Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties

BACKGROUND: High-throughput (omic) data have become more widespread in both quantity and frequency of use, thanks to technological advances, lower costs and higher precision. Consequently, computational scientists are confronted by two parallel challenges: on one side, the design of efficient methods to interpret each of these data in their own right (gene expression signatures, protein markers, etc.) and, on the other side, realization of a novel, pressing request from the biological field to design methodologies that allow for these data to be interpreted as a whole, i.e. not only as the union of relevant molecules in each of these layers, but as a complex molecular signature containing proteins, mRNAs and miRNAs, all of which must be directly associated in the results of analyses that are able to capture inter-layers connections and complexity. RESULTS: We address the latter of these two challenges by testing an integrated approach on a known cancer benchmark: the NCI-60 cell panel. Here, high-throughput screens for mRNA, miRNA and proteins are jointly analyzed using factor analysis, combined with linear discriminant analysis, to identify the molecular characteristics of cancer. Comparisons with separate (non-joint) analyses show that the proposed integrated approach can uncover deeper and more precise biological information. In particular, the integrated approach gives a more complete picture of the set of miRNAs identified and the Wnt pathway, which represents an important surrogate marker of melanoma progression. We further test the approach on a more challenging patient-dataset, for which we are able to identify clinically relevant markers. CONCLUSIONS: The integration of multiple layers of omics can bring more information than analysis of single layers alone. Using and expanding the proposed integrated framework to integrate omic data from other molecular levels will allow researchers to uncover further systemic information. The application of this approach to a clinically challenging dataset shows its promising potential

Boundary-semantic collaborative guidance network with dual-stream feedback mechanism for salient object detection in optical remote sensing imagery

With the increasing application of deep learning in various domains, salient object detection in optical remote sensing images (ORSI-SOD) has attracted significant attention. However, most existing ORSI-SOD methods predominantly rely on local information from low-level features to infer salient boundary cues and supervise them using boundary ground truth, but fail to sufficiently optimize and protect the local information, and almost all approaches ignore the potential advantages offered by the last layer of the decoder to maintain the integrity of saliency maps. To address these issues, we propose a novel method named boundary-semantic collaborative guidance network (BSCGNet) with dual-stream feedback mechanism. First, we propose a boundary protection calibration (BPC) module, which effectively reduces the loss of edge position information during forward propagation and suppresses noise in low-level features without relying on boundary ground truth. Second, based on the BPC module, a dual feature feedback complementary (DFFC) module is proposed, which aggregates boundary-semantic dual features and provides effective feedback to coordinate features across different layers, thereby enhancing cross-scale knowledge communication. Finally, to obtain more complete saliency maps, we consider the uniqueness of the last layer of the decoder for the first time and propose the adaptive feedback refinement (AFR) module, which further refines feature representation and eliminates differences between features through a unique feedback mechanism. Extensive experiments on three benchmark datasets demonstrate that BSCGNet exhibits distinct advantages in challenging scenarios and outperforms the 17 state-of-the-art (SOTA) approaches proposed in recent years. Codes and results have been released on GitHub: https://github.com/YUHsss/BSCGNet.Comment: Accepted by TGR

Overexpression of DcR3 and Its Significance on Tumor Cell Differentiation and Proliferation in Glioma

Background. Overexpression of decoy receptor 3 (DcR3) have been reported in various classes of malignancies. However, its expression and clinicopathological contribution in gliomas has not been fully elucidated. Objective. To explore the expression and clinical significance of DcR3 protein in relation to tumor cell differentiation and proliferation in glioma cell lines and tissues. Methods. One hundred and twenty-five samples of glioma patients and 18 cases of normal brain tissues were recruited. The expression of DcR3 protein was detected using immunohistochemistry. Tumor differentiation was assessed by histologic characters and the status of glial fibrillary acidic protein (GFAP). Tumor cell labeling indexes (LIs) of Ki-67 and PCNA were also obtained. The relationship between the DcR3 level and clinicopathological features was investigated, including tumor differentiation, LIs, and survival. Meanwhile, the expression of DcR3 protein was also measured in the supernatants of 8 glioma cell lines and glioma cells freshly prepared from 8 human glioblastoma specimens by using western blot. Results. The level of DcR3 protein in gliomas was significantly higher than that in normal brain tissues (P<0.01). DcR3 expression showed positive correlations with tumor pathological grade (r=0.621, P<0.01) and negative with GFAP expression (r=-0.489, P<0.01). Furthermore, there were positive correlations between DcR3 expression and Ki-67, PCNA LIs (r=0.529, P<0.01; r=0.556, P<0.01). The survival in the DcR3 negative group was 50 ± 1.79 months, longer than that of the DcR3 positive group (48.36 ± 2.90), however, without significance (P=0.149). Different levels of DcR3 could also be detected in the culturing supernatants of all the 8 glioma cell lines and glioma cells freshly obtained from 8 human glioblastoma specimens. Conclusions. The overexpression of DcR3 might play a crucial role in the tumorigenesis, differentiation, and proliferation of glioma

Antagonistic Actions of Juvenile Hormone and 20-Hydroxyecdysone Within the Ring Gland Determine Developmental Transitions in \u3cem\u3eDrosophila\u3c/em\u3e

In both vertebrates and insects, developmental transition from the juvenile stage to adulthood is regulated by steroid hormones. In insects, the steroid hormone, 20-hydroxyecdysone (20E), elicits metamorphosis, thus promoting this transition, while the sesquiterpenoid juvenile hormone (JH) antagonizes 20E signaling to prevent precocious metamorphosis during the larval stages. However, not much is known about the mechanisms involved in cross-talk between these two hormones. In this study, we discovered that in the ring gland (RG) of Drosophila larvae, JH and 20E control each other’s biosynthesis. JH induces expression of a Krüppel-like transcription factor gene Kr-h1 in the prothoracic gland (PG), a portion of the RG that produces the 20E precursor ecdysone. By reducing both steroidogenesis autoregulation and PG size, high levels of Kr-h1 in the PG inhibit ecdysteriod biosynthesis, thus maintaining juvenile status. JH biosynthesis is prevented by 20E in the corpus allatum, the other portion of the RG that produces JH, to ensure the occurrence of metamorphosis. Hence, antagonistic actions of JH and 20E within the RG determine developmental transitions in Drosophila. Our study proposes a mechanism of cross-talk between the two major hormones in the regulation of insect metamorphosis

Case Report: A novel FGFR1 fusion in acute B-lymphoblastic leukemia identified by RNA sequencing

8p11 myeloproliferative syndrome is a rare hematological malignancy with aggressive course caused by the various translocation of FGFR1. In this study, a novel FGFR1 fusion was identified by RNA sequencing in a 28-year-old male patient with acute B-lymphoblastic leukemia. The patient harbors an in-frame fusion between KIF5B exon 15 and FGFR1 exon 10. The FGFR1 fusion and its protein expression was validated by Sanger sequencing and Western blot. Meanwhile, cytogenetic analysis reported a normal karyotype and targeted DNA sequencing identified no driver mutations, respectively. Despite he achieved complete remission after induction regimen, a relapse occurred and he became refractory to chemotherapy, and salvage haploidentical hematopoietic stem cell transplantation failed to control the progressive disease. In conclusion, we present the first case of KIF5B-FGFR1 fusion in hematological malignancy. These findings extend the spectrum of translocation in 8p11 myeloproliferative syndrome, and demonstrate the great prospect of RNA sequencing in clinical practice again

Identification of a venetoclax-resistance prognostic signature base on 6-senescence genes and its clinical significance for acute myeloid leukemia

BackgroundSatisfactory responses can be obtained for acute myeloid leukemia (AML) treated by Venetoclax (VEN)-based therapy. However, there are still quite a few AML patients (AMLs) resistant to VEN, and it is critical to understand whether VEN-resistance is regulated by senescence.MethodsHere, we established and validated a signature for predicting AML prognosis based on VEN resistance-related senescence genes (VRSGs). In this study, 51 senescence genes were identified with VEN-resistance in AML. Using LASSO algorithms and multiple AML cohorts, a VEN-resistance senescence prognostic model (VRSP-M) was developed and validated based on 6-senescence genes.ResultsAccording to the median score of the signature, AMLs were classified into two subtypes. A worse prognosis and more adverse features occurred in the high-risk subtype, including older patients, non-de novo AML, poor cytogenetics, adverse risk of European LeukemiaNet (ELN) 2017 recommendation, and TP53 mutation. Patients in the high-risk subtype were mainly involved in monocyte differentiation, senescence, NADPH oxidases, and PD1 signaling pathway. The model’s risk score was significantly associated with VEN-resistance, immune features, and immunotherapy response in AML. In vitro, the IC50 values of ABT-199 (VEN) rose progressively with increasing expression of G6PD and BAG3 in AML cell lines.ConclusionsThe 6-senescence genes prognostic model has significant meaning for the prediction of VEN-resistance, guiding personalized molecularly targeted therapies, and improving AML prognosis

Constructing a Thin Disordered Self‐Protective Layer on the LiNiO₂ Primary Particles Against Oxygen Release

One of the major challenges facing the application of layered LiNiO2 (LNO) cathode materials is the oxygen release upon electrochemical cycling. Here it is shown that tailoring the provided lithium content during synthesis process can create a disordered layered Li1-xNi1+xO2 phase at the primary particle surface. The disordered surface, which serves as a self-protective layer to alleviate the oxygen loss, possesses the same layered rhombohedral structure (R m) as the inner core of primary particles of the Li1-xNi1+xO2 (x ≈ 0). With advanced synchrotron-based x-ray 3D imaging and spectroscopic techniques, a macroporous architecture within the agglomerates of LNO with ordered surface (LNO-OS) is revealed after only 40 cycles, concomitant with the reduction of nickel on the primary particle surface throughout the whole secondary particles. Such chemomechanical degradation accelerates the deterioration of LNO-OS cathodes. Comparably, there are only slight changes in the nickel valence state and interior architecture of LNO with a thin disordered surface layer (LNO-DS) after cycling, mainly arising from an improved robustness of the oxygen framework on the surface. More importantly, the disordered surface can suppress the detrimental H2 ⇋ H3 phase transition upon cycling compared to the ordered one

High-performance infrared photodetectors based on InAs/InAsSb/AlAsSb superlattice for 3.5 µm cutoff wavelength spectra

High-performance infrared p-i-n photodetectors based on InAs/InAsSb/AlAsSb superlattices on GaSb substrate have been demonstrated at 300K. These photodetectors exhibit 50% and 100% cut-off wavelength of ∼3.2 µm and ∼3.5 µm, respectively. Under -130 mV bias voltage, the device exhibits a peak responsivity of 0.56 A/W, corresponding to a quantum efficiency (QE) of 28%. The dark current density at 0 mV and -130 mV bias voltage are 8.17 × 10−2 A/cm2 and 5.02 × 10−1 A/cm2, respectively. The device exhibits a saturated dark current shot noise limited specific detectivity (D*) of 3.43 × 109 cm·Hz1/2/W (at a peak responsivity of 2.5 µm) under -130 mV of applied bias

Reduced expression of N-Myc downstream-regulated gene 2 in human thyroid cancer

<p>Abstract</p> <p>Background</p> <p><it>NDRG</it>2 (N-Myc downstream-regulated gene 2) was initially cloned in our laboratory. Previous results have shown that <it>NDRG</it>2 expressed differentially in normal and cancer tissues. Specifically, <it>NDRG</it>2 mRNA was down-regulated or undetectable in several human cancers, and over-expression of <it>NDRG</it>2 inhibited the proliferation of cancer cells. <it>NDRG</it>2 also exerts important functions in cell differentiation and tumor suppression. However, it remains unclear whether <it>NDRG</it>2 participates in carcinogenesis of the thyroid.</p> <p>Methods</p> <p>In this study, we investigated the expression profile of human <it>NDRG</it>2 in thyroid adenomas and carcinomas, by examining tissues from individuals with thyroid adenomas (n = 40) and carcinomas (n = 35), along with corresponding normal tissues. Immunohistochemistry, quantitative RT-PCR and western blot methods were utilized to determine both the protein and mRNA expression status of Ndrg2 and c-Myc.</p> <p>Results</p> <p>The immunostaining analysis revealed a decrease of Ndrg2 expression in thyroid carcinomas. When comparing adenomas or carcinomas with adjacent normal tissue from the same individual, the mRNA expression level of <it>NDRG</it>2 was significantly decreased in thyroid carcinoma tissues, while there was little difference in adenoma tissues. This differential expression was confirmed at the protein level by western blotting. However, there were no significant correlations of <it>NDRG</it>2 expression with gender, age, different histotypes of thyroid cancers or distant metastases.</p> <p>Conclusion</p> <p>Our data indicates that <it>NDRG</it>2 may participate in thyroid carcinogenesis. This finding provides novel insight into the important role of <it>NDRG2 </it>in the development of thyroid carcinomas. Future studies are needed to address whether the down-regulation of <it>NDRG</it>2 is a cause or a consequence of the progression from a normal thyroid to a carcinoma.</p