Unique genomic profile of fibrolamellar hepatocellular carcinoma

BACKGROUND & AIMS: Fibrolamellar hepatocellular carcinoma (FLC) is a rare primary hepatic cancer that develops in children and young adults without cirrhosis. Little is known about its pathogenesis, and it can be treated only with surgery. We performed an integrative genomic analysis of a large series of patients with FLC to identify associated genetic factors. METHODS: By using 78 clinically annotated FLC samples, we performed whole-transcriptome (n = 58), single-nucleotide polymorphism array (n = 41), and next-generation sequencing (n = 48) analyses; we also assessed the prevalence of the DNAJB1-PRKACA fusion transcript associated with this cancer (n = 73). We performed class discovery using non-negative matrix factorization, and functional annotation using gene-set enrichment analyses, nearest template prediction, ingenuity pathway analyses, and immunohistochemistry. The genomic identification of significant targets in a cancer algorithm was used to identify chromosomal aberrations, MuTect and VarScan2 were used to identify somatic mutations, and the random survival forest was used to determine patient prognoses. Findings were validated in an independent cohort. RESULTS: Unsupervised gene expression clustering showed 3 robust molecular classes of tumors: the proliferation class (51% of samples) had altered expression of genes that regulate proliferation and mammalian target of rapamycin signaling activation; the inflammation class (26% of samples) had altered expression of genes that regulate inflammation and cytokine enriched production; and the unannotated class (23% of samples) had a gene expression signature that was not associated previously with liver tumors. Expression of genes that regulate neuroendocrine function, as well as histologic markers of cholangiocytes and hepatocytes, were detected in all 3 classes. FLCs had few copy number variations; the most frequent were focal amplification at 8q24.3 (in 12.5% of samples), and deletions at 19p13 (in 28% of samples) and 22q13.32 (in 25% of samples). The DNAJB1-PRKACA fusion transcript was detected in 79% of samples. FLC samples also contained mutations in cancer-related genes such as BRCA2 (in 4.2% of samples), which are uncommon in liver neoplasms. However, FLCs did not contain mutations most commonly detected in liver cancers. We identified an 8-gene signature that predicted survival of patients with FLC. CONCLUSIONS: In a genomic analysis of 78 FLC samples, we identified 3 classes based on gene expression profiles. FLCs contain mutations and chromosomal aberrations not previously associated with liver cancer, and almost 80% contain the DNAJB1-PRKACA fusion transcript. By using this information, we identified a gene signature that is associated with patient survival time

Intratumoral heterogeneity and clonal evolution in liver cancer

Clonal evolution of a tumor ecosystem depends on different selection pressures that are principally immune and treatment mediated. We integrate RNA-seq, DNA sequencing, TCR-seq and SNP array data across multiple regions of liver cancer specimens to map spatio-temporal interactions between cancer and immune cells. We investigate how these interactions reflect intra-tumor heterogeneity (ITH) by correlating regional neo-epitope and viral antigen burden with the regional adaptive immune response. Regional expression of passenger mutations dominantly recruits adaptive responses as opposed to hepatitis B virus and cancer-testis antigens. We detect different clonal expansion of the adaptive immune system in distant regions of the same tumor. An ITH-based gene signature improves single-biopsy patient survival predictions and an expression survey of 38,553 single cells across 7 regions of 2 patients further reveals heterogeneity in liver cancer. These data quantify transcriptomic ITH and how the different components of the HCC ecosystem interact during cancer evolution

Multidimensional Proteomics Analysis of Amniotic Fluid to Provide Insight into the Mechanisms of Idiopathic Preterm Birth

Though recent advancement in proteomics has provided a novel perspective on several distinct pathogenetic mechanisms leading to preterm birth (inflammation, bleeding), the etiology of most preterm births still remains elusive. We conducted a multidimensional proteomic analysis of the amniotic fluid to identify pathways related to preterm birth in the absence of inflammation or bleeding.A proteomic fingerprint was generated from fresh amniotic fluid using surface-enhanced laser desorbtion ionization time of flight (SELDI-TOF) mass spectrometry in a total of 286 consecutive samples retrieved from women who presented with signs or symptoms of preterm labor or preterm premature rupture of the membranes. Inflammation and/or bleeding proteomic patterns were detected in 32% (92/286) of the SELDI tracings. In the remaining tracings, a hierarchical algorithm was applied based on descriptors quantifying similarity/dissimilarity among proteomic fingerprints. This allowed identification of a novel profile (Q-profile) based on the presence of 5 SELDI peaks in the 10-12.5 kDa mass area. Women displaying the Q-profile (mean+/-SD, gestational age: 25+/-4 weeks, n = 40) were more likely to deliver preterm despite expectant management in the context of intact membranes and normal amniotic fluid clinical results. Utilizing identification-centered proteomics techniques (fluorescence two-dimensional differential gel electrophoresis, robotic tryptic digestion and mass spectrometry) coupled with Protein ANalysis THrough Evolutionary Relationships (PANTHER) ontological classifications, we determined that in amniotic fluids with Q-profile the differentially expressed proteins are primarily involved in non-inflammatory biological processes such as protein metabolism, signal transduction and transport.Proteomic profiling of amniotic fluid coupled with non-hierarchical bioinformatics algorithms identified a subgroup of patients at risk for preterm birth in the absence of intra-amniotic inflammation or bleeding, suggesting a novel pathogenetic pathway leading to preterm birth. The altered proteins may offer opportunities for therapeutical intervention and future drug development to prevent prematurity

MicroRNA-Based Classification of Hepatocellular Carcinoma and Oncogenic Role of miR-517a

Hepatocellular carcinoma (HCC) is a heterogeneous tumor that develops via activation of multiple pathways and molecular alterations. It has been a challenge to identify molecular classes of HCC and design treatment strategies for each specific subtype. MicroRNAs (miRNAs) are involved in HCC pathogenesis and their expression profiles have been used to classify cancers. We analyzed miRNA expression in human HCC samples to identify molecular subclasses and oncogenic miRNAs

Bean Golden Mosaic: Research Advances

El frijol (Phaseolus vulgaris L.) es una de las fuentes de proteina (15-35%) y calorías (ca. 340 caI./100 gr) más importantes en la América Latina. En esta región, centro de origen de esta especie, se producen más de cuatro millones de toneladas de frijol al año, lo cual equivale al 88% de la semilla de frijol producida en las regiones tropicales del mundo. Brasil, el mayor productor de frijol del mundo, posee un consumo per capita de cerca de 20 kg/año. En America Central, el frijol es igualmente importante, siendo consumido en la mayoría de los países centroamericanos hasta tres veces por día. Proporcionalmente, en la America Central se cultiva el doble del área que en Brasil, relativo a sus extensiones territoriales. El frijol es también producido en islas del Caribe, tales como Cuba (ca. 26.000 TM), Haití (56.000 TM) y República Dominicana (55.000 TM) según datos de 1990 (CIAT). México, el segundo productor de frijol en la America Latina, consume aproximadamente 1.2 millones de toneladas métricas de frijol al año. A pesar de que México cultiva cerca de 1.800.000 hectáreas de frijol, la demanda interna no es satisfecha en algunos años dado la baja productividad del cultivo. Esta baja productividad relativa del frijol, no solo en México sino también en el resto de la América Latina (700 kg/ha vs. 1.600 kg/ha en los Estados Unidos), es una consecuencia de los múltiples problemas bióticos y abióticos que inciden en el cultivo, en el trópico Americano. Es precisamente en las regiones productoras de frijol situadas en climas cálidos, de altitud baja a intermedia (0-1200 m.s.n.m), donde el mosaico dorado del frijol alcanza su mayor incidencia.The common bean (Phaseolus vulgaris L.) is an important source of protein and calories in Latin America. In this region, the center of origin of this legume species, over 4 million tons of dry beans are produced per year. Nevertheless, many Latin American countries, including two of the largest producers of beans in the world, Brazil and Mexico, have to import beans to meet internal demand. This shortage of beans is related to the low productivity of this crop in Latin America (700 kg /ha vs. 1,600 kg/ ha average in the USA). The low productivity in the main bean production regions of tropical America is associated to the incidence of several biotic and abiotic constraints. Among the biotic constraints, bean golden mosaic virus is undoubtedly the main bean production problem in the lowland tropics, particularly, during the dry seasons of the year.Programa Cooperativo Regional de Frijol para Centroamérica, México y el Caribe (PROFRIJOL)Cooperación Suiza para el Desarrollo (COSUDE)Centro Internacional de Agricultura Tropical (CIAT)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Estación Experimental Agrícola Fabio Baudrit Moreno (EEAFBM

Proteomics Mapping of Cord Blood Identifies Haptoglobin “Switch-On” Pattern as Biomarker of Early-Onset Neonatal Sepsis in Preterm Newborns

Intra-amniotic infection and/or inflammation (IAI) are important causes of preterm birth and early-onset neonatal sepsis (EONS). A prompt and accurate diagnosis of EONS is critical for improved neonatal outcomes. We sought to explore the cord blood proteome and identify biomarkers and functional protein networks characterizing EONS in preterm newborns.We studied a prospective cohort of 180 premature newborns delivered May 2004-September 2009. A proteomics discovery phase employing two-dimensional differential gel electrophoresis (2D-DIGE) and mass spectrometry identified 19 differentially-expressed proteins in cord blood of newborns with culture-confirmed EONS (n = 3) versus GA-matched controls (n = 3). Ontological classifications of the proteins included transfer/carrier, immunity/defense, protease/extracellular matrix. The 1(st)-level external validation conducted in the remaining 174 samples confirmed elevated haptoglobin and haptoglobin-related protein immunoreactivity (Hp&HpRP) in newborns with EONS (presumed and culture-confirmed) independent of GA at birth and birthweight (P<0.001). Western blot concurred in determining that EONS babies had conspicuous Hp&HpRP bands in cord blood ("switch-on pattern") as opposed to non-EONS newborns who had near-absent "switch-off pattern" (P<0.001). Fetal Hp phenotype independently impacted Hp&HpRP. A bayesian latent-class analysis (LCA) was further used for unbiased classification of all 180 cases based on probability of "antenatal IAI exposure" as latent variable. This was then subjected to 2(nd)-level validation against indicators of adverse short-term neonatal outcome. The optimal LCA algorithm combined Hp&HpRP switch pattern (most input), interleukin-6 and neonatal hematological indices yielding two non-overlapping newborn clusters with low (≤20%) versus high (≥70%) probability of IAI exposure. This approach reclassified ∼30% of clinical EONS diagnoses lowering the number needed to harm and increasing the odds ratios for several adverse outcomes including intra-ventricular hemorrhage.Antenatal exposure to IAI results in precocious switch-on of Hp&HpRP expression. As EONS biomarker, cord blood Hp&HpRP has potential to improve the selection of newborns for prompt and targeted treatment at birth

Timing of postpartum intrauterine device placement: A cost-effectiveness analysis

©2015 by American Society for Reproductive Medicine. Objective: To determine if immediate postpartum (PP) intrauterine device (IUD) placement prevents pregnancy and is cost-effective compared with routine placement. Design: We developed a decision-analysis model to determine the number of pregnancies prevented and the cost-effectiveness of immediate PP IUD placement defi ned as within the first 10 minutes of placental expulsion compared with routine placement at the PP visit. Associated costs and probability estimates for adherence to PP follow-up, IUD placement, expulsion, and pregnancy were determined from the literature. Setting: Hospital and outpatient facility. Patient(s): Women desiring PP IUDs. Intervention(s): IUD placement. Main Outcome Measure(s): The main outcome measure was the number of pregnancies prevented per 1,000 women. The secondary outcome was an incremental cost-effectiveness ratio (ICER) defined as the marginal cost per quality-adjusted life-year (QALY) gained. An ICER of \u3c$50,000/QALY gained was considered to be cost-effective. Result(s): Immediate PP IUD placement prevented 88 unintended pregnancies per 1,000 women over a 2-year time horizon. Immediate PP IUD placement was the dominant strategy. For every 1,000 women who desired a PP IUD, attempted immediate PP placement resulted in a cost savings of$282,540 and a gain of 10 QALYs. The model is most sensitive to the cost of an undesired pregnancy. When the cost of a live birth is \u3c$6,000, immediate placement is no longer cost-saving but remains cost-effective. Monte Carlo simulation demonstrates that immediate PP IUD placement is cost-effective in 99% of simulations. Conclusion(s): Immediate PP IUD placement is a dominant strategy that prevents unintended pregnancy