Single-Cell Transcriptome Analysis Uncovers Intratumoral Heterogeneity and Underlying Mechanisms for Drug Resistance in Hepatobiliary Tumor Organoids.

Molecular heterogeneity of hepatobiliary tumor including intertumoral and intratumoral disparity always leads to drug resistance. Here, seven hepatobiliary tumor organoids are generated to explore heterogeneity and evolution via single-cell RNA sequencing. HCC272 with high status of epithelia-mesenchymal transition proves broad-spectrum drug resistance. By examining the expression pattern of cancer stem cells markers (e.g., PROM1, CD44, and EPCAM), it is found that CD44 positive population may render drug resistance in HCC272. UMAP and pseudo-time analysis identify the intratumoral heterogeneity and distinct evolutionary trajectories, of which catenin beta-1 (CTNNB1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and nuclear paraspeckle assembly transcript 1 (NEAT1) advantage expression clusters are commonly shared across hepatobiliary organoids. CellphoneDB analysis further implies that metabolism advantage organoids with enrichment of hypoxia signal upregulate NEAT1 expression in CD44 subgroup and mediate drug resistance that relies on Jak-STAT pathway. Moreover, metabolism advantage clusters shared in several organoids have similar characteristic genes (GAPDH, NDRG1 (N-Myc downstream regulated 1), ALDOA, and CA9). The combination of GAPDH and NDRG1 is an independent risk factor and predictor for patient survival. This study delineates heterogeneity of hepatobiliary tumor organoids and proposes that the collaboration of intratumoral heterogenic subpopulations renders malignant phenotypes and drug resistance.

A comparative study of clinical effect of total knee arthroplasty in the treatment of primary osteoarthritis and osteoarthritis of Kashin-Beck disease.

OBJECTIVE: To evaluate the clinical efficacy of total knee arthroplasty (TKA) in the treatment of primary osteoarthritis (OA) and osteoarthritis of Kashin-Beck disease (KBD). METHODS: This study enrolled 77 KBD patients (77 knees, KBD-TKA) and 75 OA patients (75 knees, OA-TKA) who underwent TKA from September 2008 to June 2018. Clinical assessments for each patient were performed pre-operatively and last follow-up. The efficacy measures included the visual analogue scale (VAS) pain score, range of motion (ROM), Hospital for Special Surgery (HSS) score, and short form 36 Health Survey (SF-36) as well as related influencing factors between the two groups. RESULTS: All patients were followed up; the follow-up time of KBD-TKA was 14-132 months, with an average of 72.68 ± 37.55 months; OA-TKA was 15-120 months, with an average of 49.2 ± 28.91 months. There was no difference in pre-operative VAS score (7.29 vs. 7.24) and SF-36 (PCS) score (4.87 vs. 5.49) between KBD-TKA and OA-TKA (P > 0.05), while compared with OA, KBD-TKA had significantly worse pre-operative ROM (75.48° vs. 82.87°), HSS score (36.40 vs. 41.84), and SF-36 (MCS) score (26.28 vs. 28.73) (P < 0.05). At the final follow-up, there was no significant difference in VAS score (1.13 vs. 1.16), ROM (105.79 vs. 105.79), and HSS score (92.06 vs. 92.25) between KBD-TKA and OA-TKA (P > 0.05), while compared with OA, KBD-TKA had significantly worse SF-36 (PCS) score (36.90 vs. 42.00) and SF-36 (MCS) score (55.16 vs. 59.70) (P < 0.05). In a multivariate regression, controlling for multiple potential confounders, diagnosis of KBD was associated with poor quality of life after surgery, whereas pre-operative pain was specifically associated with post-operative pain. However, preoperative gender, age, BMI, and the angles of knee prosthesis (before and after surgery) were not associated with post-operative outcome. CONCLUSION: Patients with KBD undergoing primary TKA have excellent outcomes, comparable with OA at the final follow-up, in spite of worse pre-operative ROM, HSS score, and SF-36(MCS) score. However, KBD patients are worse than OA in terms of general health. Pre-operative age, gender, BMI, and the angles of knee prosthesis were not the factors influencing the clinical efficacy of TKA. The diagnosis of KBD was an independent risk factor for poor quality of life after TKA. Pre-operative pain was a clinically important predictor of outcome.

Isoliquiritigenin inhibits the proliferation, migration and metastasis of Hep3B cells via suppressing cyclin D1 and PI3K/AKT pathway.

The overall survival rate of patients with hepatocellular carcinoma (HCC) has remained unchanged over the last several decades. Therefore, novel drugs and therapies are required for HCC treatment. Isoliquiritigenin (ISL), a natural flavonoid predominantly isolated from the traditional Chinese medicine Glycyrrhizae Radix (Licorice), has a high anticancer potential and broad application value in various cancers. Here, we aimed to investigate the anticancer role of ISL in the HCC cell line Hep3B. Functional analysis revealed that ISL inhibited the proliferation of Hep3B cells by causing G1/S cell cycle arrest in vitro. Meanwhile, the inhibitory effect of ISL on proliferation was also observed in vivo. Further analysis revealed that ISL could suppress the migration and metastasis of Hep3B cells in vitro and in vivo. Mechanistic analysis revealed that ISL inhibited cyclin D1 and up-regulated the proteins P21, P27 that negatively regulate the cell cycle. Furthermore, ISL induced apoptosis while inhibiting cell cycle transition. In addition, phosphatidylinositol 3'-kinase/protein kinase B (PI3K/AKT) signal pathway was suppressed by ISL treatment, and the epithelial marker E-cadherin was up-regulated when the mesenchymal markers Vimentin and N-cadherin were down-regulated. In brief, our findings suggest that ISL could be a promising agent for preventing HCC tumorigenesis and metastasis.

The xantha Marker Trait Is Associated with Altered Tetrapyrrole Biosynthesis and Deregulated Transcription of PhANGs in Rice.

The xantha marker trait, which is controlled by a down-regulating epi-mutation of OsGUN4, has been applied to the production of hybrid rice. However, the molecular basis for the ability of xantha mutants to attain high photosynthetic capacity even with decreased chlorophyll contents has not been characterized. In the present study, we observed that the total chlorophyll content of the xantha mutant was only 27.2% of that of the wild-type (WT) plants. However, the xantha mutant still accumulated 59.9% of the WT δ-aminolevulinic acid content, 72.8% of the WT Mg-protoporphyrin IX content, and 63.0% of the WT protochlorophyllide a content. Additionally, the protoporphyrin IX and heme contents in the mutant increased to 155.0 and 160.0%, respectively, of the WT levels. A search for homologs resulted in the identification of 124 rice genes involved in tetrapyrrole biosynthesis and photosynthesis. With the exception of OsGUN4, OsHO-1, and OsHO-2, the expression levels of the genes involved in tetrapyrrole biosynthesis were significantly higher in the xantha mutant than in the WT plants, as were all 72 photosynthesis-associated nuclear genes. In contrast, there were no differences between the xantha mutant and WT plants regarding the expression of all 22 photosynthesis-associated chloroplast genes. Furthermore, the abundance of 1O2 and the expression levels of 1O2-related genes were lower in the xantha mutant than in the WT plants, indicating 1O2-mediated retrograde signaling was repressed in the mutant plants. These results suggested that the abundance of protoporphyrin IX used for chlorophyll synthesis decreased in the mutant, which ultimately decreased the amount of chlorophyll in the xantha mutant. Additionally, the up-regulated expression of photosynthesis-associated nuclear genes enabled the mutant to attain a high photosynthetic capacity. Our findings confirm that OsGUN4 plays an important role in tetrapyrrole biosynthesis and photosynthesis in rice. GUN4, chlorophyll synthesis pathways, and photosynthetic activities are highly conserved in plants and hence, novel traits (e.g., xantha marker trait) may be generated in other cereal crops by modifying the GUN4 gene.

A microRNA expression profile for vascular invasion can predict overall survival in hepatocellular carcinoma.

BACKGROUND: The presence of vascular invasion (VI) in pathology specimens is a well-known unfavorable prognostic factor of hepatocellular carcinoma (HCC) recurrence and overall survival (OS). We investigated the vascular invasion related microRNA (miRNA) expression profiles and potential of prognostic value in HCC. METHODS: MiRNA and mRNA expression data for HCC were accessed from The Cancer Genome Atlas (TCGA). LASSO logistic regression models were used to develop a miRNA-based classifier for predicting VI. The predictive capability was accessed by area under receiver operating characteristics (AUC). Concordance index (C-index) and time-dependent receiver operating characteristic (td-ROC) were used to determine its prognostic value. We validated the predictive and prognostic accuracy of this classifier in an external independent cohort of 127 patients. Functionally relevant targets of miRNAs were determined using miRNA target prediction, experimental validation and correlation of miRNA and mRNA expression data. RESULTS: A 16-miRNA-based classifier was developed which identified VI accurately, with AUC of 0.731 and 0.727 in TCGA set and validation cohort, respectively. C-index and td-ROC showed that the classifier was able to stratify patients into risk groups strongly associated with OS. When stratified by tumor characteristics, the classifier was still a clinically and statistically significant prognostic model. The predictive and prognostic accuracy of the classifier was confirmed in validation cohort. Vascular invasion related miRNA/target pairs were identified by integrating expression patterns of predicted targets, which were validated in cell lines. CONCLUSIONS: A multi-miRNA-based classifier developed based on the presence of VI, which could effectively predict OS in HCC.

A MELD-based nomogram for predicting 3-month mortality of patients with acute-on-chronic hepatitis B liver failure.

BACKGROUND: Acute-on-chronic hepatitis B liver failure (ACHBLF) is associated with poor short-term prognosis. The aim of the present study was to construct and validate a model for end-stage liver disease (MELD)-based nomogram for the 3-month mortality estimation for patients with ACHBLF. METHODS: A total of 551 patients with ACHBLF were prospectively enrolled from 2 independent medical centers and divided into 2 cohorts of training and validation, respectively. The 3-month mortality was recorded as the outcome. The MELD-based nomogram was constructed to predict the 3-month mortality for ACHBLF using the training group of 335 patients and validated using an independent cohort of 216 patients. The predictive capability of MELD-based nomogram was compared with the MELD score system by calibration analysis, receiver operating characteristics (ROC) and decision curve analysis in both training cohort and validation cohort. RESULTS: Multivariate analysis suggested that age, serum sodium, and MELD score were independent prognostic indicators associated with the 3-month mortality for ACHBLF, and therefore used for developing the nomogram. In terms of calibration, the predicted survival by the MELD-based nomogram was found to be extremely in line with the observed 3-month mortality both in training cohort and validation cohort. Additionally, both ROC and decision curve analyses showed that the MELD-based nomogram was better than MELD, MELD-Na, MELDNa, and iMELD for ACHBLF prognosis prediction. The results were confirmed in the external cohort of validation. CONCLUSIONS: The MELD-based nomogram provided a user-friendly, accurate and reproducible tool for predicting 3-month mortality of patients with ACHBLF.

[Simulation of AquaCrop model and management practice optimization for dryland maize production under whole plastic-film mulching on double ridges]. / æ—±åœ°å ¨è†œåŒåž„æ²ŸçŽ‰ç±³ç”Ÿäº§çš„AquaCrop模型模拟及管理措施优化.

In order to study the applicability of AquaCrop model for simulating dryland whole plastic-film mulching in double ridges cultivation mode and to find the best agronomic management measures, the data of nitrogen gradient test in 2014 and 2015 were selected to validate the variety and stress parameters in the model. The change trends of yield were simulated under different mana-gement measures. The results showed that the root mean square error (RMSE), normalized root mean square error (NRMSE) and the compliance index (d) of the measured and simulated production for all treatments were 717 kg·hm-2, 10.0% and 0.96, respectively, the RMSE, NRMSE and d of the total biomass were 951 kg·hm-2, 6.5% and 0.98, respectively, which indicated that the cultivation characteristics of the whole plastic-film mulching on double ridges maize in the dryland could be well reflected. The best fitting degree was 270 kg N·hm-2 from dynamic simulation analysis of canopy cover degrees and biomass, and with the increase of N stress, the simulation accuracy gradually declined. The best sowing time of the whole plastic-film mulching on double ridges maize in the middle part of Gansu Province was from late April to early May, the seeding density was 45000-65000 plants·hm-2, the growth period was 130-145 days, and the nitrogen application rate was 240-280 kg·hm-2. The results of this study had a certain reference value for the application of AcquaCrop model in arid region of Gansu, and would contribute to the transformation and popularization of agricultural cultivation techniques.

C-reactive protein-to-albumin ratio is a predictor of hepatitis B virus related decompensated cirrhosis: time-dependent receiver operating characteristics and decision curve analysis.

BACKGROUND AND AIMS: Hepatitis B virus (HBV) infection remains a major health problem and HBV-related-decompensated cirrhosis (HBV-DC) usually leads to a poor prognosis. Our aim was to determine the utility of inflammatory biomarkers in predicting mortality of HBV-DC. MATERIALS AND METHODS: A total of 329 HBV-DC patients were enrolled. Survival estimates for the entire study population were generated using the Kaplan-Meier method. The prognostic values for model for end-stage liver disease (MELD) score, Child-Pugh score, and inflammatory biomarkers neutrophil/lymphocyte ratio, C-reactive protein-to-albumin ratio (CAR), and lymphocyte-to-monocyte ratio (LMR) for HBV-DC were compared using time-dependent receiver operating characteristic curves and time-dependent decision curves. RESULTS: The survival time was 23.1±15.8 months. Multivariate analysis identified age, CAR, LMR, and platelet count as prognostic independent risk factors. Kaplan-Meier analysis indicated that CAR of at least 1.0 (hazard ratio, 7.19; 95% confidence interval, 4.69-11.03), and LMR less than 1.9 (hazard ratio, 2.40; 95% confidence interval, 1.69-3.41) were independently associated with mortality of HBV-DC. The time-dependent receiver operating characteristic indicated that CAR showed the best performance in predicting mortality of HBV-DC compared with LMR, MELD score, and Child-Pugh score. The results were also confirmed by time-dependent decision curves. CONCLUSION: CAR and LMR were associated with the prognosis of HBV-DC. CAR was superior to LMR, MELD score, and Child-Pugh score in HBV-DC mortality prediction.

Development and validation of a prognostic nomogram for acute-on-chronic hepatitis B liver failure.

BACKGROUND AND AIM: Determining individual risk of short-term mortality in patients with acute-on-chronic hepatitis B liver failure (ACHBLF) is a difficult task. We aimed to develop and externally validate a prognostic nomogram for ACHBLF patients. METHODS: The nomogram was built to estimate the probability of 30-day, 60-day, 90-day, and 60-month survival based on an internal cohort of 246 patients with ACHBLF. The predictive accuracy and discriminative ability of nomogram were determined by a concordance index (C-index), calibration curve, and time-dependent receiver operating characteristics (tdROC), comparing with model for end-stage liver disease (MELD) score. The results were validated using bootstrap resampling and an external cohort of 138 patients. Furthermore, we plotted decision curves to evaluate the clinical usefulness of nomogram. RESULTS: Independent factors derived from multivariable Cox analysis of training cohort to predict mortality were age, total bilirubin, serum sodium, and prothrombin activity, which were all assembled into nomogram. The calibration curves for probability of survival showed optimal agreement between nomogram prediction and actual observation. The C-index of nomogram was higher than that of MELD score for predicting survival (30-day, 0.809 vs 0.717, P < 0.001; 60-day, 0.792 vs 0.685, P < 0.001; 90-day, 0.779 vs 0.678, P < 0.001; 6-month, 0.781 vs 0.677, P < 0.001). Additionally, tdROC and decision curves also showed that nomogram was superior to MELD score. The results were confirmed in validation cohort. CONCLUSIONS: The prognostic nomogram provided an individualized risk estimate of short-term survival in patients with ACHBLF, offering to clinicians to improve their abilities to assess patient prognosis.

Onjisaponin B derived from Radix Polygalae enhances autophagy and accelerates the degradation of mutant α-Synuclein and Huntingtin in PC-12 cells / 中国药理学与毒理学杂志

OBJECTIVE To investigate the autophagic effect of the compounds from the Chinese medicinal herbs, Radix polygalae as a potential neuroprotective agent that enhances the clearance of mutant Huntingtin and α- synuclein in PC- 12 cells. METHODS Radix polygalae was extracted with 75% ethanol using refluxing method, and its quality was assayed by UHPLC-TOF-MS. The autophagic effect of Radix polygalae extract, and its major components including polygalacic acid, senegenin and onjisaponin B were investigated using the green fluorescent protein-light chain 3 (GFP-LC3) autophagy detection and Western blot platforms for detecting the autophagic markers, GFP-LC3 puncta formation and LC3 II expression. The degradation of A53T α- synuclein and the inhibition ofα-synuclein oligo merization related to the Parkinson disease were assayed using Western blot and flow cytometer analysis, respectively. While the cytotoxicity and the degradation of the mutant Huntingtin associated with the Huntingtin disease were investigated using MTT method and flow cytometer analysis. RESULTS Radix polygalae ethanol extract and onjisaponin B improved the GFP-LC3 puncta formation and expression of LC3Ⅱ with time and dose manner, and this induction was activated via AMPK-mTOR and Atg 7 gene pathway. Furthermore, the clearance of α-synuclein and mutant Huntingtin was enhanced via autophagy induction with the treatment of Radix polygalae ethanol extract and onjisaponin B. CONCLUSION Findings in the current study provide detailed insights into the protective mechanism of a novel autophagy inducer, onjisaponin B, which is valuable for further investigation as a new candidate agent for modulating neurodegenerative disorders through the reduction of toxicity and clearance of mutant proteins in the cellular level.

The ROCK/GGTase Pathway Are Essential to the Proliferation and Differentiation of Neural Stem Cells Mediated by Simvastatin.

Simvastatin, a lipophilic and fermentation-derived natural statin, is reported to treat neurological disorders, such as traumatic brain injury, Parkinson's disease (PD), Alzheimer disease (AD), etc. Recently, research also indicated that simvastatin could promote regeneration in the dentate gyrus of adult mice by Wnt/ß-catenin signaling (Robin et al. in Stem Cell Reports 2:9-17, 2014). However, the effect and mechanisms by which simvastatin may affect the neural stem cells (NSCs; from the embryonic day 14.5 (E14.5) SD rat brain) are not fully understood. Here, we investigated the effects of different doses of simvastatin on the survival, proliferation, differentiation, migration, and cell cycle of NSCs as well as underlying intracellular signaling pathways. The results showed that simvastatin not only inhibits the proliferation of NSCs but also enhances the ßIII-tubulin+ neuron differentiation rate. Additionally, we find that simvastatin could also promote NSC migration and induce cell cycle arrest at M2 phrase. All these effects of simvastatin on NSCs were mimicked with an inhibitor of Rho kinase (ROCK) and a specific inhibitor of geranylgeranyl transferase (GGTase). In conclusion, these data indicate that simvastatin could promote neurogenesis of neural stem cells, and these effects were mediated through the ROCK/GGTase pathway.

[Effect of Acupuncture Stimulation of Different Acupoint Groups on Levels of Stress Hormones and Serum Brain-derived Neurotrophic Factor in Depression Rats].

OBJECTIVE: To screen the effective acupoints for anti-depression in depression rats and to explore the mechanisms of acupuncture for relieving depression. METHODS: Fifty rats were randomly divided into normal control, model, "Yin-tang" (EX-HN 3)-"Baihui" (GV 20, 2-acupoints), EX-HN 3-GV 20-"Fengchi" (GB 20)-"Shenshu" (BL 23, 4-acupoints) and medication groups, with 10 rats in each group. The depression model was established by unpredictable chronic mild stress (UCMS) for 28 days. For rats of the 2-acupoints and 4-acupoints groups, EX-HN 3 and GV 20, and EX-HN 3, GV 20, GB 20 and BL 23 were punctured with filiform needles respectively before performing mild stress every time. The acupuncture needles were retained for 30 min during each intervention and the treatment was conducted once daily for 28 days. The rats of the medication group were treated by intragastric administration of Fluoxetine (0.18 mg/kg) once a day for 28 days. The rats' anxiety-like behavior (rearing and crossing times) was detected by open-field test. The contents of adrenocorticotropic hormone (ACTH) in the pituitary, 5-hydroxytryptamine (5-HT) in the hippocampus, the cortisol (CORT) in the adrenal gland, and the brain derived neurotrophic factor (BDNF) in the serum were examined by ELISA. RESULTS: Compared to the normal control group, the numbers of both rearing and crossing motions in the model group were significantly decreased (P<0.01, P<0.05), while in comparison with the model group, the rearing and crossing numbers of rats in the 2-acupoints and 4-acupoints and medication groups were significantly increased (P<0.01). ELISA showed that after modeling, the content of adrenal CORT was significantly increased (P<0.01), and those of hippocampal 5-HT and serum BDNF were obviously down-regulated in the model group (P<0.01). After the treatment, the adrenal CORT levels in the three intervention groups were notably down-regulated, and hippocampal 5-HT and serum BONE evidently up-regulated in these 3 intervention groups (P<0.05, P<0.01). No marked changes were found in the pituitary ACTH contents of the model and 3 intervention groups (P>0.05), and no significant differences were shown among the three intervention groups in the levels of the aforementioned 6 indexes (P>0.05). CONCLUSION: Acupuncture intervention can effectively improve the unprompted activates of the depression rats, which may be related to its effects in up-regulating hippocampal 5-HT and serum BONE levels, and in down-regulating adrenal CORT content.

Pattern of mutation rates in the germline of Drosophila melanogaster males from a large-scale mutation screening experiment.

The sperm or eggs of sexual organisms go through a series of cell divisions from the fertilized egg; mutations can occur at each division. Mutations in the lineage of cells leading to the sperm or eggs are of particular importance because many such mutations may be shared by somatic tissues and also may be inherited, thus having a lasting consequence. For decades, little has been known about the pattern of the mutation rates along the germline development. Recently it was shown from a small portion of data that resulted from a large-scale mutation screening experiment that the rates of recessive lethal or nearly lethal mutations differ dramatically during the germline development of Drosophila melanogaster males. In this paper the full data set from the experiment and its analysis are reported by taking advantage of a recent methodologic advance. By analyzing the mutation patterns with different levels of recessive lethality, earlier published conclusions based on partial data are found to remain valid. Furthermore, it is found that for most nearly lethal mutations, the mutation rate at the first cell division is even greater than previous thought compared with those at other divisions. There is also some evidence that the mutation rate at the second division decreases rapidly but is still appreciably greater than those for the rest of the cleavage stage. The mutation rate at spermatogenesis is greater than late cleavage and stem-cell stages, but there is no evidence that rates are different among the five cell divisions of the spermatogenesis. We also found that a modestly biased sampling, leading to slightly more primordial germ cells after the eighth division than those reported in the literature, provides the best fit to the data. These findings provide conceptual and numerical basis for exploring the consequences of differential mutation rates during individual development.

Controlled attenuation parameter for the detection of steatosis severity in chronic liver disease: a meta-analysis of diagnostic accuracy.

BACKGROUND AND AIM: Controlled attenuation parameter (CAP) is a novel ultrasound-based elastography method for detection of steatosis severity. This meta-analysis aimed to assess the performance of CAP. METHODS: PubMed, the Cochrane Library, and the Web of Knowledge were searched to find studies, published in English, relating to accuracy evaluations of CAP for detecting stage 1 (S1), stage 2 (S2), or stage 3 (S3) hepatic steatosis which was diagnosed by liver biopsy. Sensitivities, specificities, and hierarchical summary receiver operating characteristic (HSROC) curves were used to examine CAP performance. The clinical utility of CAP was also evaluated. RESULTS: Nine studies, with 11 cohorts were analyzed. The summary sensitivities and specificities values were 0.78 (95% confidence interval [CI], 0.69-0.84) and 0.79 (95% CI, 0.68-0.86) for ≥ S1, 0.85 (95% CI, 0.74-0.92) and 0.79 (95% CI, 0.71-0.85) for ≥ S2, and 0.83 (95% CI, 0.76-0.89) and 0.79 (95% CI, 0.68-0.87) for ≥ S3. The HSROCs were 0.85 (95% CI, 0.81-88) for ≥ S1, 0.88 (95% CI, 0.85-0.91) for ≥ S2, and 0.87 (95% CI, 0.84-0.90) for ≥ S3. Following a "positive" measurement (over the threshold value) for ≥ S1, ≥ S2, and ≥ S3, the corresponding post-test probabilities for the presence of steatosis (pretest probability was 50%) were 78%, 80% and 80%, respectively; if the values were below these thresholds ("negative" results), the post-test probabilities were 22%, 16%, and 17%, respectively. CONCLUSIONS: CAP has good sensitivity and specificity for detecting hepatic steatosis; however, based on a meta-analysis, CAP was limited in their accuracy of steatosis, which precluded widespread use in clinical practice.

Possible formation of mitochondrial-RNA containing chimeric or trimeric RNA implies a post-transcriptional and post-splicing mechanism for RNA fusion.

Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs. We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. In some trimeric ESTs, the downstream partner was fused to the poly-A tail of the upstream partner, which, together with the mtRNA-nRNA fusions, suggests a possible new mechanism for RNA fusion that occurs after both transcription and splicing have been terminated, and possibly outside the nucleus, in contrast to the two current hypothetical mechanisms, trans-splicing and transcriptional-slippage, that occur in the nucleus. The mt-sequences in the mtRNA-nRNA fusions had pseudogenes in the nucleus but, surprisingly, localized mainly in chromosomes 1 and 5. In some mtRNA-nRNA fusions, as well as in some ESTs that were derived only from mtRNA, the mt-sequences might be cis- or trans-spliced. Actually, we cloned a new cis-spliced mtRNA, coined as 16SrRNA-s. Hence, mtDNA may not always be intron-less. Fusion of three or more RNAs to one, fusion of nRNA to mtRNA, and cis- or trans-splicing of mtRNA should all enlarge the cellular RNA repertoire, in turn enlarging the cellular functions. Therefore, future experimental verification of the existence of these novel classes of fusion RNAs and spliced mtRNAs in human cells should significantly advance our understanding of biology and medicine.

[Polymorphs of clopidogrel bisulfate].

This paper is to report the polymorphism of raw materials of clopidogrel bisulfate at home and abroad. By the analysis of Fourier transform infrared spectroscopy (FTIR) and powder X-ray diffraction (p-XRD), samples are roughly classified into two groups, except one patent material. And the differential scanning calorimeter (DSC) examination showed more detailed information for these materials. The results of the study could provide comprehensive basis for the quality evaluation of clopidogrel bisulfate.

Meta-analysis of the association between a polymorphism in microRNA-196a2 and susceptibility to colorectal cancer.

BACKGROUND/AIMS: To accurately evaluate the impact of the C/T polymorphism in microRNA (miRNA)-196a2 on the colorectal cancer (CRC) risk, by meta-analysis. METHODS: An electronic search for articles was conducted in PubMed, EMBASE, ISI Web of Science, and the Cochrane Library. The pooled odds ratio (OR) and its 95% confidence interval (CI) were used to assess the association through meta-analysis. RESULTS: 5 studies were used for analysis. The results showed a significant association between the miRNA-196a2 C/T polymorphism and CRC risk in the genetic models (C vs. T: OR = 1.168, 95% CI = 1.106-1.282, p = 0.001; CC vs. TT: OR = 1.368, 95% CI = 1.132-1.654, p = 0.001; TC/CC vs. TT: OR = 1.206, 95% = CI 1.035-1.405, p = 0.016; CC vs. TC/TT: OR = 1.254, 95% CI = 1.077-1.461, p = 0.004), with the exception of the TC-versus-TT model (TC vs. TT: OR = 1.130, 95% CI = 0.961-1.329, p = 0.138). In a subgroup analysis based on ethnicity, we identified a significant overrepresentation of the polymorphism in individuals of Asian ethnicity. CONCLUSION: This meta-analysis indicates a significant association between the miRNA-196a2 polymorphism and CRC risk.

Cyclin-dependent kinase 4 may be expressed as multiple proteins and have functions that are independent of binding to CCND and RB and occur at the S and G 2/M phases of the cell cycle.

Cyclin-dependent kinase 4 (CDK4) is known to be a 33 kD protein that drives G 1 phase progression of the cell cycle by binding to a CCND protein to phosphorylate RB proteins. Using different CDK4 antibodies in western blot, we detected 2 groups of proteins around 40 and 33 kD, respectively, in human and mouse cells; each group often appeared as a duplet or triplet of bands. Some CDK4 shRNAs could decrease the 33 kD wild-type (wt) CDK4 but increase some 40 kD proteins, whereas some other shRNAs had the opposite effects. Liquid chromatography-mass spectrometry/mass spectrometry analysis confirmed the existence of CDK4 isoforms smaller than 33 kD but failed to identify CDK4 at 40 kD. We cloned one CDK4 mRNA variant that lacks exon 2 and encodes a 26 kD protein without the first 74 amino acids of the wt CDK4, thus lacking the ATP binding sequence and the PISTVRE domain required for binding to CCND. Co-IP assay confirmed that this ΔE2 protein lost CCND1- and RB1-binding ability. Moreover, we found, surprisingly, that the wt CDK4 and the ΔE2 could inhibit G 1-S progression, accelerate S-G 2/M progression, and enhance or delay apoptosis in a cell line-specific manner in a situation where the cells were treated with a CDK4 inhibitor or the cells were serum-starved and then replenished. Hence, CDK4 seems to be expressed as multiple proteins that react differently to different CDK4 antibodies, respond differently to different shRNAs, and, in some situations, have previously unrecognized functions at the S-G 2/M phases of the cell cycle via mechanisms independent of binding to CCND and RB.

Capture, enrichment, and mass spectrometric detection of low-molecular-weight biomarkers with nanoporous silicon microparticles.

Mining the disease information contained in the low-molecular-weight range of a proteomic profile is becoming of increasing interest in cancer research. This work evaluates the ability of nanoporous silicon microparticles (NPSMPs) to capture, enrich, protect, and detect low-molecular-weight peptides (LMWPs) sieved from a pool of highly abundant plasma proteins. The average pore size and porosity of NPSMPs are controlled by the electrochemical preparation conditions, and the critical parameters for admission or exclusion of protein with a definite molecular weight are determined by reflectometric-interference Fourier transform spectroscopy (RIFTS). Sodium dodecyl sulfate polyacrylamide-gel electrophoresis (SDS-PAGE) and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) analysis of the proteins captured by the NPSMPs show that the chemical nature of the NPSMPs surface and the solution pH also play vital roles in determining the affinity of NPSMPs for target analytes. It is found that carboxyl-terminated porous microparticles with a porosity of 26% (pore diameter around 9.0 nm) specifically fractionate, enrich and protect LMWPs sieved from either simulated samples or human serum samples. Moreover, NPSMPs containing captured peptides can be directly spotted onto a MALDI plate. When placed in a conventional MALDI matrix, laser irradiation of the particles results in the release of the target peptides confined in the nanopores, which are then ionized and detected in the MALDI experiment. As a proof-of-principle test case, mass spectra of NPSMPs prepared using serum from colorectal cancer patients and from control patients can be clearly distinguished by statistical analysis. The work demonstrates the utility of the method for discovery of biomarkers in the untapped LMWP fraction of human serum, which can be of significant value in the early diagnosis and management of diseases.