THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration.

The mechanisms by which the relatively conserved spliceosome manages the enormously large number of splicing events that occur in humans (∼200 000 versus ∼300 in yeast) are poorly understood. Here, we show deposition of one RNA modification-N2-methylguanosine (m2G) on the G72 of U6 snRNA (the catalytic center of the spliceosome) promotes efficient pre-mRNA splicing activity in human cells. This modification was identified to be conserved among vertebrates. Further, THUMPD2 was demonstrated as the methyltransferase responsible for U6 m2G72 by explicitly recognizing the U6-specific sequences and structural elements. The knock-out of THUMPD2 eliminated U6 m2G72 and impaired the pre-mRNA splicing activity, resulting in thousands of changed alternative splicing events of endogenous pre-mRNAs in human cells. Notably, the aberrantly spliced pre-mRNA population elicited the nonsense-mediated mRNA decay pathway. We further show that THUMPD2 was associated with age-related macular degeneration and retinal function. Our study thus demonstrates how an RNA epigenetic modification of the major spliceosome regulates global pre-mRNA splicing and impacts physiology and disease.

Targeted therapy for intractable cancer on the basis of molecular profiles: An open-label, phase II basket trial (Long March Pathway).

Purpose: We evaluated he effects of molecular guided-targeted therapy for intractable cancer. Also, the epidemiology of druggable gene alterations in Chinese population was investigated. Materials and methods: The Long March Pathway (ClinicalTrials.gov identifier: NCT03239015) is a non-randomized, open-label, phase II trial consisting of several basket studies examining the molecular profiles of intractable cancers in the Chinese population. The trial aimed to 1) evaluate the efficacy of targeted therapy for intractable cancer and 2) identify the molecular epidemiology of the tier II gene alterations among Chinese pan-cancer patients. Results: In the first stage, molecular profiles of 520 intractable pan-cancer patients were identified, and 115 patients were identified to have tier II gene alterations. Then, 27 of these 115 patients received targeted therapy based on molecular profiles. The overall response rate (ORR) was 29.6% (8/27), and the disease control rate (DCR) was 44.4% (12/27). The median duration of response (DOR) was 4.80 months (95% CI, 3.33-27.2), and median progression-free survival (PFS) was 4.67 months (95% CI, 2.33-9.50). In the second stage, molecular epidemiology of 17,841 Chinese pan-cancer patients demonstrated that the frequency of tier II gene alterations across cancer types is 17.7%. Bladder cancer had the most tier-II alterations (26.1%), followed by breast cancer (22.4%), and non-small cell lung cancer (NSCLC; 20.2%). Conclusion: The Long March Pathway trial demonstrated a significant clinical benefit for intractable cancer from molecular-guided targeted therapy in the Chinese population. The frequency of tier II gene alterations across cancer types supports the feasibility of molecular-guided targeted therapy under basket trials.

Boosting Hydrogen Evolution Electrocatalysis via Regulating the Electronic Structure in a Crystalline-Amorphous CoP/CeOx p-n Heterojunction.

The modulation of the electronic structure is the effective access to achieve highly active electrocatalysts for the hydrogen evolution reaction (HER). Transition-metal phosphide-based heterostructures are very promising in enhancing HER performance but the facile fabrication and an in-depth study of the catalytic mechanisms still remain a challenge. In this work, the catalytically inactive n-type CeOx is successfully combined with p-type CoP to form the CoP/CeOx heterojunction. The crystalline-amorphous CoP/CeOx heterojunction is fabricated by the phosphorization of predesigned Co(OH)2/CeOx via the as-developed reduction-hydrolysis strategy. The p-n CoP/CeOx heterojunction with a strong built-in potential of 1.38 V enables the regulation of the electronic structure of active CoP within the space-charge region to enhance its intrinsic activity and facilitate the electron transfer. The functional CeOx entity and the negatively charged CoP can promote the water dissociation and optimize H adsorption, synergistically boosting the electrocatalytic HER output. As expected, the heterostructured CoP/CeOx-20:1 with the optimal ratio of Co/Ce shows significantly improved HER activity and favorable kinetics (overpotential of 118 mV at a current density of 10 mA cm-2 and Tafel slope of 77.26 mV dec-1). The present study may provide new insight into the integration of crystalline and amorphous entities into the p-n heterojunction as a highly efficient electrocatalyst for energy storage and conversion.

THUMPD3-TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates.

Post-transcriptional modifications affect tRNA biology and are closely associated with human diseases. However, progress on the functional analysis of tRNA modifications in metazoans has been slow because of the difficulty in identifying modifying enzymes. For example, the biogenesis and function of the prevalent N2-methylguanosine (m2G) at the sixth position of tRNAs in eukaryotes has long remained enigmatic. Herein, using a reverse genetics approach coupled with RNA-mass spectrometry, we identified that THUMP domain-containing protein 3 (THUMPD3) is responsible for tRNA: m2G6 formation in human cells. However, THUMPD3 alone could not modify tRNAs. Instead, multifunctional methyltransferase subunit TRM112-like protein (TRMT112) interacts with THUMPD3 to activate its methyltransferase activity. In the in vitro enzymatic assay system, THUMPD3-TRMT112 could methylate all the 26 tested G6-containing human cytoplasmic tRNAs by recognizing the characteristic 3'-CCA of mature tRNAs. We also showed that m2G7 of tRNATrp was introduced by THUMPD3-TRMT112. Furthermore, THUMPD3 is widely expressed in mouse tissues, with an extremely high level in the testis. THUMPD3-knockout cells exhibited impaired global protein synthesis and reduced growth. Our data highlight the significance of the tRNA: m2G6/7 modification and pave a way for further studies of the role of m2G in sperm tRNA derived fragments.

Serum tumor markers for the prediction of concordance between genomic profiles from liquid and tissue biopsy in patients with advanced lung adenocarcinoma.

BACKGROUND: The concordance between mutations detected from plasma and tissue is critical for treatment choices of patients with advanced lung adenocarcinoma. METHODS: We prospectively analyzed the association of the serum tumor markers with the concordance between blood and tissue genomic profiles from 185 patients with advanced lung adenocarcinoma. The concordance was defined according to 3 criteria. Class 1 included all targetable driver mutations in 8 genes; class 2 included class 1 mutations plus mutations in KRAS, STK11, and TP53; class 3 included class 2 mutations plus tumor mutation burden (TMB) status. RESULTS: Collectively, 150 out of 185 patients had mutations in both tissue and plasma samples, while one patient was mutation-negative for both, resulting a concordance of 81.6%. The concordance rate for class 1 mutations was 80%, and 65% and 69% for class 2 and class 3, respectively. Carbohydrate antigen 19-9 (CA19-9) or cytokeratin 19 (CYFRA21-1) levels higher than the normal upper limit predicted the concordance of tissue and blood results in class 1 (P=0.005, P=0.011), class 2 (P=0.011, P<0.001), and class 3 (P=0.001, P=0.014). In class 1, the cutoff values of CA19-9 were 30, 36, and 284 U/mL to reach the concordance thresholds of 90%, 95%, and 100%, respectively (P=0.032, P=0.003, P=0.043). For CYFRA21-1, the cutoff values were 6, 18, and 52 µg/L (P=0.005, P=0.051, P=0.354). In class 2, the cutoff values for CYFRA21-1 were 18, 22, and 52 µg/L (P=0.001, P=0.001, P=0.052). In class 3, the cutoff values for CA19-9 were 36, 39, and 85 U/mL (P=0.003, P=0.001, P=0.008). For CYFRA21-1, the cutoff values were 22, 52, and 52 µg/L (P=0.900, P>0.99, P>0.99). When the sum score for 4 serum tumor markers was greater than 35, both class 1, class 2, and class 3 reached a predictive threshold of 90%. CONCLUSIONS: Serum tumor markers can be used as easy and practical clinical predictors of concordance in mutation profiles between blood and tissue samples from patients with advanced lung adenocarcinoma.

The occurrence order and cross-talk of different tRNA modifications.

Chemical modifications expand the composition of RNA molecules from four standard nucleosides to over 160 modified nucleosides, which greatly increase the complexity and utility of RNAs. Transfer RNAs (tRNAs) are the most heavily modified cellular RNA molecules and contain the largest variety of modifications. Modification of tRNAs is pivotal for protein synthesis and also precisely regulates the noncanonical functions of tRNAs. Defects in tRNA modifications lead to numerous human diseases. Up to now, more than 100 types of modifications have been found in tRNAs. Intriguingly, some modifications occur widely on all tRNAs, while others only occur on a subgroup of tRNAs or even only a specific tRNA. The modification frequency of each tRNA is approximately 7% to 25%, with 5-20 modification sites present on each tRNA. The occurrence and modulation of tRNA modifications are specifically noticeable as plenty of interplays among different sites and modifications have been discovered. In particular, tRNA modifications are responsive to environmental changes, indicating their dynamic and highly organized nature. In this review, we summarized the known occurrence order, cross-talk, and cooperativity of tRNA modifications.

Injectable Magnesium-Zinc Alloy Containing Hydrogel Complex for Bone Regeneration.

Gelatin methacryloyl (GelMA) has been widely used in bone engineering. It can also be filled into the calvarial defects with irregular shape. However, lack of osteoinductive capacity limits its potential as a candidate repair material for calvarial defects. In this study, we developed an injectable magnesium-zinc alloy containing hydrogel complex (Mg-IHC), in which the alloy was fabricated in an atomization process and had small sphere, regular shape, and good fluidity. Mg-IHC can be injected and plastically shaped. After cross-linking, it contents the elastic modulus similar to GelMA, and has inner holes suitable for nutrient transportation. Furthermore, Mg-IHC showed promising biocompatibility according to our evaluations of its cell adhesion, growth status, and proliferating activity. The results of alkaline phosphatase (ALP) activity, ALP staining, alizarin red staining, and real-time polymerase chain reaction (PCR) further indicated that Mg-IHC could significantly promote the osteogenic differentiation of MC3T3-E1 cells and upregulate the genetic expression of collagen I (COL-I), osteocalcin (OCN), and runt-related transcription factor 2 (RUNX2). Finally, after applied to a mouse model of critical-sized calvarial defect, Mg-IHC remarkably enhanced bone formation at the defect site. All of these results suggest that Mg-IHC can promote bone regeneration and can be potentially considered as a candidate for calvarial defect repairing.

A Systematic Inflammation-based Model in Advanced Pancreatic Ductal Adenocarcinoma.

Emerging evidence revealed the critical role of systematic inflammation in pancreatic ductal adenocarcinoma (PDAC). In the present study, we reviewed the records of 279 patients with advanced PDAC. Among them, 147 cases were used as the training cohort and another 132 as the validation cohort. In the training cohort, distant metastasis, carbohydrate antigen 19-9 (CA19-9), Glasgow prognostic score (GPS), neutrophil-to-lymphocyte ratio (NLR), and lymphocyte-to-monocyte ratio (LMR) were independent prognostic factors in Cox regression. A nomogram based on these factors was generated to predict median survival time and survival probabilities at 6, 12, and 18 months. The nomogram showed a better discriminatory ability than the American Joint Committee on Cancer (AJCC) TNM staging (C-index: 0.727 vs. 0.610). In the validation cohort, a nomogram composed of the same variables also showed a high discriminatory ability (C-index: 0.784). In the low-risk group with a nomogram total point (NTP) value of more than 175, patients receiving combination therapy showed better prognosis than those receiving monotherapy (P=0.015). In conclusion, the nomogram based on inflammatory biomarkers can serve as useful prognostic tool for advanced PDAC. In addition, patients with high NTP can greater benefit from combination chemotherapy than monotherapy.

Routine Hemostasis and Hemogram Parameters: Valuable Assessments for Coagulation Disorder and Chemotherapy in Cancer Patients.

BACKGROUND: The clotting system abnormalities are the common complication in cancer patients. The aim of this retrospective study was to evaluate the coagulation state, clinical features, and treatment in cancer patients by routine tests. METHODS: A total of 2328 patients with different types of cancer were classified as the positive group (n = 1419, including 53 patients with thrombosis) and the negative group (n = 909) based on D-dimer (DD) value. Of the 2328 cases, 354 were admitted for chemotherapy. Hemostasis test and complete blood count (CBC) were performed during treatment or following-up. RESULTS: This study showed that the hypercoagulable state was affected not only by clinical staging (P < 0.0001) but also by metastasis site (P < 0.0001 for bone vs. lung). Compared to negative DD group, the higher fibrinogen level, the extended activated partial thromboplastin time, and prothrombin time interacted markedly with disease clinical stage (P < 0.05) in the positive group. Between positive DD groups with and without thrombus, the significantly statistic difference in white blood cell (WBC) and DD (P < 0.05) rather than in red blood cell (RBC) and platelet count was observed. However, the higher DD level was not correlated with WBC, RBC, and platelet count in the positive DD group. Furthermore, the hypercoagulable plasma profile in cancer patients was moderated 2-3 weeks after chemotherapy (P < 0.05 for first six cycles). CONCLUSIONS: The routine hemostatic parameters and CBC are valuable to assessment for thrombosis and chemotherapy even for disease prognosis.

Size-dependent toxicity and interactions of calcium oxalate dihydrate crystals on Vero renal epithelial cells.

Urinary crystals in normal and kidney stone patients often have varying sizes; the interaction between renal epithelial cells and COD crystals generated in the tubular fluid could play an initiating role in the pathophysiology of calcium oxalate nephrolithiasis. This study aims to compare the cytotoxicity of micro/nano-calcium oxalate dihydrate (COD) crystals (50 nm, 100 nm, 600 nm, 3 µm, and 10 µm) toward African green monkey renal epithelial (Vero) cells to reveal the mechanism of kidney stone formation at the molecular and cellular levels. METHODS: Vero cells were exposed to COD crystals of varying sizes at a concentration of 200 µg mL-1 for 6 h. The effects of COD crystals on Vero cell viability, apoptosis rate, and cellular biochemical parameters [lactate dehydrogenase (LDH), superoxide dismutase (SOD), reactive oxygen species (ROS), hyaluronic acid (HA), osteopontin (OPN), and mitochondrial membrane potential (Δψm)] were determined using biochemical and morphological analyses. RESULTS: Vero cell viability and apoptotic rate were closely associated with the size of COD crystals; lower cell viability and higher apoptosis rate were observed in cells exposed to smaller COD crystal size. The expression of SOD, ROS, HA and OPN also changed in a size-dependent manner after exposure to the five different sizes of COD crystals. The area ratio of the (100) face with a high density of Ca2+ ions to the total surface area was also found to influence the severity of cell injury. Cell injury induced by COD crystals was mainly caused by excessive expression of intracellular ROS and reduction of free-radical scavenger SOD. Moreover, binding of large crystals on the cell membrane surface takes more time to cause cell injury than internalized small-sized crystals. The cell death rate was found to be positively correlated with the amount of internalized COD crystals. CONCLUSIONS: although the COD toxicity is often disregarded, the size-dependent cytotoxicity of COD crystals toward Vero cells is demonstrated in this study.

Inhibition on calcium oxalate crystallization and repair on injured renal epithelial cells of degraded soybean polysaccharide.

This paper investigated the inhibitory effect of degraded soybean polysaccharide (DPS) on the growth of calcium oxalate (CaOxa) crystals. The results were compared with that of soybean polysaccharide without degradation (SPS). The data showed that DPS exhibited a much higher efficiency to inhibit CaOxa growth and stabilize calcium oxalate dihydrate (COD) compared with SPS. As DPS concentration increased, the soluble Ca(2+) ions significantly increased, the aggregation degree of calcium oxalate monohydrate (COM) crystals decreased, the shape of COD crystals became round and blunt, and the Zeta potential on CaOxa crystal surface reduced. The above results were all conducive for the inhibition of CaOxa crystallization. In addition, DPS displayed a distinct repairing effect on oxidative injured renal epithelial cells in African green monkey (Vero), with enhanced cell viability and extracellular superoxide dismutase activity after repair. The morphologies of the repaired cells and their regulatory capability on CaOxa growth were between the control and injured cells. The results indicated that the risk of stone formation can be reduced by DPS, and that DPS may be a potential green drug to prevent the formation of CaOxa stones.

[Establishment of permanent lymphoblastoid cell lines of 47 patients with abnormal chromosome karyotype].

To increase the efficiency of in vitro transformation of human lymphocytes by Epstein-Barr virus (EBV) and establish permanent lymphoblastoid cell lines from patients with abnormal chromosome karyotype, B lymphoid cells were prepared from cryopreserved heparinized blood samples. The lymphoid cell pellet was resuspended with 0.5 ml medium of RPMI with 20% fetal calf serum(FCS), and added 2 ml virus-containing superatant of the EB virus-producing cell lines by filtrated, and mixed. Four 25 cm2 cell culture bottles were put upright. A total of 2.5 ml of RPMI with 20% FCS was put in each of them. The blood-virus mixture was distributed among the four cell culture bottles as follows: Bottle I, Bottle II, Bottle III and Bottle IV were added with 0.3 ml, 0.6 ml, 1.2 ml and the rest respectively. The cells culture bottles were put into the cell culture incubator in an upright position. After 3 days the cells were puting new medium with 20% FCS as follows: Bottle I 3 ml, Bottle II 4 ml, Bottle III 5 ml and Bottle IV 6 ml. After one week, the medium was changed again as described above. The medium change was conducted until the cells grew very fast. The right ratio between blood cells and virus titer can not be exactly determined for every blood sample, and therefore a dilution series with four different blood/virus ratios was set up. Due to the dilution series, addition of immune inhibitors like cyclosporine, was not necessary. Forty-seven permanent lymphoblastoid cell lines of patients with abnormal chromosome karyotype. Transformed cells were found in only one or two of the four cell culture bottles. The total successive rate increased up to 97.87%. Of the four cell culture bottles, Bottle I, Bottle II, Bottle III and Bottle IV, the successive rates were 6.39%, 61.70%, 31.91% and 8.51% respectively. This method can be used for preserving large number of lymphoblastoid cell lines, and also provide enough research materials for further studies.

[Genetic polymorphisms of human short tandem repeat vWA].

We researched the genetic polymorphisms of vWA in Henan population and its usefulness in forensic science.DNA extracted from non-relative persons in Henan population with Chelex was amplified by polymerase chain reaction and was typed by nondenaturing polyacrylamide gel electrophoresis silver staining.A total of 8 alleles and 19 genotypes were found in Henan population,its heterozygosity is high and the locus can be used in forensic genetics. We obtained the allelic frequency of the locus vWA in Henan population. The results of amniotic fluid,villus,blood stain indicate vWA is a good locus for forensic study.

[Genetic polymorphism of six STR loci in the Han population in Henan province].

To investigate the allele frequencies of six short tandem repeats (STR) loci: F13A1, F13B, D8S1179, CSF1PO, D5S818 and TPOX in Han population in Henan province, DNA was extracted with chelex from EDTA-blood samples of the unrelated individuals in Henan province and amplified with PCR technique. The PCR product was analyzed with the undenatured PAGE vertical electrophoresis and silverstain. The results were obtained through genetical analysis. The authors got the number of allele of six loci, Three alleles of F13A1 could be detected in this population. The F13A1 * 7 is the most common allele with a frequency of 45.2%, followed by F13A1 * 5 and F13A1 * 4 respectively. F13B had four alleles among which F13B * 10 has the highest frequency, followed by F13B * 9, F13B * 8, F13B * 11. The 8 alleles of D8S1179 in the order from high to low frequency is D8S1179 * 14, * 15, * 12, * 11, * 10. And the most common frequencies of alleles of CSF1PO, D5S818, TPOX ore CSF1PO * 12, D5S818 * 11, TPOX * 8, respectively followed by the allele of * 11, * 14, * 10, * 13 in CSF1PO locus, and * 12, * 13, * 10, * 9, * 14, * 8, * 15, * 7 in D5S818 locus, * 11, * 9, * 12, * 10 in TPOX locus. The heterozygosities of the six loci were 0.62, 0.46, 0.83, 0.59, 0.78 and 0.65; the discrimination powers were 0.78, 0.66, 0.95, 0.79, 0.92 and 0.82. The heterozygosities of the six loci are high and the frequencies are in good agreement with Hardy-Weinberg equilibrium. The six loci are good as genetic markers. We can use these loci in dividualidentification and partenity test in forensic area.