Long noncoding RNA expression in acute lymphoblastic leukemia: A systematic review.

Long noncoding RNAs (lncRNAs), as gene expression modulators, are potential players in Acute Lymphoblastic Leukemia (ALL) pathogenesis. We systematically explored current literature on lncRNA expression in ALL to identify lncRNAs consistently reported as differentially expressed (DE) either in ALL versus controls or between ALL subtypes. By comparing articles that provided global expression data for DE lncRNAs in the ETV6::RUNX1-positive ALL subtype, we identified four DE lncRNAs in three independent studies (two versus other subtypes and one versus controls), showing concordant expression of LINC01013, CRNDE and lnc-KLF7-1. Additionally, LINC01503 was consistently downregulated on ALL versus controls. Within RT-qPCR studies, twelve lncRNA were DE in more than one source. Thus, several lncRNAs were supported as DE in ALL by multiple sources, highlighting their potential role as candidate biomarkers or therapeutic targets. Finally, as lncRNA annotation is rapidly expanding, standardization of reporting and nomenclature is urgently needed to improve data verifiability and compilation.

Sequential order dependent dark-exciton modulation in bi-layered TMD heterostructure.

We report the emergence of dark-excitons in transition-metal-dichalcogenide (TMD) heterostructures that strongly rely on the stacking sequence, i.e., momentum-dark K-Q exciton located exclusively at the top layer of the heterostructure. The feature stems from band renormalization and is distinct from those of typical neutral excitons or trions, regardless of materials, substrates, and even homogeneous bilayers, which is further confirmed by scanning tunneling spectroscopy. To understand the unusual stacking sequence, we introduce the excitonic Elliot formula by imposing strain exclusively on the top layer that could be a consequence of the stacking process. We further find that the intensity ratio of Q- to K-excitons in the same layer is inversely proportional to laser power, unlike for conventional K-K excitons. This can be a metric for engineering the intensity of dark K-Q excitons in TMD heterostructures, which could be useful for optical power switches in solar panels.

Interface engineering of charge-transfer excitons in 2D lateral heterostructures.

The existence of bound charge transfer (CT) excitons at the interface of monolayer lateral heterojunctions has been debated in literature, but contrary to the case of interlayer excitons in vertical heterostructure their observation still has to be confirmed. Here, we present a microscopic study investigating signatures of bound CT excitons in photoluminescence spectra at the interface of hBN-encapsulated lateral MoSe2-WSe2 heterostructures. Based on a fully microscopic and material-specific theory, we reveal the many-particle processes behind the formation of CT excitons and how they can be tuned via interface- and dielectric engineering. For junction widths smaller than the Coulomb-induced Bohr radius we predict the appearance of a low-energy CT exciton. The theoretical prediction is compared with experimental low-temperature photoluminescence measurements showing emission in the bound CT excitons energy range. We show that for hBN-encapsulated heterostructures, CT excitons exhibit small binding energies of just a few tens meV and at the same time large dipole moments, making them promising materials for optoelectronic applications (benefiting from an efficient exciton dissociation and fast dipole-driven exciton propagation). Our joint theory-experiment study presents a significant step towards a microscopic understanding of optical properties of technologically promising 2D lateral heterostructures.

New Insights on the Regulatory Gene Network Disturbed in Central Areolar Choroidal Dystrophy-Beyond Classical Gene Candidates.

Central areolar choroidal dystrophy (CACD) is a rare hereditary disease that mainly affects the macula, resulting in progressive and usually profound visual loss. Being part of congenital retinal dystrophies, it may have an autosomal dominant or recessive inheritance and, until now, has no effective treatment. Given the shortage of genotypic information about the disease, this work systematically reviews the literature for CACD-causing genes. Three independent researchers selected 33 articles after carefully searching and filtering the Scielo, Pubmed, Lilacs, Web of Science, Scopus, and Embase databases. Mutations of six genes (PRPH2, GUCA1A, GUCY2D, CDHR1, ABCA4, and TTLL5) are implicated in the monogenic dominant inheritance of CACD. They are functionally related to photoreceptors (either in the phototransduction process, as in the case of GUCY2D, or the recovery of retinal photodegradation in photoreceptors for GUCA1A, or the formation and maintenance of specific structures within photoreceptors for PRPH2). The identified genetic variants do not explain all observed clinical features, calling for further whole-genome and functional studies for this disease. A network analysis with the CACD-related genes identified in the systematic review resulted in the identification of another 20 genes that may influence CACD onset and symptoms. Furthermore, an enrichment analysis allowed the identification of 13 transcription factors and 4 long noncoding RNAs interacting with the products of the previously mentioned genes. If mutated or dysregulated, they may be directly involved in CACD development and related disorders. More than half of the genes identified by bioinformatic tools do not appear in commercial gene panels, calling for more studies about their role in the maintenance of the retina and phototransduction process, as well as for a timely update of these gene panels.

Dark exciton anti-funneling in atomically thin semiconductors.

Transport of charge carriers is at the heart of current nanoelectronics. In conventional materials, electronic transport can be controlled by applying electric fields. Atomically thin semiconductors, however, are governed by excitons, which are neutral electron-hole pairs and as such cannot be controlled by electrical fields. Recently, strain engineering has been introduced to manipulate exciton propagation. Strain-induced energy gradients give rise to exciton funneling up to a micrometer range. Here, we combine spatiotemporal photoluminescence measurements with microscopic theory to track the way of excitons in time, space and energy. We find that excitons surprisingly move away from high-strain regions. This anti-funneling behavior can be ascribed to dark excitons which possess an opposite strain-induced energy variation compared to bright excitons. Our findings open new possibilities to control transport in exciton-dominated materials. Overall, our work represents a major advance in understanding exciton transport that is crucial for technological applications of atomically thin materials.

Electron Dynamics in a Two-Dimensional Nanobubble: A Two-Level System Based on Spatial Density.

Nanobubbles formed in monolayers of transition metal dichalcogenides (TMDCs) on top of a substrate feature localized potentials in which electrons can be captured. We show that the captured electronic density can exhibit a nontrivial spatiotemporal dynamics, whose movements can be mapped to states in a two-level system illustrated as points of an electronic Poincaré sphere. These states can be fully controlled, i.e, initialized and switched, by multiple electronic wave packets. Our results could be the foundation for novel implementations of quantum circuits.

Non-equilibrium diffusion of dark excitons in atomically thin semiconductors.

Atomically thin semiconductors provide an excellent platform to study intriguing many-particle physics of tightly-bound excitons. In particular, the properties of tungsten-based transition metal dichalcogenides are determined by a complex manifold of bright and dark exciton states. While dark excitons are known to dominate the relaxation dynamics and low-temperature photoluminescence, their impact on the spatial propagation of excitons has remained elusive. In our joint theory-experiment study, we address this intriguing regime of dark state transport by resolving the spatio-temporal exciton dynamics in hBN-encapsulated WSe2 monolayers after resonant excitation. We find clear evidence of an unconventional, time-dependent diffusion during the first tens of picoseconds, exhibiting strong deviation from the steady-state propagation. Dark exciton states are initially populated by phonon emission from the bright states, resulting in creation of hot (unequilibrated) excitons whose rapid expansion leads to a transient increase of the diffusion coefficient by more than one order of magnitude. These findings are relevant for both fundamental understanding of the spatio-temporal exciton dynamics in atomically thin materials as well as their technological application by enabling rapid diffusion.

Nonclassical Exciton Diffusion in Monolayer WSe_{2}.

We experimentally demonstrate time-resolved exciton propagation in a monolayer semiconductor at cryogenic temperatures. Monitoring phonon-assisted recombination of dark states, we find a highly unusual case of exciton diffusion. While at 5 K the diffusivity is intrinsically limited by acoustic phonon scattering, we observe a pronounced decrease of the diffusion coefficient with increasing temperature, far below the activation threshold of higher-energy phonon modes. This behavior corresponds neither to well-known regimes of semiclassical free-particle transport nor to the thermally activated hopping in systems with strong localization. Its origin is discussed in the framework of both microscopic numerical and semiphenomenological analytical models illustrating the observed characteristics of nonclassical propagation. Challenging the established description of mobile excitons in monolayer semiconductors, these results open up avenues to study quantum transport phenomena for excitonic quasiparticles in atomically thin van der Waals materials and their heterostructures.

Non-syndromic Oculocutaneous Albinism: Novel Genetic Variants and Clinical Follow Up of a Brazilian Pediatric Cohort.

Oculocutaneous albinism (OCA) is a genetic disorder characterized by skin, hair, and eye hypopigmentation due to a reduction or absence of melanin. Clinical manifestations include vision problems and a high susceptibility to skin cancer. In its non-syndromic form, OCA is associated with six genes and one chromosomal region. Because OCA subtypes are not always clinically distinguishable, molecular analysis has become an important tool for classifying types of OCA, which facilitates genetic counseling and can guide the development of new therapies. We studied eight Brazilian individuals aged 1.5-18 years old with clinical diagnosis of OCA. Assessment of ophthalmologic characteristics showed results consistent with albinism, including reduced visual acuity, nystagmus, and loss of stereoscopic vision. We also observed the appearance of the strabismus and changes in static refraction over a 2-year period. Dermatologic evaluation showed that no participants had preneoplastic skin lesions, despite half of the participants reporting insufficient knowledge about skin care in albinism. Whole-exome and Sanger sequencing revealed eight different mutations: six in the TYR gene and two in the SLC45A2 gene, of which one was novel and two were described in a population study but were not previously associated with the OCA phenotype. We performed two ophthalmological evaluations, 2 years apart; and one dermatological evaluation. To the best of our knowledge, this is the first study to perform clinical follow-up and genetic analysis of a Brazilian cohort with albinism. Here, we report three new OCA causing mutations.

Negative effective excitonic diffusion in monolayer transition metal dichalcogenides.

While exciton relaxation in monolayers of transition metal dichalcogenides (TMDs) has been intensively studied, spatial exciton diffusion has received only a little attention - in spite of being a key process for optoelectronics and having already shown interesting unconventional behaviours (e.g. spatial halos). Here, we study the spatiotemporal dynamics in TMD monolayers and track optically excited excitons in time, momentum, and space. In particular, we investigate the temperature-dependent exciton diffusion including the remarkable exciton landscape constituted by bright and dark states. Based on a fully quantum mechanical approach, we show at low temperatures an unexpected negative effective diffusion characterized by a shrinking of the spatial exciton distributions. This phenomenon can be traced back to the existence of dark exciton states in TMD monolayers and is a result of an interplay between spatial exciton diffusion and intervalley exciton-phonon scattering.

Penetrance of the TP53 R337H Mutation and Pediatric Adrenocortical Carcinoma Incidence Associated with Environmental Influences in a 12-Year Observational Cohort in Southern Brazil.

The TP53 R337H mutation is associated with increased incidence of pediatric adrenocortical tumor (ACT). The different environmental conditions where R337H carriers live have not been systematically analyzed. Here, the R337H frequencies, ACT incidences, and R337H penetrance for ACT were calculated using the 2006 cohort with 4165 R337H carriers living in Paraná state (PR) subregions. The effectiveness of a second surveillance for R337H probands selected from 42,438 tested newborns in PR (2016 cohort) was tested to detect early stage I tumor among educated families without periodical exams. Estimation of R337H frequencies and ACT incidence in Santa Catarina state (SC) used data from 50,115 tested newborns without surveillance, ACT cases from a SC hospital, and a public cancer registry. R337H carrier frequencies in the population were 0.245% (SC) and 0.306% (PR), and 87% and 95% in ACTs, respectively. The ACT incidence was calculated as ~6.4/million children younger than 10 years per year in PR (95% CI: 5.28; 7.65) and 4.15/million in SC (CI 95%: 2.95; 5.67). The ACT penetrance in PR for probands followed from birth to 12 years was 3.9%. R337H carriers living in an agricultural subregion (C1) had a lower risk of developing pediatric ACT than those living in industrial and large urban subregion (relative risk = 2.4). One small ACT (21g) without recurrence (1/112) was detected by the parents in the 2016 cohort. ACT incidence follows R337H frequency in each population, but remarkably environmental factors modify these rates.

The Prognostic Role of CD8+ T Lymphocytes in Childhood Adrenocortical Carcinomas Compared to Ki-67, PD-1, PD-L1, and the Weiss Score.

Adrenocortical carcinoma (ACC) is a rare disease among children. Our goal was to identify prognostic biomarkers in 48 primary ACCs from children (2.83 ± 2.3 y; mean age ± SD) by evaluating the tumor stage and outcome for an age of diagnosis before or after 3 years, and association with ACC cluster of differentiation 8 positive (CD8+) cytotoxic T lymphocytes (CD8+-CTL) and Ki-67 immunohistochemical expression (IHC). Programmed death 1(PD-1)/Programmed death-ligand 1 (PD-L1) immunohistochemistry (IHC) in ACC was analyzed in a second, partially overlapping cohort (N = 19) with a similar mean age. All patients and control children were carriers of the germline TP53 R337H mutation. Survival without recurrence for less than 3 years and death unrelated to disease were excluded. Higher counts of CD8+-CTL were associated with patients diagnosed with ACC at a younger age and stage I, whereas a higher percentage of the Ki-67 labeling index (LI) and Weiss scores did not differentiate disease free survival (DFS) in children younger than 3 years old. No PD-1 staining was observed, whereas weakly PD-L1-positive immune cells were found in 4/19 (21%) of the ACC samples studied. A high CD8+-CTL count in ACC of surviving children is compelling evidence of an immune response against the disease. A better understanding of the options for enhancement of targets for CD8+ T cell recognition may provide insights for future pre-clinical studies.

Exciton Propagation and Halo Formation in Two-Dimensional Materials.

The interplay of optics, dynamics, and transport is crucial for the design of novel optoelectronic devices, such as photodetectors and solar cells. In this context, transition-metal dichalcogenides (TMDs) have received much attention. Here, strongly bound excitons dominate optical excitation, carrier dynamics, and diffusion processes. While the first two have been intensively studied, there is a lack of fundamental understanding of nonequilibrium phenomena associated with exciton transport that is of central importance (e.g., for high-efficiency light harvesting). In this work, we provide microscopic insights into the interplay of exciton propagation and many-particle interactions in TMDs. On the basis of a fully quantum mechanical approach and in excellent agreement with photoluminescence measurements, we show that Auger recombination and emission of hot phonons act as a heating mechanism giving rise to strong spatial gradients in excitonic temperature. The resulting thermal drift leads to an unconventional exciton diffusion characterized by spatial exciton halos.

Spatial trends in congenital malformations and stream water chemistry in Southern Brazil.

The incidence of variable congenital malformation (CM) among 399 municipalities in the state of Paraná, southern Brazil, suggests the etiological role of environmental factors. This study examined a) environmental concentrations of chlorine anions (Cl-) associated with organochlorines (OCs) and b) associations between these chemicals and agricultural output with CMs using a geographical information system. In one of the three years during the sampling period (2008, 2009 or 2010) Cl-, dichlorodiphenyltrichloroethane (p,p'-DDT), dichlorodiphenyldichloroethylene (p,p'-DDE), dichlorodiphenyldichloroethane (p,p'-DDD), and endosulfan levels were measured in 465 (465/736, 63%) catchment basins. Agricultural outputs for crops during 2006-2010 were also evaluated (t/km2). Further, CM kernel density for the 399 municipalities in Paraná during 2007-2014 was investigated. Cl- levels increased significantly in one of the three years (2008, 2009 or 2010) in western catchment basins, compared to 1996 (p < 0.0001). The municipalities were divided according to the obtained Cl- levels, where sub-region C2 (central-southern) < 1.8 mg/L ≤ sub-regions C1 (northern-western) and C3 (eastern-southern). We identified 8756 cases of CMs among 1,221,287 newborns (NB) in all sub-regions. C1 had higher DDT-DDE-DDD (p,p'-DDT + p,p'-DDE + p,p'-DDD) concentrations, agricultural output, and CM kernel density. C2 and C3 had minor agricultural outputs (per square kilometer) and CM densities. A 2.96 mg/L increase in Cl- between sub-regions C1 and C2 was co-localized with a 45% increase in CM density (spatial relative risk = 1.45, CI 95%: 1.36-1.55). C1 had the highest log likelihood ratios (p = 0.001) identified via SaTScan clustering analyses. Organochlorines and other toxic chlorinated chemicals may contribute to CMs in humans, and these chemicals are ultimately transformed and release Cl- in rivers. Higher Cl- levels were correlated significantly with higher agricultural productivity, DDT-DDE-DDD levels, and CMs in some parts of the northern and western sub-regions (C1).

Impact of neonatal screening and surveillance for the TP53 R337H mutation on early detection of childhood adrenocortical tumors.

PURPOSE: The incidence of pediatric adrenocortical tumors (ACTs) is remarkably high in southern Brazil, where more than 90% of patients carry the germline TP53 mutation R337H. We assessed the impact of early detection of this mutation and of surveillance of carriers. PATIENTS AND METHODS: Free newborn screening was offered at all hospitals in the state of Paraná. Parents of positive newborns were tested, and relatives in the carrier line were offered screening. Positive newborns and their relatives age < 15 years were offered surveillance (periodic clinical, laboratory, and ultrasound evaluations). ACTs detected by imaging were surgically resected. RESULTS: Of 180,000 newborns offered screening, 171,649 were screened, and 461 (0.27%) were carriers. As of April 2012, ACTs had been diagnosed in 11 of these carriers but in only two neonatally screened noncarriers (P < .001); six patient cases were identified among 228 carrier relatives age < 15 years (total, 19 ACTs). Surveillance participants included 347 (49.6%) of 699 carriers. Tumors were smaller in surveillance participants (P < .001) and more advanced in nonparticipants (four with stage III disease; two deaths). Neonatally screened carriers also had neuroblastoma (n = 1), glioblastoma multiforme (n = 1), choroid plexus carcinoma (n = 2), and Burkitt lymphoma (n = 1). Cancer histories and pedigrees were obtained for 353 families that included 1,704 identified carriers. ACTs were the most frequent cancer among carrier children (n = 48). CONCLUSION: These findings establish the prevalence of the TP53 R337H mutation in Paraná state and the penetrance of ACTs among carriers. Importantly, screening and surveillance of heterozygous carriers are effective in detecting ACTs when readily curable.

Controversies about the chromosomal stability of cultivated mesenchymal stem cells: their clinical use is it safe?

The usefulness of adult stem cells in research and therapeutic applications highly relies on their genomic integrity and stability. Many laboratories including ours have addressed this concern using methods such as karyotyping, Qbanding, fluorescent in situ hybridization, array CGH, flow cytometry and Pap test to evaluate number and structure of chromosomes and cellular phenotype. This review attempts to summarize the findings reported so far for the studies on chromosomal aberrations in adult stem cells and warrant to perform certain basic tests before transplantation to avoid any adverse reactions, which will thus aid in better therapeutic output after cellular transplantation in the treatment of various diseases.

Identity by descent mapping of founder mutations in cancer using high-resolution tumor SNP data.

Dense genotype data can be used to detect chromosome fragments inherited from a common ancestor in apparently unrelated individuals. A disease-causing mutation inherited from a common founder may thus be detected by searching for a common haplotype signature in a sample population of patients. We present here FounderTracker, a computational method for the genome-wide detection of founder mutations in cancer using dense tumor SNP profiles. Our method is based on two assumptions. First, the wild-type allele frequently undergoes loss of heterozygosity (LOH) in the tumors of germline mutation carriers. Second, the overlap between the ancestral chromosome fragments inherited from a common founder will define a minimal haplotype conserved in each patient carrying the founder mutation. Our approach thus relies on the detection of haplotypes with significant identity by descent (IBD) sharing within recurrent regions of LOH to highlight genomic loci likely to harbor a founder mutation. We validated this approach by analyzing two real cancer data sets in which we successfully identified founder mutations of well-characterized tumor suppressor genes. We then used simulated data to evaluate the ability of our method to detect IBD tracts as a function of their size and frequency. We show that FounderTracker can detect haplotypes of low prevalence with high power and specificity, significantly outperforming existing methods. FounderTracker is thus a powerful tool for discovering unknown founder mutations that may explain part of the "missing" heritability in cancer. This method is freely available and can be used online at the FounderTracker website.

SNP array profiling of childhood adrenocortical tumors reveals distinct pathways of tumorigenesis and highlights candidate driver genes.

CONTEXT: Childhood adrenocortical tumors (ACT) are rare malignancies, except in southern Brazil, where a higher incidence rate is associated to a high frequency of the founder R337H TP53 mutation. To date, copy number alterations in these tumors have only been analyzed by low-resolution comparative genomic hybridization. OBJECTIVE: We analyzed an international series of 25 childhood ACT using high-resolution single nucleotide polymorphism arrays to: 1) detect focal copy number alterations highlighting candidate driver genes; and 2) compare genetic alterations between Brazilian patients carrying the R337H TP53 mutation and non-Brazilian patients. RESULTS: We identified 16 significantly recurrent chromosomal alterations (q-value < 0.05), the most frequent being -4q34, +9q33-q34, +19p, loss of heterozygosity (LOH) of chromosome 17 and 11p15. Focal amplifications and homozygous deletions comprising well-known oncogenes (MYC, MDM2, PDGFRA, KIT, MCL1, BCL2L1) and tumor suppressors (TP53, RB1, RPH3AL) were identified. In addition, eight focal deletions were detected at 4q34, defining a sharp peak region around the noncoding RNA LINC00290 gene. Although non-Brazilian tumors with a mutated TP53 were similar to Brazilian tumors, those with a wild-type TP53 displayed distinct genomic profiles, with significantly fewer rearrangements (P = 0.019). In particular, three alterations (LOH of chromosome 17, +9q33-q34, and -4q34) were significantly more frequent in TP53-mutated samples. Finally, two of four TP53 wild-type tumors displayed as sole rearrangement a copy-neutral LOH of the imprinted region at 11p15, supporting a major role for this region in ACT development. CONCLUSIONS: Our findings highlight potential driver genes and cellular pathways implicated in childhood ACT and demonstrate the existence of different oncogenic routes in this pathology.

NPM1 deletion is associated with gross chromosomal rearrangements in leukemia.

BACKGROUND: NPM1 gene at chromosome 5q35 is involved in recurrent translocations in leukemia and lymphoma. It also undergoes mutations in 60% of adult acute myeloid leukemia (AML) cases with normal karyotype. The incidence and significance of NPM1 deletion in human leukemia have not been elucidated. METHODOLOGY AND PRINCIPAL FINDINGS: Bone marrow samples from 145 patients with myelodysplastic syndromes (MDS) and AML were included in this study. Cytogenetically 43 cases had isolated 5q-, 84 cases had 5q- plus other changes and 18 cases had complex karyotype without 5q deletion. FISH and direct sequencing investigated the NPM1 gene. NPM1 deletion was an uncommon event in the "5q- syndrome" but occurred in over 40% of cases with high risk MDS/AML with complex karyotypes and 5q loss. It originated from large 5q chromosome deletions. Simultaneous exon 12 mutations were never found. NPM1 gene status was related to the pattern of complex cytogenetic aberrations. NPM1 haploinsufficiency was significantly associated with monosomies (p<0.001) and gross chromosomal rearrangements, i.e., markers, rings, and double minutes (p<0.001), while NPM1 disomy was associated with structural changes (p=0.013). Interestingly, in complex karyotypes with 5q- TP53 deletion and/or mutations are not specifically associated with NPM1 deletion. CONCLUSIONS AND SIGNIFICANCE: NPM1/5q35 deletion is a consistent event in MDS/AML with a 5q-/-5 in complex karyotypes. NPM1 deletion and NPM1 exon 12 mutations appear to be mutually exclusive and are associated with two distinct cytogenetic subsets of MDS and AML.