Single-cell and whole-transcriptome sequencing of lymph node metastasis-related gene signature: A large-scale pan-cancer cohort, machine learning and experimental study.

BACKGROUND: Lymph node metastasis (LNM) is an independent prognostic factor in numerous types of cancer. Therefore, a LNM-related gene-based nomogram may precisely predict survival and drug sensitivity, and reveal the mechanism underlying LNM. MATERIALS AND METHODS: Gene sequencing profiles of pan-cancer data (33 cancer types) were acquired from The Cancer Genome Atlas UCSC Xena database. Patients were classified into primary (N = 10,071) and testing (N = 5,036) cohorts. The lymph node score (LNscore) was established via single-cell RNA sequencing, whole-transcriptome sequencing, machine learning, and Cox regression analyses. A novel prognosis model, formulated by incorporating the LNscore and clinical characteristics, was evaluated using the concordance index, calibration curve, and decision curve analysis. Moreover, patients were assigned into high- and low-risk groups according to the median LNscore. We investigated these two groups for survival prognosis, functional enrichment, immune infiltration, and drug sensitivity. In addition, we silenced and overexpressed insulin like growth factor 2 mRNA binding protein 2 (IGF2BP2). We also analyzed the behavior of breast cancer (BRCA) cells regarding lymphatic metastasis and lymphangiogenesis in vitro. IGF2BP2 stimulated the proliferation of BRCA cells via 5-Ethynyl-2'-deoxyuridine and Cell Counting Kit-8 experiments. RESULTS: A LNM-related set of 12 genes was identified and utilized to determine the LNscore. The concordance-index of both cohorts in the LNscore-based model was >0.7. The immune landscape revealed that the sensitivity to immunotherapy might be better in the high-risk group versus the low-risk group. In addition, we discovered that IGF2BP2 was overexpressed in BRCA tissues and significantly associated with poor survival. Functional analysis indicated that IGF2BP2 promoted BRCA cell migration and proliferation. Additionally, IGF2BP2 accelerated lymphatic metastasis and lymphangiogenesis in vivo. CONCLUSIONS: A novel LNscore-based model was established via comprehensive analysis of LNM-related genes. This model can accurately predict patient survival and drug sensitivity, and reveal the mechanism of LNM in the pan-cancer setting.

Integrative analysis of lactylation-related genes and establishment of a novel prognostic signature for hepatocellular carcinoma.

BACKGROUND: Lactylation has been found to involve in regulating many types of biological process in cancers. However, research on lactylation-related genes in predicting the prognosis of hepatocellular carcinoma (HCC) remains limited. METHODS: The differential expression of lactylation-related genes (EP300 and HDAC1-3) in pan-cancer were examined in public databases. HCC patient tissues were obtained for mRNA expression and lactylation level detection by RT-qPCR and western blotting. Transwell migration assay, CCK-8 assay, EDU staining assay and RNA-seq were performed to verify the potential function and mechanisms in HCC cell lines after lactylation inhibitor apicidin treatment. lmmuCellAI, quantiSeq, xCell, TIMER and CIBERSOR were used to analyze the correlation between transcription levels of lactylation-related genes and immune cell infiltration in HCC. Risk model of lactylation-related genes was constructed by LASSO regression analysis, and prediction effect of the model was evaluated. RESULT: The mRNA levels of lactylation-related genes and lactylation levels were higher in HCC tissues than normal samples. The lactylation levels, cell migration, and proliferation ability of HCC cell lines were suppressed after apicidin treatment. The dysregulation of EP300 and HDAC1-3 was associated with proportion of immune cell infiltration, especially B cell. Upregulation of HDAC1 and HDAC2 was closely associated with poorer prognosis. Finally, a novel risk model, based on HDAC1 and HDAC2, was developed for prognosis prediction in HCC. CONCLUSION: HDAC1 and HDAC2 are expected to become new biomarkers for HCC. Risk scoring model based on HDAC1 and HDAC2 can be used to predict the prognosis of HCC patients.

Construction and validation of chemoresistance-associated tumor- infiltrating exhausted-like CD8+ T cell signature in breast cancer: cr-TILCD8TSig.

Background: Accumulating evidence has revealed that CD8+ T cell exhaustion (Tex) results in worse immunotherapy outcomes. However, the molecular functions and mechanisms of action of Tex in chemoresistance needed to be elucidated. Methods: The populations of tumor-infiltrating CD8+ T cells (TILCD8Ts) in chemoresistant and chemosensitive groups of the GSE25066 dataset were calculated using CIBERSORT. Differentially expressed genes (DEGs) between TILCD8Ts and other immune cells were explored by integrating 16 immune cell datasets downloaded from the gene expression omnibus (GEO) database. Gene ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, univariate and multivariate Cox regression, and least absolute shrinkage and selection operator (LASSO) regression of TILCD8T-specific upregulated genes were used to construct a chemoresistant TILCD8T signature (cr-TILCD8TSig). Clinical prognostic data, genomic alterations, chemotherapy response, and immunotherapy response were compared between the different cr-TILCD8TSig subgroups in the GSE25066 and the cancer genome atlas breast cancer (TCGA-BRCA) cohorts. Results: A cr-TILCD8TSig with exhausted features was identified, consisting of seven genes (TCF7, RARRES3, ARL4C, ITK, CDH3, GZMB, and KLRD1), which were identified from 104 TILCD8Ts-specific DEGs. Our results showed that compared to the cr-TILCD8TSig-low subgroup, the -high subgroup had a poorer distant relapse-free survival (DRFS) in the GSE25066 cohort and worse progression-free survival (PFS) in the TCGA-BRCA cohort. Univariate and multivariate Cox regression analyses also demonstrated that cr-TILCD8TSig was an independent prognostic factor in the two independent cohorts. Furthermore, cr-TILCD8TSig-low patients benefited more from chemotherapy and immunotherapy than cr-TILCD8TSig-high patients. Besides, we found cell transmembrane signal transduction and the ECM may provide the molecular basis for resistance to antitumor agents in the cr-TILCD8Sig-high subgroup. For genomic alterations, we revealed that mutations in PIK3CA, DMD, and APOB were more common in the cr-TILCD8Sig-high subgroup than in the cr-TILCD8Sig-low subgroup. A nomogram was finally constructed with good discrimination and calibration. Conclusions: cr-TILCD8TSig is a useful tool to independently predict prognosis, chemotherapy response, and immunotherapy outcomes in patients with breast cancer.

[Analysis of the influence factors of school-age children's refractive status].

Objective: To analyze the influence of the eye biological parameters, height, and weight on the school-age children's refractive status. Methods: Cross-sectional study. A total of 1 656 children (1 656 eyes), aged from 7 to 14 years, were selected from 8 schools in Wenzhou during June 2012 and June 2013. The height and weight of each child were measured, and the body mass index (BMI) was calculated. The eye biological parameters, including axial length (AL), corneal power (C=1/CR), anterior chamber depth (ACD), and white to white (WTW), were measured by IOLMaster (version 5.0, Carl Zeiss, Germany), and the AL/CR was calculated. Refraction was measured by fast cycloplegic retinoscopy, and the spherical equivalent (SE) was calculated. Only right eyes were included in the analysis. SPSS16.0 was used to analyze the data. The correlations of the equivalent spherical power, the eye biological parameters, height, weight, and BMI were evaluated. Linear regression analysis was used for the SE, AL, and AL/CR. Results: The prevalence of myopia in 7- to 14-year-old school-age children was 50.2% on the average, 48.4% in boys, and 51.7% in girls. The average SE was (-1.07±1.74) D. With adjustment of the age, gender, urban and rural areas, there was an association between the SE and AL, AL/CR, ACD, height and weight. The correlation coefficient was -0.663, -0.730, -0.416, -0.365, and -0.281, respectively (P<0.05). There was no significant correlation between the SE and WTW, corneal power and BMI. Regarding the different refractive statuses, there was a stronger correlation between the SE and AL, AL/CR in children with hyperopia, moderate myopia or high myopia than those with emmetropia or mild myopia (P< 0.01). In the older children, the correlation between the SE and AL, AL/CR was stronger. Linear regression analysis showed SE= 26.55-9.11·AL/CR and 23.0-1.02·AL. Conclusions: There was an association between the SE and AL, AL/CR, ACD, height and weight in school-age children. In children with hyperopia, moderate myopia, high myopia or at an older age, the correlation was more significant between the SE and AL, AL/CR. (Chin J Ophthalmol, 2016, 52:831-835).

HMG-CoA reductase inhibitors induce apoptosis of lymphoma cells by promoting ROS generation and regulating Akt, Erk and p38 signals via suppression of mevalonate pathway.

Statins, the inhibitors of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, are widely used cholesterol-lowering drugs. Convincing evidence indicates that statins stimulate apoptotic cell death in several types of proliferating tumor cells in a cholesterol-lowering-independent manner. The objective here was to elucidate the molecular mechanism by which statins induce lymphoma cells death. Statins (atorvastatin, fluvastatin and simvastatin) treatment enhanced the DNA fragmentation and the activation of proapoptotic members such as caspase-3, PARP and Bax, but suppressed the activation of anti-apoptotic molecule Bcl-2 in lymphoma cells including A20 and EL4 cells, which was accompanied by inhibition of cell survival. Both increase in levels of reactive oxygen species (ROS) and activation of p38 MAPK and decrease in mitochondrial membrane potential and activation of Akt and Erk pathways were observed in statin-treated lymphoma cells. Statin-induced cytotoxic effects, DNA fragmentation and changes of activation of caspase-3, Akt, Erk and p38 were blocked by antioxidant (N-acetylcysteine) and metabolic products of the HMG-CoA reductase reaction, such as mevalonate, farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP). These results suggests that HMG-CoA reductase inhibitors induce lymphoma cells apoptosis by increasing intracellular ROS generation and p38 activation and suppressing activation of Akt and Erk pathways, through inhibition of metabolic products of the HMG-CoA reductase reaction including mevalonate, FPP and GGPP.

Comparative proteomic analysis identifies protein disulfide isomerase and peroxiredoxin 1 as new players involved in embryonic interdigital cell death.

In this study, we used comparative proteomics to identify proteins that were involved in the regulation of interdigital cell death. The protein profiles of embryonic day (E) 12.5 and 13.5 mouse hindlimb interdigital tissues were compared to identify proteins that were differentially expressed. The interdigital cells are irreversibly committed to programmed cell death (PCD) at E13.5, whereas they are developmentally plastic at E12.5. We established that protein disulfide isomerase (PDI) expression was up-regulated at E13.5, while peroxiredoxin 1 (Prdx1) expression was down-regulated at this time point. Semiquantitative reverse transcriptase-polymerase chain reaction and Western blot analyses confirmed the data obtained from the two-dimensional electrophoresis gels. Furthermore, we were able to up-regulate PDI expression by manipulating the E12.5 interdigital tissues to die during culture, although this up-regulation was not possible when cell survival was promoted. In addition, we could inhibit interdigital cell death and expression of proapoptotic genes (Bmp-4 and Bambi) by treating interdigital tissues with PDI antibodies and bacitracin (a PDI enzyme inhibitor). These findings suggested that PDI was involved in the activation and maintenance of interdigital cell death. Conversely, we determined that Prdx1 expression was maintained when interdigital cultures were manipulated to survive but down-regulated when the cultures were permitted to die. The result suggested that Prdx1 was involved in maintaining interdigital cell survival. However, we were unable to induce interdigital cell death by means of RNA interference-mediated silencing of Prdx1 expression, indicating that Prdx1 down-regulation is not sufficient for PCD to occur. Proteomic analysis of the Prdx1 knock-down cells revealed that the level of NF-kappaB inhibitor epsilon (IkappaBepsilon) was dramatically reduced. Furthermore, we found an increase in NFkappaB activation and reactive oxygen species (ROS) levels in the cytoplasm as a result of Prdx1 knockdown. We also found that silencing Prdx1 made the interdigital cells more susceptible to ROS-induced cell death. Taken together, our study identifies two new players in interdigital cell death and highlights that PCD is regulated by a delicate balance of proapoptotic and survival-promoting activities.

Heart-type fatty acid binding proteins are upregulated during terminal differentiation of mouse cardiomyocytes, as revealed by proteomic analysis.

At birth, the cardiomyocytes in the mouse neonatal heart still retain their ability to proliferate. However, this lasts only a few days and then the cardiomyocytes irreversibly lose their potential to divide. It is still not fully understood what factors are involved in the cessation of cardiomyocyte proliferation. Using proliferating cell nuclear antigen (PCNA) antibodies, we established that cardiomyocytes could divide extensively in 2-day-old mouse neonatal hearts and to a lesser extent in 6-day-old hearts. By 13 days, the cardiomyocytes have mostly stopped dividing. Comparative two-dimensional gel electrophoresis (2-DE) was performed on total proteins extracted from the 2-day- and 13-day-old hearts, in order to identify peptides that might be involved in the inhibition of cardiomyocyte proliferation. Using matrix-assisted laser desorption ionization mass spectroscopy (MALDI-TOF), we identified two protein spots that have the same molecular weight (approximately 14 kDa) but different pIs (5.9 and 6.1). Mass spectra analysis determined the proteins to be isoforms of the heart-type fatty acid binding protein (H-FABP). The pI 6.1 H-FABP is also known as mammary-derived growth inhibitor (MDGI; Specht et al. 1996). MGDI is a breast tumour growth suppressor gene capable of inhibiting tumour cell proliferation (Huynh et al. 1995). Both H-FABP isoforms were expressed in 2-day-old hearts but became strongly upregulated in 13-day-old hearts. We examined whether H-FABPs and PCNA were coexpressed in 2-, 6- and 13-day-old heart histological sections, using MDGI antibodies. The antibody could detect both forms of H-FABPs. It was established that there was a correlation between an increase in H-FABP expression and a decrease in PCNA expression. Hence, we tentatively propose that H-FABP isoforms are involved in regulating cardiomyocyte growth and differentiation in mouse neonatal hearts.

Growth arrest-specific 2 gene expression during patellar tendon healing.

We examined the cellular and molecular processes involved in patellar tendon healing following induced injury. A wound was surgically created at the center of the patellar tendon of adult rats. The wound site was examined at selected time intervals by immunohistochemical and in situ hybridization techniques. It was found that, between the 2nd and 7th day postoperation, fibroblast-like cells invaded the wound site. DiI-labelling experiments suggested that the majority of cells that occupied the wound originated from the edges of the wound. Furthermore, immunohistochemical studies revealed that at the wound site a meshwork of fibronectin developed that can support the migration of the DiI-labelled cells. We also examined the spatial and temporal expression patterns of the growth arrest specific 2 (GAS2) gene during patellar tendon healing. GAS2 was found strongly expressed in the tenocytes of unoperated patellar tendons. The gene was also expressed in the intact regions of operated tendons but not in the fibroblast-like cells that occupied the wound site, when examined 2 days postoperation. In addition the strip of intact tendon directly opposite the wound site also did not express GAS2. Examination of the experimental tendon at the 3rd month, when cells had completely occupied the wound site, revealed that Gas2 was expressed by all cells found in the wound. Bromodeoxyuridine (BrdU) incorporation analysis revealed that the presence of Brdu-positive cells in the wound indirectly correlated with the absence of Gas2 expression. We speculate that the GAS2 gene might play a role in regulating tenocyte proliferation during tendon healing.

Limitations on the s-state approach to the interpretation of sub-angstrom resolution electron microscope images and microanalysis.

The s-state approach is useful for analysing transmission electron microscope images of a thin crystalline foil consisting of well-separated atomic columns. It assumes that the signal collected (e.g., the annular dark-field image, the EELS spectrum) can be attributed to only the lowest-energy bound eigenstate of the two-dimensional projected potential of a single column. When, however, columns are close, the form of the bound states depends on more than one column, which implies that interpretation of the signal may not be so simple. For closely spaced columns we show that the simple s-state approach fails for the case of a sub-Angstrom probe initially centred on one column of a pair, because two bound states are excited. The energy in the probe is almost completely transferred to the neighbouring column after it has propagated some tens of nanometres through the foil and then is transferred back. Signals which relate directly to the local probe intensity (e.g. annular dark-field formed by thermal diffuse scattering, EELS) must be analysed in terms of the two bound states. Accurate calculations of bound states of pairs of columns are more demanding than for a single column but sufficient accuracy can be achieved from knowledge of the 1s-states of isolated columns. We provide formulae for the bound states of a column pair. These can be used to determine if image analysis requires the extension to the s-state approach described in this paper.

Fibroblast growth factor-8b-stimulated myogenic cell proliferation is suppressed by the promyelocytic leukemia gene.

Muscle cell growth is regulated by growth-promoting and -inhibiting factors. In this study, the physiological effects of fibroblast growth factor (FGF)-8b and the promyelocytic leukemia (PML) gene on G8 myogenic cells were examined. FGF-8b was found to strongly stimulate myogenic cell proliferation. Signal transduction assays using AP-1/SEAP and E-box/SEAP reporters revealed that the transcriptional factors junB/c-fos and c-myc were involved in FGF-8b-stimulated G8 cell growth. Besides examining factors that positively stimulate myogenic cell growth, we also examined genes that negatively affect cell growth. PML is a growth suppressor gene and we studied its expression in G8 cells under different growth conditions. Immunohistochemical staining revealed that in the presence of low serum, PML was expressed in approximately 23.2% of all cultured G8 cells. However, under normal culture conditions (10% serum), PML expression dropped to about 2.6%. We found that the PML gene acted antagonistically to FGF-8b, as the overexpression of PML in G8 cells significantly inhibited FGF-8b-stimulated cell proliferation. It also inhibited AP-1 and E-box transactivation. However, we believe that PML functions as a stress-response gene in G8 cells rather than as a gene normally involved in regulating muscle development.

Parvalbumin expression is downregulated in rat fast-twitch skeletal muscles during aging.

In this study, the protein expression profile of extensor digitorum longous (EDL) and Soleus (SOL) muscles, representing fast- and slow-twitch skeletal muscles, respectively, was established using high resolution two-dimensional electrophoresis (2-DE). One protein spot was found uniquely expressed in EDL muscle. N-terminal sequence analysis identified the protein as parvalbumin. Parvalbumin is a high affinity calcium binding protein that regulates muscle contraction and relaxation. Our experiments revealed that parvalbumin expression in EDL muscle was down-regulated during aging. In addition, high-intensity exercise could reverse this age-related change. Soleus muscles do not normally express parvalbumin, but high-intensity exercise could ectopically induce its expression in both young and old SOL muscles. We have also confirmed our 2-DE findings by immunohistochemistry on muscle sections. Our results suggest that high-intensity training could be used to improve muscle functions during aging because parvalbumin play an important role in regulating skeletal muscle contraction and relaxation.

Functions of the growth arrest specific 1 gene in the development of the mouse embryo.

The growth arrest specific 1 (gas1) gene is highly expressed in quiescent mammalian cells (Schneider et al., 1988, Cell 54, 787-793). Overexpression of gas1 in normal and some cancer cell lines could inhibit G(0)/G(1) transition. Presently, we have examined the functions of this gene in the developing mouse embryo. The spatial-temporal expression patterns for gas1 were established in 8.5- to 14.5-day-old embryos by immunohistochemical staining and in situ hybridization. Gas1 was found heterogeneously expressed in most organ systems including the brain, heart, kidney, limb, lung, and gonad. The antiproliferative effects of gas1 on 10.5 and 12.5 day limb cells were investigated by flow cytometry. In 10.5 day limbs cells, gas1 overexpression could not prevent G(0)/G(1) progression. It was determined that gas1 could only induce growth arrest if p53 was also coexpressed. In contrast, gas1 overexpression alone was able to induce growth arrest in 12.5 day limb cells. We also examined the cell cycle profile of gas1-expressing and nonexpressing cells by immunochemistry and flow cytometry. For 10.5 day Gas1-expressing heart and limb cells, we did not find these cells preferentially distributed at G0/G1, as compared with Gas1-negative cells. However, in the 12.5 day heart and limb, we did find significantly more Gas1-expressing cells distributed at G0/G1 phase than Gas1-negative cells. These results implied that Gas1 alone, during the early stages of development, could not inhibit cell growth. This inhibition was only established when the embryo grew older. We have overexpressed gas1 in subconfluent embryonic limb cells to determine the ability of gas1 to cross-talk with various response elements of important transduction pathways. Specifically, we have examined the interaction of gas1 with Ap-1, NFkappaB, and c-myc responsive elements tagged with a SEAP reporter. In 10.5 day limb cells, gas1 overexpression had little effect on Ap-1, NFkappaB, and c-myc activities. In contrast, gas1 overexpression in 12.5 day limb cells enhanced AP-1 response while it inhibited NFkappaB and c-myc activities. These responses were directly associated with the ability of gas1 to induce growth arrest in embryonic limb cells. In the 12.5 day hindlimb, gas1 was found strongly expressed in the interdigital tissues. We overexpressed gas1 in these tissues and discovered that it promoted interdigital cell death. Our in situ hybridization studies of limb sections and micromass cultures revealed that, during the early stages of chondrogenesis, only cells surrounding the chondrogenic condensations expressed gas1. The gene was only expressed by chondrocytes after the cartilage started to differentiate. To understand the function of gas1 in chondrogenesis, we overexpressed the gene in limb micromass cultures. It was found that cells overexpressing gas1/GFP could not participate in cartilage formation, unlike cells that just express the GFP reporter. We speculated that the reason gas1 was expressed outside the chondrogenic nodules was to restrict cells from being recruited into the nodules and thereby defining the boundary between chondrogenic and nonchondrogenic forming regions.

Hepatocyte growth factor stimulates chemotactic response in mouse embryonic limb myogenic cells in vitro.

In this study we investigate the influence of Hepatocyte Growth Factor (HGF) on the motility of embryonic forelimb myoblasts. Using Blindwell chemotactic chambers, it was found that HGF at concentrations of 1-50 ng/ml dramatically enhanced the ability of myogenic cells to migrate. This stimulatory effect was elicited in a dose-dependent fashion and the effect was reversed with the addition of HGF neutralizing antibodies. A checkerboard analysis was performed and it revealed that HGF's effect on limb myoblast motility was through both chemokinesis and chemotaxis. HGF was also examined for its ability to stimulate myogenic cell proliferation, using MF20 antibody as the myogenic marker. At all concentrations tested, HGF did not stimulate an overall increase in the numbers of MF20-positive myoblasts in culture. To examine the chemokinetic effect of HGF on cell migration in the limb, cells were isolated from the proximal regions of the limb (areas rich in myogenic cells), exposed to HGF, labeled with DiI and transplanted into 11.5 day mouse forelimbs. After 36 h of culture, it was found that DiI-labeled limb cells, pretreated with HGF, migrated significantly further in the limb than labeled cells that have not been exposed to HGF. The chemotactic effect of HGF was also investigated by implanting beads loaded with and without HGF into the 11.5 day limb. Proximal to the beads, DiI-labeled limb cells were also transplanted. It was found that HGF was able to chemotactically attract and direct the migration of DiI-labeled limb cells. Immunohistological staining was performed with HGF antibodies to determine the distribution of HGF in the 11.5 day mouse forelimb. It was found that HGF was strongly expressed by the apical ectodermal ridge (AER), the ectoderm and the mesenchyme directly beneath the AER. Positive staining was also obtained for the myogenic regions. However, the pattern was heterogeneous--punctuated with myogenic cells expressing and not expressing HGF.

Desmin transgene expression in mouse somites requires the presence of the neural tube.

Transgenic mice were used to study the effect of the neural tube on somite myogenesis. These mice express a transgene in which the 1 kb DNA 5' regulatory sequence of the desmin gene is linked to a reporter gene which codes for E. coli beta-galactosidase. In order to determine whether the developmental fate of cells, specifically the prospective myogenic population, in newly developed somites was pre-determined, newly formed somites were isolated from the caudal region of day 9.5 transgenic embryos and transplanted into 8.5 day non-transgenic host embryos. Even though the implanted somites were not oriented in the host embryos, all the specimens examined developed normally at the graft site forming a dermatome, myotome and sclerotome in the correct anatomical positions. The myotome even expressed the desmin transgene. In addition, we isolated the 3 most caudal somites, that is, the most recently developed somites, from day 9.5 transgenic embryos and maintained them on gelatin-coated coverslips in culture for up to 4 days. While these somite explants did not develop myoblasts, it was possible to induce myogenesis by introducing pieces of neural tube into the explant cultures. These results suggest that the developmental fate of cells within the newly formed somite is not predetermined, but is dependent on the microenvironment surrounding the developing somite.