Artificial intelligence-based non-invasive tumor segmentation, grade stratification and prognosis prediction for clear-cell renal-cell carcinoma

Due to the complicated histopathological characteristics of clear-cell renal-cell carcinoma (ccRCC), non-invasive prognosis before operative treatment is crucial in selecting the appropriate treatment. A total of 126 345 computerized tomography (CT) images from four independent patient cohorts were included for analysis in this study. We propose a V Bottleneck multi-resolution and focus-organ network (VB-MrFo-Net) using a cascade framework for deep learning analysis. The VB-MrFo-Net achieved better performance than VB-Net in tumor segmentation, with a Dice score of 0.87. The nuclear-grade prediction model performed best in the logistic regression classifier, with area under curve values from 0.782 to 0.746. Survival analysis revealed that our prediction model could significantly distinguish patients with high survival risk, with a hazard ratio (HR) of 2.49 [95% confidence interval (CI): 1.13-5.45, P = 0.023] in the General cohort. Excellent performance had also been verified in the Cancer Genome Atlas cohort, the Clinical Proteomic Tumor Analysis Consortium cohort, and the Kidney Tumor Segmentation Challenge cohort, with HRs of 2.77 (95%CI: 1.58-4.84, P = 0.0019), 3.83 (95%CI: 1.22-11.96, P = 0.029), and 2.80 (95%CI: 1.05-7.47, P = 0.025), respectively. In conclusion, we propose a novel VB-MrFo-Net for the renal tumor segmentation and automatic diagnosis of ccRCC. The risk stratification model could accurately distinguish patients with high tumor grade and high survival risk based on non-invasive CT images before surgical treatments, which could provide practical advice for deciding treatment options.</p

Identification of QTLs and candidate genes for rice seed germinability under low temperature using high‐density genetic mapping and RNA‐seq

Abstract Reduced temperatures during germination adversely affect rice (Oryza sativa L.) production. Little is known, however, of the genes or genetic loci involved. Here, QTLs were investigated in a recombinant inbred line (RIL) resulting from a 02428 (japonica)‐YZX (indica) cross. The phenotypes of the cultivars differ significantly when exposed to low temperatures during germination. Mapping with a high‐density bin map identified 11 loci associated with low‐temperature germination of which loci 2 and 4 were identified by multiple traits over two seasons. Locus 2 was a major genetic locus, explaining 22.36% of phenotypic variation. The haplotype results showed that the pyramiding of favorable alleles of these two loci was beneficial to improving the rice seeds' low‐temperature germinability. RNA‐seq analysis was performed on the second day of germination at low temperature for both parents. Three DGEs (Os03g0119800, Os03g0120900, and Os03g0121300) were obtained for locus 2 and were confirmed as the most likely candidates by qRT‐PCR verification, gene sequence alignment, and haplotype analysis. Collectively, these quantitative trait loci and candidate genes may be valuable for the breeding of cold‐tolerant rice lines as well as broadening our knowledge of the genetics underlying germination at low temperatures

Interferon-γ Induces Senescence in Normal Human Melanocytes

<div><p>Background</p><p>Interferon-γ (IFN-γ) plays an important role in the proceedings of vitiligo through recruiting lymphocytes to the lesional skin. However, the potential effects of IFN-γ on skin melanocytes and the subsequent contribution to the vitiligo pathogenesis are still unclear.</p><p>Objective</p><p>To investigate the effects of IFN-γ on viability and cellular functions of melanocytes.</p><p>Methods</p><p>Primary human melanocytes were treated with IFN-γ. Cell viability, apoptosis, cell cycle melanin content and intracellular reactive oxygen species (ROS) level were measured. mRNA expression was examined by real-time PCR. The release of interleukin 6 (IL-6) and heat shock protein 70 (HSP-70) was monitored by ELISA. β-galactosidase staining was utilized to evaluate melanocyte senescence.</p><p>Results</p><p>Persistent IFN-γ treatment induced viability loss, apoptosis, cell cycle arrest and senescence in melanocytes. Melanocyte senescence was characterized as the changes in pigmentation and morphology, as well as the increase of β-galactosidase activity. Increase of p21^Cip1/Waf1 protein was evident in melanocytes after IFN-γ treatment. IFN-γ induction of senescence was attenuated by siRNAs against p21, Janus kinase 2 (JAK2) or signal transducer and activator of transcription 1 (STAT1), but not by JAK1 siRNA nor by p53 inhibitor pifithrin-α. IFN-γ treatment increased the accumulation of intracellular ROS in melanocytes, while ROS scavenger N-acetyl cysteine (NAC) effectively inhibited IFN-γ induced p21 expression and melanocyte senescence. IL-6 and HSP-70 release was significantly induced by IFN-γ treatment, which was largely inhibited by NAC. The increase of IL-6 and HSP-70 release could also be observed in senescent melanocytes.</p><p>Conclusion</p><p>IFN-γ can induce senescence in melanocytes and consequently enhance their immuno-competency, leading to a vitiligo-prone milieu.</p></div

Effects of IFN-γ on melanogenesis in normal melanocytes.

<p>(A) Melanocytes were treated with various concentrations of IFN-γ (0, 100 or 1000 U/ml) for 3 or 7days before melanin content was measured. The melanin content was normalized on the basis of protein concentration. (b–g) Total RNA was extracted from melanocytes treated with or without IFN-γ for 24 hours. Real-time PCR was then performed to evaluate the relative mRNA levels of (B) tyrosinase (TYR), (C) tyrosinase-related protein 1 (TYRP1), (D) Melan-A, (E) melanocyte protein 17 (PMEL17), (F) microphthalmia-associated transcription factor (MITF), and (G) dopachrome tautomerase (DCT). The values shown represent the mean ± SD of three independent melanocyte cultures. *P<0.05 and **P<0.01.</p

IFN-γ decreased viability of melanocytes, caused apoptosis and cell cycle arrest.

<p>Primary normal human Melanocytes were treated with various concentrations of IFN-γ (0, 100 or 1000 U/ml) for 72 h. Cell viability was then examined by MTS assay (A). Apoptosis was analyzed by flow cytometry after cells were stained with PI and Annexin V-FITC (B). (C) Cell cycle distribution of melanocytes was measured 24 h post IFN-γ treatment. Results are presented as mean ± SD from at least three independent melanocyte cultures. *P<0.05, **P<0.01, Student's t-test compared with controls.</p

JAK2 and STAT1 activities are necessary for IFN-γ caused melanocyte senescence.

<p>Melanocytes were transfected with JAK1, JAK2, STAT1 siRNAs or scrambled control siRNA (Ctrl). After 48 h, cells were treated with or without 100 U/ml IFN-γ for additional 7 days. (A) Cell viability of melancytes was measured by MTS assay. (B) Protein level of p21 was evaluated by Western blot. β-actin was probed as the loading control. (C) Percentages of SA-β-gal-positive cells were determined based on microscopic analysis.</p

Involvement of Reactive Oxygen Species (ROS) in the IFN-γ induced senescence.

<p>(A) Melancytes were stimulated with indicated concentration of IFN-γ for 24 h. Generated ROS was detected with flow cytometer after labelled with the ROS sensor DCFH-DA. (B,C) Melanocytes were treated with or without 100 U/ml IFN-γ for 7 days in the presence of vehicle or 1 mM NAC. (B) Protein level of p21 was evaluated by Western blot. β-actin was probed as the loading control. (C) Percentages of SA-β-gal-positive cells were determined based on microscopic analysis. CON represents the cell culture without IFN-γ.</p