although the Kamlet-Taft parameters indicate that [M1,2O2][TFSI] has a higher polarity, this IL preferably adopts trans-[TFSI], which is normally stabilised with the cations having a lower polarity. This may be due to the presence of the oxygen in the cationic ring which delocalises the electron density of the lowest unoccupied molecular orbitals (LUMO) and increases the conformational freedom of the hydrogen bonds between cations and anions. Moreover, the mixtures of pure ILs with a suitable Li-salt were also investigated to analyze the effect of the Li salt on the polarity and the ion conformers.

Tailoring the physical properties of the mixtures of ionic liquids: a microscopic point of view.

A detailed investigation of the phase diagram of the mixtures of the two ionic liquids N-trimethyl-N-propylammonium bis(trifluoromethylsulfonyl)imide (TMPA-TFSI) and N-trimethyl-N-hexylammonium bis(trifluoromethylsulfonyl)imide (TMHA-TFSI) has been performed in the temperature range between 140 and 330 K by means of DSC and infrared spectroscopy measurements. In the low temperature crystalline states, a large concentration of the trans-TFSI conformer is present in TMPA-TFSI, while almost only cis-TFSI is retained in TMHA-TFSI. For the mixtures (TMPA-TFSI)100-x (TMHA-TFSI)x, at concentrations close to the extremes, solid crystalline phases are still present and they show a strong predominance of the trans conformer of the TFSI ion for x < 15 or a large concentration of the cis conformer of TFSI for x > 85. At intermediate concentrations (33 < x < 67) no crystalline phase develops at low temperatures and both conformers of TFSI survive in the whole temperature range investigated here. We suggest that the competition between the two TFSI conformers at low temperatures can be the origin of the lack of crystalline phases for intermediate concentrations and can be exploited as a valid tool to tailor the physical properties of the mixtures of ionic liquids.

Phase Transitions of PYR14-TFSI as a Function of Pressure and Temperature: the Competition between Smaller Volume and Lower Energy Conformer.

A detailed Raman study has been carried out on the ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide (PYR14-TFSI) over a wide pressure (0-8 GPa) and temperature (100-300 K) range. The explored thermodynamic region allowed us to study the evolution of the system across different solid and liquid phases. Calculated Raman spectra remarkably helped in the spectral data analysis. In particular, the pressure behavior of the most intense Raman peak and the shape analysis of the ruby fluorescence (used as a local pressure gauge) allowed us to identify a liquid-solid transition around 2.2 GPa at T = 300 K. The low-frequency Raman signal as well as the absence of remarkable spectral shape modifications on crossing the above threshold and the comparison with the spectra of the crystalline phase suggest a glassy nature of the high-pressure phase. A detailed analysis of the pressure dependence of the relative concentration of two conformers of TFSI allowed us to obtain an estimate of the volume variation between trans-TFSI and the smaller cis-TFSI, which is the favored configuration on applying the pressure. Finally, the combined use of both visual inspection and Raman spectroscopy confirmed the peculiar sequence of phase transitions observed as a function of temperature at ambient pressure and the different spectral/morphological characteristics of the two crystalline phases.

The Complex Dance of the Two Conformers of Bis(trifluoromethanesulfonyl)imide as a Function of Pressure and Temperature.

Absorbance spectra of two ionic liquids, the short alkyl chain N-trimethyl-N-propylammonium bis(trifluoromethanesulfonyl)imide (TMPA-TFSI) and the longer chain N-trimethyl-N-hexylammonium bis(trifluoromethanesulfonyl)imide (TMHA-TFSI) are reported as a function of pressure and temperature. The occurrence of various phase transitions is evidenced by the changes in the relative concentration of the cisoid and transoid conformers of their common TFSI anion. The infrared spectrum of TMPA-TFSI was measured at 300 K with an applied pressure varying over the 0-5 GPa range. Above 0.2 GPa only the trans conformer is detected, suggesting the occurrence of a pressure induced crystallization. When pressure is applied to TMHA-TFSI at T = 310 K, both TFSI conformers subsist up to ∼11 GPa. However, the clear change of their intensity ratio observed around 2 GPa, suggests the onset of a glass phase as supported by measurements carried out at 4.2 GPa along a cooling/heating cycle. A careful analysis of the spectra collected along different p-T thermodynamic paths shows the occurrence of a cold crystallization at 295 K on heating from 139 K along the p = 0.5 GPa isobar. The rich phase diagrams of the two ionic liquids is the result of the competition among the anion-cation intermolecular interactions, the lower energy of trans-TFSI with respect to cis-TFSI and the smaller volume of cis-TFSI with respect to trans-TFSI.

miRNA profiling in serum and tissue samples to assess noninvasive biomarkers for NSCLC clinical outcome.

In NSCLC, the altered expression of some miRNAs in primary tumor tissues has been correlated with diagnosis and prognosis, while the role of circulating miRNAs as cancer biomarkers is currently emerging. MiRNA expression profile through miRNA Affymetrix array was evaluated on a training set formed by the tumor component (n = 30 NSCLC serum, n = 11/30 tumor tissues) and the control component (n = 10 healthy serum and n = 11/30 noncancerous counterparts). Statistical analyses highlighted the following: a = 55 miRNAs deregulated in tumor serum, b = 27 miRNAs deregulated in tumor tissues, and c = 2 miRNAs deregulated both in tumor serum and in tumor tissues. MiRwalk tool and enrichment pathway analyses selected some miRNAs whose target genes are correlated with the main pathways involved in NSCLC tumorigenesis. The altered expression of the selected miR-486-5p (a), miR-29c* (b), and miR-133a (c) was confirmed in the validation set (n = 40). MiR-486-5p had a higher expression in tumor serum than in tumor tissues (P = 0.004), and miR-29c* showed a lower expression in tumor tissues than in tumor serum (P < 0.001). MiR-133a had a not different expression in both tumor serum and tumor tissues (P = 0.07). The low level of miR-486-5p expression in the serum of affected patients was associated with a worse time to progression of disease (P = 0.010), and serum level of miR-486-5p was a significant prognostic indicator of NSCLC (adjusted hazard ratio = 0.179, P = 0.019). These data suggest the possibility to monitor affected patients through serum and/or tissue samples, analyzing the altered expression of specific miRNAs, in order to detect prognostic biomarkers in the NSCLC.

Relaxation Dynamics and Phase Transitions in Ionic Liquids: Viscoelastic Properties from the Liquid to the Solid State.

In the present work we performed low-frequency mechanical spectroscopy experiments to measure the mechanical modulus of two ionic liquids and its variation during the main phase transitions occurring by varying the temperature, in the both liquid and the solid states. The liquids share the same anion, the bis(trifluoromethanesulfonyl)imide, and present different cations, 1-butyl-1-methylpyrrolidinium and 1-allyl-3-H-imidazolium. A thermally activated relaxation process is found in the liquid phase and is analyzed in terms of a modified Debye model. The obtained parameters provide indications about the nature and the mechanism giving rise to the peak, which is attributed to the ions motion by means of hopping processes. Moreover, density functional calculations were performed, and the comparison with the analysis of the experimental data suggests that the anion conformers are likely to be involved in the different configurations among which the ions can rearrange.

Interaction of 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide with an electrospun PVdF membrane: Temperature dependence of the concentration of the anion conformers.

We measured the temperature dependence of the infrared absorption spectrum of 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide (PY R14-TFSI) between 160 and 330 K, through all the phase transitions presented by this compound. The comparison of the experimental spectra with the calculated vibration modes of different conformers of the ions composing the ionic liquid allowed to detect the presence of both conformers of TFSI in the liquid, supercooled, and glass phases, while only the trans-conformer is retained in both solid phases. When the ionic liquid swells a polyvinylidenefluoride (PVdF) electrospun membrane, the cis-rotamer is detected in all phases, since the interaction between the polymer and the ionic liquid inhibits the complete transformation of TFSI into the trans-conformer in the solid phases. Computational results confirm that in the presence of a PVdF chain, cis-TFSI becomes the lowest energy conformer. Therefore, the interaction with the polymer alters the physical properties of the ionic liquid.

MicroRNA expression profiling in male and female familial breast cancer.

BACKGROUND: Gender-associated epigenetic alterations are poorly investigated in male and female familial breast cancer (fBC). MicroRNAs may contribute to the different biology in men and women particularly related to RASSF1A pathways. METHODS: Microarray technology was used to evaluate miRNA profile in 24 male and 43 female fBC. Key results were validated using RT-qPCR in an external samples set. In vitro studies were carried out to verify microRNA-target gene interaction. RESULTS: Pathway enrichment analysis with the 287 differentially expressed microRNAs revealed several signalling pathways differently regulated in male and female cases. Because we previously hypothesised a peculiar involvement of RASSF1A in male fBC pathogenesis, we focussed on the MAPK and the Hippo signalling pathways that are regulated by RASSF1A. Male miR-152 and miR-497 upregulation and RASSF1A and NORE1A interacting gene downregulation were observed, confirming a possible indirect interaction between miRNAs and the two genes. CONCLUSIONS: For the first time, a different microRNA expression pattern in male and female fBC has been shown. Moreover, the importance of RASSF1A pathway in male fBC carcinogenesis has been confirmed, highlighting a possible role for miR-152 and miR-497 in controlling MAPK and Hippo signalling pathways, regulated by RASSF1A.

Stabilization of different conformers of bis(trifluoromethanesulfonyl)imide anion in ammonium-based ionic liquids at low temperatures.

The infrared absorption spectra of two ionic liquids with bis(trifluoromethanesulfonyl)imide (TFSI) as an anion and ammonium with different alkyl chains as cations are reported as a function of temperature. Using the comparison with ab initio calculations of the infrared-active intramolecular vibrations, the experimental lines were ascribed to the various ions composing the ionic liquids. In the liquid state of the samples, both conformers of the TFSI ion are present. In the solid state, however, the two conformers survive in N-trimethyl-N-propylammonium bis(trifluoromethanesulfonyl)imide (TMPA-TFSI), while only cis-TFSI is retained in N-trimethyl-N-hexylammonium bis(trifluoromethanesulfonyl)imide (TMHA-TFSI). We suggest that the longer alkyl chains of the former compound stabilize the less stable conformer of TFSI by means of stronger interactions between anions and cations.

A de novo 11p13 Microduplication in a Patient with Some Features Invoking Silver-Russell Syndrome.

Patients with Silver-Russell syndrome (SRS) show an intrauterine and postnatal growth restriction associated with a variable spectrum of additional features. Genetic or epigenetic alterations on chromosomes 7 and 11 can be detected in several SRS patients; however, a large fraction of cases remains with unknown genetic etiology. Here, we describe the clinical and molecular findings of a patient with a phenotype invoking SRS showing intrauterine and postnatal growth retardation, psychomotor retardation, relative macrocephaly, slightly triangular face with pointed chin, clinodactyly, and a slight body asymmetry, in whom single-nucleotide polymorphism oligonucleotide array analysis led to the identification of a de novo 11p13 duplication containing many genes that could be functionally related with the observed clinical features. Many deletions of chromosome 11p13, resulting in WAGR (Wilms tumor, aniridia, genital anomalies, mental retardation) syndrome, have been described, while only few duplications spanning the same region have been reported so far. To our knowledge, this is the first reported case presenting a SRS carrier of an 11p13 duplication. We propose candidate genes for the observed traits, and in particular, we discuss the possible role of the involvement of 2 noncoding RNAs in the etiology of the phenotype.

A novel microdeletion syndrome at 3q13.31 characterised by developmental delay, postnatal overgrowth, hypoplastic male genitals, and characteristic facial features.

BACKGROUND: Congenital deletions affecting 3q11q23 have rarely been reported and only five cases have been molecularly characterised. Genotype-phenotype correlation has been hampered by the variable sizes and breakpoints of the deletions. In this study, 14 novel patients with deletions in 3q11q23 were investigated and compared with 13 previously reported patients. METHODS: Clinical data were collected from 14 novel patients that had been investigated by high resolution microarray techniques. Molecular investigation and updated clinical information of one cytogenetically previously reported patient were also included. RESULTS: The molecular investigation identified deletions in the region 3q12.3q21.3 with different boundaries and variable sizes. The smallest studied deletion was 580 kb, located in 3q13.31. Genotype-phenotype comparison in 24 patients sharing this shortest region of overlapping deletion revealed several common major characteristics including significant developmental delay, muscular hypotonia, a high arched palate, and recognisable facial features including a short philtrum and protruding lips. Abnormal genitalia were found in the majority of males, several having micropenis. Finally, a postnatal growth pattern above the mean was apparent. The 580 kb deleted region includes five RefSeq genes and two of them are strong candidate genes for the developmental delay: DRD3 and ZBTB20. CONCLUSION: A newly recognised 3q13.31 microdeletion syndrome is delineated which is of diagnostic and prognostic value. Furthermore, two genes are suggested to be responsible for the main phenotype.

Clock gene expression levels and relationship with clinical and pathological features in colorectal cancer patients.

The clock gene machinery controls cellular metabolism, proliferation, and key functions, such as DNA damage recognition and repair. Dysfunction of the circadian clock is involved in tumorigenesis, and altered expression of some clock genes has been found in cancer patients. The aim of this study was to evaluate the expression levels of core clock genes in colorectal cancer (CRC). Quantitative real-time polymerase chain reaction (qPCR) was used to examine ARNTL1, CLOCK, PER1, PER2, PER3, CRY1, CRY2, Timeless (TIM), TIPIN, and CSNK1? expression levels in the tumor tissue and matched apparently healthy mucosa of CRC patients. In the tumor tissue of CRC patients, compared to their matched healthy mucosa, expression levels of ARNTL1 (p=.002), PER1 (p=.002), PER2 (p=.011), PER3 (p=.003), and CRY2 (p=.012) were lower, whereas the expression level of TIM (p=.044) was higher. No significant difference was observed in the expression levels of CLOCK (p=.778), CRY1 (p=.600), CSNK1 (p=.903), and TIPIN (p=.136). As to the clinical and pathological features, a significant association was found between low CRY1 expression levels in tumor mucosa and age (p=.026), and female sex (p=.005), whereas high CRY1 expression levels in tumor mucosa were associated with cancer location in the distal colon (p?=?.015). Moreover, high TIM mRNA levels in the tumor mucosa were prevalent whenever proximal lymph nodes were involved (p= .013) and associated with TNM stages III-IV (p=.005) and microsatellite instability (p=.015). Significantly poorer survival rates were evidenced for CRC patients with lower expression in the tumor tissue of PER1 (p=.010), PER3 (p= .010), and CSNKIE (p=.024). In conclusion, abnormal expression levels of core clock genes in CRC tissue may be related to the process of tumorigenesis and exert an influence on host/tumor interactions.

22q11.2 Distal Deletion Syndrome: Description of a New Case with Truncus Arteriosus Type 2 and Review.

22q11.2 deletion syndrome is mainly characterized by conotruncal congenital heart defects, velopharyngeal insufficiency, hypocalcemia and a characteristic craniofacial appearance. The etiology in the majority of patients is a 3-Mb recurrent deletion in region 22q11.2. Nevertheless, recently some cases of infrequent deletions with various sizes have been reported with a different phenotype. We report on a patient with congenital heart disease (truncus arteriosus type 2) in whom a de novo 1.3-Mb 22q11.2 deletion was detected by array comparative genomic hybridization. The deletion described corresponds to an atypical and distal deletion which spans low copy repeat (LCR) 4 and is associated with breakpoint sites that do not correspond to known LCRs of 22q11.2. We examine the clinical phenotype of our case and compare our findings with those published in the literature. The most prevalent clinical features in this type of deletion are a history of prematurity, pre-natal and post-natal growth retardation, slight facial dysmorphic features, microcephaly and developmental delay, with a speech defect in particular. These are clearly different from those found in the classic 22q11.2 deletion syndrome, and we believe that the main differential diagnosis should be with Silver-Russel syndrome. In our case we observe the cardiac phenotype with truncus arteriosus communis usually seen in the classic 22q11.2 deletion syndrome, and so far associated with the TBX1 gene. Significantly, however, TBX1 is not included in our patient's deletion. The possible roles of a position effect or other genes are discussed.