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

Molecular Cloning and Expression Analysis of a Hexokinase Gene, MdHXK1 in Apple

A hexokinase gene named MdHXK1 (MDP0000309677) was cloned from ‘Gala’ apple (Malus × domestica Borkh.). Sequence analysis showed that the MdHXK1 gene was 1 497 bp long and encoded 499 amino acids. The predicted molecular mass of this protein was 54.05 kD, and the pI was 5.76. A phylogenetic tree indicated apple MdHXK1 exhibited the highest sequence similarity to Pyrus bretschneideri PbHXK1. Analysis of the functional domain showed that the MdHXK1 protein included two conserved kinase domains. The prediction of subcellular localization suggested that the MdHXK1 protein was mainly localized in the cytoplasm. There was an indication that MdHXK1 existed as one copy in the apple genome by Southern blotting. Silico analysis suggested that the promoter sequence contained several typical cis-acting elements, including defense, sugar signaling and phytohormone responsive elements. Quantitative real-time PCR analysis demonstrated that the MdHXK1 gene was mainly expressed in stem and flower tissues. During the development of apple fruits, the expression of the MdHXK1 gene initially increased and then decreased. The changes on Glc phosphorylation relative activity and glucose concentration showed the same trend. In addition, the expression of this gene was induced by salt stress, low temperature, and abscisic acid (ABA). Finally, we obtained and purified the fused MdHXK1 protein by recombinant prokaryotic expression. Studies have demonstrated that MdHXK1 may participate in sugar metabolism in apple fruits. Enzyme encoded by MdHXK1 is a key factor in the mediation of sugar accumulation. Recently, researchers on hexokinase at home and abroad mainly focused on model plants, such as Arabidopsis, tobacco and rice, but orchard fruit like apple were underresearched. Our research established the foundation for the further study of the functions of MdHXK1

Expression Analysis of the MdCIbHLH1 Gene in Apple Flower Buds and Seeds in the Process of Dormancy

A bHLH transcription factor that is induced by low temperature was found in apple (Malus × domestica Borkh.). To understand the sequence characteristics of the gene, bioinformatics analysis was performed. Furthermore, gene expression patterns of the laminated apple seeds and lateral flower buds were analyzed during the period of dormancy release with semi-quantitative RT-PCR. Based on secondary structure predictions, the results showed that the MdCIbHLH1 protein structure mainly included α-helix and random coil, while β-sheet and extended strand content was less. Semi-quantitative RT-PCR analysis showed that the expression patterns of MdCIbHLH1 were similar in laminated apple seeds and lateral flower buds during the period of dormancy release. Before dormancy release, expression levels of MdCIbHLH1 were high and gradually decreased during the period of dormancy release. These results indicated that MdCIbHLH1 might play an important role during dormancy release in apple seeds and apple buds

Functional Characterization of the Apple RING E3 Ligase MdMIEL1 in Transgenic Arabidopsis

E3 ubiquitin ligases are involved in various physiological processes, and they play pivotal roles in growth and development. In this study, we identified a previously unknown gene in the apple fruit (Malus × domestica) and named it MdMIEL1. The MdMIEL1 gene encoded a protein that contained a zinc-finger domain at its N-terminus and a RING-finger motif at its C-terminus. To investigate MdMIEL1 functions, we generated transgenic Arabidopsis lines expressing the MdMIEL1 gene under the control of the Cauliflower mosaic virus 35S promoter. Interestingly, ectopic expression of MdMIEL1 in Arabidopsis produced multiple phenotypes, including early germination, early flowering and a lateral root number increase relative to wild-type plants. Further analysis indicated that MdMIEL1 regulated lateral root initiation by increasing auxin accumulation in the roots. In a word, these results suggest that, MdMIEL1 as a novel RING-finger ubiquitin ligase influences plant growth and development, and highlight that MdMIEL1 regulates lateral root growth

Comparative Analysis of GF-5 and Sentinel-2A Fusion Methods for Lithological Classification: The Tuanjie Peak, Xinjiang Case Study

This study investigates the application of hyperspectral image space–spectral fusion technology in lithologic classification, using data from China’s GF-5 and Europe’s Sentinel-2A. The research focuses on the southern region of Tuanjie Peak in the Western Kunlun Range, comparing five space–spectral fusion methods: GSA, SFIM, CNMF, HySure, and NonRegSRNet. To comprehensively evaluate the effectiveness and applicability of these fusion methods, the study conducts a comprehensive assessment from three aspects: evaluation of fusion effects, lithologic classification experiments, and field validation. In the evaluation of fusion effects, the study uses an index analysis and comparison of spectral curves before and after fusion, concluding that the GSA fusion method performs the best. For lithologic classification, the Random Forest (RF) classification method is used, training with both area and point samples. The classification results from area sample training show significantly higher overall accuracy compared to point samples, aligning well with 1:50,000 scale geological maps. In field validation, the study employs on-site verification combined with microscopic identification and comparison of images with actual spectral fusion, finding that the classification results for the five lithologies are essentially consistent with field validation results. The “GSA+RF” method combination established in this paper, based on data from GF-5 and Sentinel-2A satellites, can provide technical support for lithological classification in similar high-altitude regions

Genome-Wide Identification, Characterization, and Expression Analysis of Calmodulin-Like Proteins (CMLs) in Apple

Calcium (Ca2+), a crucial second messenger in plants, is involved in diverse signaling pathways including biotic and abiotic stress responses. However, the functions of most calcium sensors including calcium-dependent protein kinases (CDPKs), calmodulins (CaMs), calmodulin-like proteins (CMLs), and calcineurin B-like proteins (CBLs) remain limited in plants, particularly in woody plants. Currently, a total of 83 CMLs and seven CaMs were discovered in the apple genome in this study. Functional domain analysis showed that these CMLs and CaMs contain a highly conserved EF-hand motif. qRT-PCR assays indicated that these CMLs were expressed ubiquitously in apple, including in the roots, stems, leaves, flowers, and fruits, and also possessed spatial specificity. Finally, most of these CMLs were induced by hormonal and abiotic stress, suggesting their potential roles in the regulation of growth, development, and the stress response in apple. In summary, our findings provide potential evidence that apple CMLs may be involved in abiotic stress and the regulation of plant growth and development

Lithium-Bearing Pegmatite Identification, Based on Spectral Analysis and Machine Learning: A Case Study of the Dahongliutan Area, NW China

Lithium (Li) resources are widely used in many strategic emerging fields; recently, several large-scale to super-large-scale pegmatite-type lithium deposits have been discovered in Dahongliutan, NW China. However, the natural environmental conditions in the Dahongliutan area are extremely harsh; hence, manpower in field exploration is difficult to achieve. Efficient and rapid methods for identifying Li-rich pegmatites, based on hyperspectral remote sensing technology, have great potential for promoting the discovery of lithium resources. Ground spectral research is the cornerstone of regional hyperspectral imaging (HSI) for geological mapping. Direct observation and analysis by the naked eye are part of a process that is mainly dependent upon abundant experience and knowledge from experts. Machine learning (ML) technology has the advantages of automatic feature extraction and relationship characterization. Therefore, identifying the spectral features of Li-rich pegmatite via ML can accurately and efficiently distinguish the spectral characteristics of Li-rich pegmatites and Li-poor pegmatites, enabling further excavation to identify the strongest predictors of Li-pegmatite and laying a foundation for the accurate extraction of Li-rich pegmatites in the West Kunlun region using HSI. The spectral characteristics of pegmatite in the visible near-infrared and shortwave infrared (VNIR–SWIR) spectra were observed and analyzed. Li-rich pegmatite was identified based on the diagnostic spectral waveform characteristic parameters of the local wavelength range. The results demonstrated that the pegmatite ML recognition model was based on spectral characteristic parameters of the local wavelength range, with good model explicability, and the area under the curve (AUC) calculated for the model is 0.843. A recognition model based on full-range spectrum data achieved a higher precision, and the AUC value was up to 0.977. The evaluation of the Gini coefficient presented the strongest predictors, which were used to map the spatial distribution lithology, based on GF-5, in Akesayi and the 509 mines, producing encouraging lithological mapping results (Kappa > 0.9, OA > 94%)

The Characterization, Authentication, and Gene Expression Pattern of the MdCER Family in Malus domestica

Plant cuticular wax is an important determinant factor of fruit quality. Cuticular wax can protect the fruit from UV radiation, drought, and disease and increase the storage period of fruit. In many species, CER gene is associated with wax and can affect plant response to stress, but no characterization of CER gene and its family has been reported in apples. In this study, we identified 10 MdCER genes in Malus domestica based on the sequences of 10 CER genes in Arabidopsis thaliana. Three-dimensional structures were then defined, and root-mean-square deviation (RMSD) scoring matrixes were used to evaluate the matches. These 10 genes were divided into three classes using phylogenetic methods; namely, class I, II, and III. The predicted MdCER genes were distributed across 7 out of 17 chromosomes with different densities. Furthermore, the gene structures and motif compositions of the MdCER genes were analyzed. The quantitative real-time PCR results indicated that MdCER family genes were mainly expressed in the leaves and stems and rarely in the roots. Most of the MdCER members responded to salicylic acid and polyethylene glycol treatment, indicating that the MdCER family is associated with disease resistance (biotic) and abiotic stress. Keywords: apple, wax, MdCER gene family, expressio

A Genome-Wide Analysis of the LBD (LATERAL ORGAN BOUNDARIES Domain) Gene Family in <em>Malus domestica</em> with a Functional Characterization of <em>MdLBD11</em>

<div><p>The plant-specific LBD (LATERAL ORGAN BOUNDARIES domain) genes belong to a major family of transcription factor that encode a zinc finger-like domain. It has been shown that LBD genes play crucial roles in the growth and development of <i>Arabidopsis</i> and other plant species. However, no detailed information concerning this family is available for apple. In the present study, we analyzed the apple (<i>Malus domestica</i>) genome and identified 58 <i>LBD</i> genes. This gene family was tested for its phylogenetic relationships with homologous genes in the <i>Arabidopsis</i> genome, as well as its location in the genome, structure and expression. We also transformed one <i>MdLBD</i> gene into <i>Arabidopsis</i> to evaluate its function. Like <i>Arabidopsis</i>, apple <i>LBD</i> genes also have a conserved CX₂CX₆CX₃C zinc finger-like domain in the N terminus and can be divided into two classes. The expression profile indicated that apple <i>LBD</i> genes exhibited a variety of expression patterns, suggesting that they have diverse functions. At the same time, the expression analysis implied that members of this apple gene family were responsive to hormones and stress and that they may participate in hormone-mediated plant organogenesis, which was demonstrated with the overexpression of the apple <i>LBD</i> gene <i>MdLBD11</i>, resulting in an abnormal phenotype. This phenotype included upward curling leaves, delayed flowering, downward-pointing flowers, siliques and other abnormal traits. Based on these data, we concluded that the <i>MdLBD</i> genes may play an important role in apple growth and development as in <i>Arabidopsis</i> and other species.</p> </div

Application of horizontal development wells in reserves evaluation and development of offshore oilfields

In the early stage of offshore oilfield development, due to the lack of drilling, limited data admission, and lack of dynamic data, there is great uncertainty in the understanding of oilfield reserves. With increased degree of development, production is usually inconsistent with reserves, and reserve re-evaluation is an important way to resolve this problem. In order to improve the development efficiency and reduce costs, offshore oilfields are dominated by horizontal wells, resulted in limited data acquisition. Therefore, new horizontal well data has become the key to obtainnew geological reservoir parameters and improve the accuracy of reserve estimation. In order to further obtain reliable reserve evaluation results and resolve the dynamic and static contradictions of the oilfield, based on analyzing the main controlling parameters of reserve change in the Pearl River Mouth Basin, this study fully excavates the role of horizontal development wells in improving the accuracy of primary controlling parameters.Our results show that the oil-bearing area and effective thickness are the most uncertain in the reserve assessment, and cause the change of reserves. Horizontal development well is critical in improving the production capacity of the oilfield, determining the lower limit of effective thickness, investigating microstructure, and identifying lithological boundary and fluid interface, etc. In the case of limited data access, the utilizationof horizontal development wells can effectively improve the accuracy of major controlling parameters to obtain relatively reasonable geological reserves, and solve the dynamic contradictions of oilfield production. It also points out the direction for late exploration and development of oilfields. Application examples from multiple oil fields in the eastern South China Sea also confirm this understanding