RankCompV3: a differential expression analysis algorithm based on relative expression orderings and applications in single-cell RNA transcriptomics.

BACKGROUND: Effective identification of differentially expressed genes (DEGs) has been challenging for single-cell RNA sequencing (scRNA-seq) profiles. Many existing algorithms have high false positive rates (FPRs) and often fail to identify weak biological signals. RESULTS: We present a novel method for identifying DEGs in scRNA-seq data called RankCompV3. It is based on the comparison of relative expression orderings (REOs) of gene pairs which are determined by comparing the expression levels of a pair of genes in a set of single-cell profiles. The numbers of genes with consistently higher or lower expression levels than the gene of interest are counted in two groups in comparison, respectively, and the result is tabulated in a 3 × 3 contingency table which is tested by McCullagh's method to determine if the gene is dysregulated. In both simulated and real scRNA-seq data, RankCompV3 tightly controlled the FPR and demonstrated high accuracy, outperforming 11 other common single-cell DEG detection algorithms. Analysis with either regular single-cell or synthetic pseudo-bulk profiles produced highly concordant DEGs with the ground-truth. In addition, RankCompV3 demonstrates higher sensitivity to weak biological signals than other methods. The algorithm was implemented using Julia and can be called in R. The source code is available at https://github.com/pathint/RankCompV3.jl . CONCLUSIONS: The REOs-based algorithm is a valuable tool for analyzing single-cell RNA profiles and identifying DEGs with high accuracy and sensitivity.

Distinctive p-d Orbital Hybridization in CuSb Porous Nanonetworks for Enhanced Nitrite Electroreduction to Ammonia.

Electrochemical nitrite reduction reaction ( NO 2 - RR ${\mathrm{NO}}_{\mathrm{2}}^{\mathrm{ - }}{\mathrm{RR}}$ ), as a green and sustainable ammonia synthesis technology, has broad application prospects and environmental friendliness. Herein, an unconventional p-d orbital hybridization strategy is reported to realize the fabrication of defect-rich CuSb porous nanonetwork (CuSb PNs) electrocatalyst for NO 2 - RR ${\mathrm{NO}}_{\mathrm{2}}^ - {\mathrm{RR}}$ . The crystalline/amorphous heterophase structure is cleverly introduced into the porous nanonetworks, and this defect-rich structure exposes more atoms and activated boundaries. CuSb PNs exhibit a large NH3 yield ( r N H 3 ${{r}_{{\mathrm{N}}{{{\mathrm{H}}}_{\mathrm{3}}}}}$ ) of 946.1 µg h-1 m cat - 1 ${\mathrm{m}}_{{\mathrm{cat}}}^{ - {\mathrm{1}}}$ and a high faradaic efficiency (FE) of 90.7%. Experimental and theoretical studies indicate that the excellent performance of CuSb PNs results from the defect-rich porous nanonetworks structure and the p-d hybridization of Cu and Sb elements. This work describes a powerful pathway for the fabrication of p-d orbital hybrid defect-rich porous nanonetworks catalysts, and provides hope for solving the problem of nitrogen oxide pollution in the field of environment and energy.

Application of individualized differential expression analysis in human cancer proteome.

Liquid chromatography-mass spectrometry-based quantitative proteomics can measure the expression of thousands of proteins from biological samples and has been increasingly applied in cancer research. Identifying differentially expressed proteins (DEPs) between tumors and normal controls is commonly used to investigate carcinogenesis mechanisms. While differential expression analysis (DEA) at an individual level is desired to identify patient-specific molecular defects for better patient stratification, most statistical DEP analysis methods only identify deregulated proteins at the population level. To date, robust individualized DEA algorithms have been proposed for ribonucleic acid data, but their performance on proteomics data is underexplored. Herein, we performed a systematic evaluation on five individualized DEA algorithms for proteins on cancer proteomic datasets from seven cancer types. Results show that the within-sample relative expression orderings (REOs) of protein pairs in normal tissues were highly stable, providing the basis for individualized DEA for proteins using REOs. Moreover, individualized DEA algorithms achieve higher precision in detecting sample-specific deregulated proteins than population-level methods. To facilitate the utilization of individualized DEA algorithms in proteomics for prognostic biomarker discovery and personalized medicine, we provide Individualized DEP Analysis IDEPAXMBD (XMBD: Xiamen Big Data, a biomedical open software initiative in the National Institute for Data Science in Health and Medicine, Xiamen University, China.) (https://github.com/xmuyulab/IDEPA-XMBD), which is a user-friendly and open-source Python toolkit that integrates individualized DEA algorithms for DEP-associated deregulation pattern recognition.

Effects of pressure on hydrogen diffusion behaviors in MgO.

Hydrogen, as the smallest atom and a key component of water, can penetrate into materials in various forms (e.g., atoms, molecules), which has significant effects on their properties; hence, the diffusion behavior of hydrogen has aroused widespread attention. One of the major compositions in the Earth's interior is MgO. Thus, the diffusion behavior of hydrogen in MgO under high pressure is vital for understanding the water cycle in the Earth's interior. However, the hydrogen diffusion behavior in MgO under high pressure is still poorly understood. Herein, the hydrogen diffusion behaviors in MgO with increasing pressure are systematically investigated in the framework of first-principles methods. Our results show that separated H atoms tend to converge to form H2 molecules, and H2 molecules tend to gather together. The energy barriers of both H and H2 diffusion in MgO increase with pressure. Notably, our results illustrate that hydrogen prefers to diffuse in solid MgO in its molecular state even under high pressure. Furthermore, the attempt frequency of hydrogen in MgO increases with temperature, while it decreases with pressure. This study will deepen our understanding of hydrogen diffusion behavior in MgO under high pressure and provide guidance for studies on particle diffusion in solid materials under extreme conditions.

Perfusion measurement in brain gliomas using velocity-selective arterial spin labeling: comparison with pseudo-continuous arterial spin labeling and dynamic susceptibility contrast MRI.

OBJECTIVES: To evaluate the performance of velocity-selective (VS) ASL among patients with untreated gliomas by comparing with both pseudo-continuous (PC) ASL and dynamic susceptibility contrast-enhanced perfusion-weighted imaging (DSC-PWI). METHODS: Forty-four consecutive patients with newly diagnosed glioma who underwent preoperative perfusion MRI including VSASL, PCASL, and DSC-PWI between 2017 and 2019 were retrospectively evaluated. Visual inspection was performed to evaluate the tumor signal intensity relative to gray matter based on 1-5 score criteria and weighted kappa was used to evaluate the pair-wise concordance between VSASL or PCASL and DSC-PWI. The relative tumor blood flow (rTBF) was measured from sampling intra-tumoral areas of hot-spot on the blood flow map and normalized against the contralateral normal gray matter blood flow. Linear regression and Bland-Altman analyses were performed to evaluate the correlation and agreement of rTBF measurements between ASL methods and DSC-PWI. The ROC analysis was constructed to determine the diagnostic performance of three perfusion methods for grading gliomas. RESULTS: TBF maps derived from VSASL were more comparable with DSC-PWI than PCASL on visual inspection (weighted kappa of 0.90 vs 0.68). In quantitative analysis, VSASL-rTBF yielded higher correlation with the values from DSC-PWI than PCASL-rTBF (R2 = 80% vs 47%, p < 0.001 for both). Both ASL and DSC-derived rTBF showed good distinction between low-grade and high-grade gliomas (p < 0.001). Compared to PCASL, VSASL yielded superior diagnostic sensitivity, specificity, and accuracy in glioma grading. CONCLUSIONS: VSASL showed great promise for accurate quantification of TBF and could potentially improve the diagnostic performance of ASL in preoperative grading of gliomas. KEY POINTS: • VSASL demonstrated a greater agreement with DSC-PWI than with PCASL on visual inspection and perfusion quantification. • VSASL showed a higher diagnostic sensitivity, negative predictive value, and accuracy than PCASL for glioma grading. • With the advantages of insensitivity to transit delay and no need of prescribing a labeling plane, VSASL could potentially improve the diagnostic performance of ASL for a more accurate, noninvasive quantification of TBF in patients with glioma.

Unusual Intramolecular Motion of ReH92- in K2ReH9 Crystal: Circle Dance and Three-Arm Turnstile Mechanisms Revealed by Computational Studies.

The nonahydridorhenate dianion ReH92- is a unique rhenium polyhydride complex due to its remarkably high coordination number; however, its detailed polytopal rearrangement process in either solution or crystal is so far unclear. In this work, our quantum chemical calculations have identified two previously unreported fluxional mechanisms for the ReH92- dianion in the K2ReH9 crystal: three-arm turnstile rotation and circle dance mechanism. These two polytopal rearrangements in the crystal offer an alternative interpretation to the pulse and wide-line NMR spectra (Farrar et al. J. Chem. Phys. 1969, 51, 3595). The previously postulated hindered rotation of the whole ReH92- dianion in K2ReH9 (White et al. J. Chem. Soc., Faraday Trans. 2 1972, 68, 1414) turns out to be a combination of the above-mentioned two elementary fluxional processes. In addition, our calculations have confirmed the Muetterties' D3h⇌C4v rearrangement as the intramolecular motion for the ReH92- dianion in solution.

Neuronal SETD2 activity links microtubule methylation to an anxiety-like phenotype in mice.

Gene discovery efforts in autism spectrum disorder have identified heterozygous defects in chromatin remodeller genes, the 'readers, writers and erasers' of methyl marks on chromatin, as major contributors to this disease. Despite this advance, a convergent aetiology between these defects and aberrant chromatin architecture or gene expression has remained elusive. Recently, data have begun to emerge that chromatin remodellers also function directly on the cytoskeleton. Strongly associated with autism spectrum disorder, the SETD2 histone methyltransferase for example, has now been shown to directly methylate microtubules of the mitotic spindle. However, whether microtubule methylation occurs in post-mitotic cells, for example on the neuronal cytoskeleton, is not known. We found the SETD2 α-tubulin lysine 40 trimethyl mark occurs on microtubules in the brain and in primary neurons in culture, and that the SETD2 C-terminal SRI domain is required for binding and methylation of α-tubulin. A CRISPR knock-in of a pathogenic SRI domain mutation (Setd2SRI) that disables microtubule methylation revealed at least one wild-type allele was required in mice for survival, and while viable, heterozygous Setd2SRI/wtmice exhibited an anxiety-like phenotype. Finally, whereas RNA-sequencing (RNA-seq) and chromatin immunoprecipitation-sequencing (ChIP-seq) showed no concomitant changes in chromatin methylation or gene expression in Setd2SRI/wtmice, primary neurons exhibited structural deficits in axon length and dendritic arborization. These data provide the first demonstration that microtubules of neurons are methylated, and reveals a heterozygous chromatin remodeller defect that specifically disables microtubule methylation is sufficient to drive an autism-associated phenotype.

The magnetic properties of pressurized CsV3Sb5 calculated by using a hybrid functional.

Based on the hybrid functional, we find that at 0 GPa, pristine CsV3Sb5 has a magnetic moment of 0.28 µB per vanadium atom, which is suppressed at a pressure of 2.5 GPa resulting in a spin-crossover. Since the ground state of CsV3Sb5 with charge density wave (CDW) distortion is a non-magnetic state, the magnetic moment of V atoms in pristine CsV3Sb5 will be suppressed by the temperature-induced CDW transition at 94 K. The schematic evolution of magnetic moments as functions of pressure and temperature is presented. At low temperature, CsV3Sb5 is a rare example of materials hosting a pressure-induced magnetic moment, and we suggest that the effects of magnetic moments of V atoms should be considered for understanding its properties.

Proteogenomics connects somatic mutations to signalling in breast cancer.

Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. Here we describe quantitative mass-spectrometry-based proteomic and phosphoproteomic analyses of 105 genomically annotated breast cancers, of which 77 provided high-quality data. Integrated analyses provided insights into the somatic cancer genome including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. Interrogation of the 5q trans-effects against the Library of Integrated Network-based Cellular Signatures, connected loss of CETN3 and SKP1 to elevated expression of epidermal growth factor receptor (EGFR), and SKP1 loss also to increased SRC tyrosine kinase. Global proteomic data confirmed a stromal-enriched group of proteins in addition to basal and luminal clusters, and pathway analysis of the phosphoproteome identified a G-protein-coupled receptor cluster that was not readily identified at the mRNA level. In addition to ERBB2, other amplicon-associated highly phosphorylated kinases were identified, including CDK12, PAK1, PTK2, RIPK2 and TLK2. We demonstrate that proteogenomic analysis of breast cancer elucidates the functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies therapeutic targets.

A rank-based algorithm of differential expression analysis for small cell line data with statistical control.

To detect differentially expressed genes (DEGs) in small-scale cell line experiments, usually with only two or three technical replicates for each state, the commonly used statistical methods such as significance analysis of microarrays (SAM), limma and RankProd (RP) lack statistical power, while the fold change method lacks any statistical control. In this study, we demonstrated that the within-sample relative expression orderings (REOs) of gene pairs were highly stable among technical replicates of a cell line but often widely disrupted after certain treatments such like gene knockdown, gene transfection and drug treatment. Based on this finding, we customized the RankComp algorithm, previously designed for individualized differential expression analysis through REO comparison, to identify DEGs with certain statistical control for small-scale cell line data. In both simulated and real data, the new algorithm, named CellComp, exhibited high precision with much higher sensitivity than the original RankComp, SAM, limma and RP methods. Therefore, CellComp provides an efficient tool for analyzing small-scale cell line data.

Link synthetic lethality to drug sensitivity of cancer cells.

Synthetic lethal (SL) interactions occur when alterations in two genes lead to cell death but alteration in only one of them is not lethal. SL interactions provide a new strategy for molecular-targeted cancer therapy. Currently, there are few drugs targeting SL interactions that entered into clinical trials. Therefore, it is necessary to investigate the link between SL interactions and drug sensitivity of cancer cells systematically for drug development purpose. We identified SL interactions by integrating the high-throughput data from The Cancer Genome Atlas, small hairpin RNA data and genetic interactions of yeast. By integrating SL interactions from other studies, we tested whether the SL pairs that consist of drug target genes and the genes with genomic alterations are related with drug sensitivity of cancer cells. We found that only 6.26%∼34.61% of SL interactions showed the expected significant drug sensitivity using the pooled cancer cell line data from different tissues, but the proportion increased significantly to approximately 90% using the cancer cell line data for each specific tissue. From an independent pharmacogenomics data of 41 breast cancer cell lines, we found three SL interactions (ABL1-IFI16, ABL1-SLC50A1 and ABL1-SYT11) showed significantly better prognosis for the patients with both genes being altered than the patients with only one gene being altered, which partially supports the SL effect between the gene pairs. Our study not only provides a new way for unraveling the complex mechanisms of drug sensitivity but also suggests numerous potentially important drug targets for cancer therapy.

Spin-crossover induced ferromagnetism and layer stacking-order change in pressurized 2D antiferromagnet MnPS3.

Spin-crossover combined with metal-insulator transition and superconductivity has been found in 2D transition-metal phosphorous trichalcogenides when tuning them by high pressure. Simulation of such intriguing spin-crossover behaviors is crucial to understanding the mechanism. The Hubbard U correction is widely used to describe the strong on-site Coulomb interaction in the d electrons of transition-metal compounds, while the U values are sensitive to the crystal field and spin state varying greatly with pressure. In this work, we show that taking MnPS3 as an example and based on a uniform parameter set, the hybrid functional calculations give a spin-crossover pressure of 35 GPa consistent with experimental observation (30 GPa), which is less than half of the existing reported value (63 GPa) using the Hubbard U correction. Notably, we find a spin-crossover induced transition from an antiferromagnetic semiconductor with monoclinic stacking-order to a ferromagnetic semiconductor with rhombohedral stacking-order, and the ferromagnetism originates from the partially occupied t2g orbitals. Different from previous understanding, the Mott metal-insulator transition of MnPS3 does not occur simultaneously with the spin-crossover but in a pressurized low-spin phase.

The RNA polymerase III repressor MAF1 is regulated by ubiquitin-dependent proteasome degradation and modulates cancer drug resistance and apoptosis.

MAF1 homolog, negative regulator of RNA polymerase III (MAF1) is a key repressor of RNA polymerase (pol) III-dependent transcription and functions as a tumor suppressor. Its expression is frequently down-regulated in primary human hepatocellular carcinomas (HCCs). However, this reduction in MAF1 protein levels does not correlate with its transcript levels, indicating that MAF1 is regulated post-transcriptionally. Here, we demonstrate that MAF1 is a labile protein whose levels are regulated through the ubiquitin-dependent proteasome pathway. We found that MAF1 ubiquitination is enhanced upon mTOR complex 1 (TORC1)-mediated phosphorylation at Ser-75. Moreover, we observed that the E3 ubiquitin ligase cullin 2 (CUL2) critically regulates MAF1 ubiquitination and controls its stability and subsequent RNA pol III-dependent transcription. Analysis of the phenotypic consequences of modulating either CUL2 or MAF1 protein expression revealed changes in actin cytoskeleton reorganization and altered sensitivity to doxorubicin-induced apoptosis. Repression of RNA pol III-dependent transcription by chemical inhibition or knockdown of BRF1 RNA pol III transcription initiation factor subunit (BRF1) enhanced HCC cell sensitivity to doxorubicin, suggesting that MAF1 regulates doxorubicin resistance in HCC by controlling RNA pol III-dependent transcription. Together, our results identify the ubiquitin proteasome pathway and CUL2 as important regulators of MAF1 levels. They suggest that decreases in MAF1 protein underlie chemoresistance in HCC and perhaps other cancers and point to an important role for MAF1 and RNA pol III-mediated transcription in chemosensitivity and apoptosis.

Qualitative transcriptional signature for predicting pathological response of colorectal cancer to FOLFOX therapy.

FOLFOX (5-fluorouracil, leucovorin and oxaliplatin) is one of the main chemotherapy regimens for colorectal cancer (CRC), but only half of CRC patients respond to this regimen. Using gene expression profiles of 96 metastatic CRC patients treated with FOLFOX, we first selected gene pairs whose within-sample relative expression orderings (REO) were significantly associated with the response to FOLFOX using the exact binomial test. Then, from these gene pairs, we applied an optimization procedure to obtain a subset that achieved the largest F-score in predicting pathological response of CRC to FOLFOX. The REO-based qualitative transcriptional signature, consisting of five gene pairs, was developed in the training dataset consisting of 96 samples with an F-score of 0.90. In an independent test dataset consisting of 25 samples with the response information, an F-score of 0.82 was obtained. In three other independent survival datasets, the predicted responders showed significantly better progression-free survival than the predicted non-responders. In addition, the signature showed a better predictive performance than two published FOLFOX signatures across different datasets and is more suitable for CRC patients treated with FOLFOX than 5-fluorouracil-based signatures. In conclusion, the REO-based qualitative transcriptional signature can accurately identify metastatic CRC patients who may benefit from the FOLFOX regimen.

Transcriptional signatures for coupled predictions of stage II and III colorectal cancer metastasis and fluorouracil-based adjuvant chemotherapy benefit.

The current study suggests that the identification of predictive signatures of fluorouracil (5-FU) response for stage II and III colorectal cancer (CRC) could be confounded by chemotherapy-irrelevant low relapse risk. Using the samples of patients with stage II and III CRC who were treated with curative surgery only, we identified a signature with which to predict chemotherapy-irrelevant relapse risk for patients after curative surgery. By applying this signature to the samples of patients with stage II and III CRC who were treated with 5-FU-based adjuvant chemotherapy (ACT) after surgery, we predicted the relapse risk if treated with surgery only. From high-risk samples, we further identified another signature with which to predict therapeutic benefit from 5-FU-based ACT. On the basis of the relative expression orderings of gene pairs, a postsurgery relapse risk signature that consisted of 44 gene pairs was developed and verified in 3 independent data sets. A 5-FU therapeutic benefit signature that consisted of 4 gene pairs was then developed to predict the response of 5-FU-based ACT for those patients with high relapse risk after curative surgery. The signature was verified in 4 independent datasets. For patients with stage II and III CRC, the coupled signatures can first identify patients with high relapse risk after curative surgery, then predict therapeutic benefit from 5-FU-based ACT.-Song, K., Guo, Y., Wang, X., Cai, H., Zheng, W., Li, N., Song, X., Ao, L., Guo, Z., Zhao, W. Transcriptional signatures for coupled predictions of stage II and III colorectal cancer metastasis and fluorouracil-based adjuvant chemotherapy benefit.

Transcriptomic analysis on the effects of melatonin in gastrointestinal carcinomas.

BACKGROUND: Melatonin has been shown with anticancer property and therapeutic potential for tumors. However, there lacks a systematic study on the molecular pathways of melatonin and its antitumor effects in gastrointestinal carcinomas. METHODS: Using the gene expression profiles of four cancer cell lines from three types of gastrointestinal carcinomas before and after melatonin treatment, including gastric carcinoma (GC), colorectal carcinoma (CRC) and hepatocellular carcinoma (HCC), differentially expressed genes (DEGs) and biological pathways influenced by melatonin were identified. The qRT-PCR analyses were performed to validate the effects of melatonin on 5-FU resistance-related genes in CRC. RESULTS: There were 17 pathways commonly altered by melatonin in the three cancer types, including FoxO signaling pathways enriched by the upregulated DEGs and cell cycle signaling pathways enriched by the downregulated DEGs, confirmed the dual role of melatonin to tumor growth, pro-apoptosis and anti-proliferation. DEGs upregulated in the three types of cancer tissues but reversely downregulated by melatonin were commonly enriched in RNA transport, spliceosome and cell cycle signaling pathways, which indicate that melatonin might exert antitumor effects through these pathways. Our results further showed that melatonin can downregulate the expression levels of 5-FU resistance-related genes, such as thymidylate synthase in GC and ATR, CHEK1, BAX and MYC in CRC. The qRT-PCR results demonstrated that melatonin enhanced the sensitivity of CRC 5-FU resistant cells by decreasing the expression of ATR. CONCLUSIONS: Melatonin exerts the effects of pro-apoptosis and anti-proliferation on gastrointestinal carcinomas, and might increase the sensitivity of 5-FU in GC and CRC patients.

Comparison of outcomes in intrauterine insemination, in vitro fertilisation and intracytoplasmic sperm injection in men with and without varicocele.

Objectives: To investigate the differences in clinical pregnancy, miscarriage, and live birth rates when male partners were diagnosed with a varicocele and to compare these outcomes to those without and study the outcomes based on the grade of varicocele. Methods: The retrospective study was based on a cohort of consecutive infertile couples undergoing assisted reproductive technology (ART) at the Reproductive Center of Shandong Provincial Hospital affiliated to the Shandong University during the period between January 2017 and December 2018. A total of 4203 couples comprised of men with and without varicocele undergoing the first ART cycle (1501 intrauterine inseminations (IUI), 1623 in vitro fertilisations (IVF) and 1079 intracytoplasmic sperm injections (ICSI)) were included. Semen parameters and ART outcomes were determined. Results: ICSI (26.5%) originated from men with a significant lower level in sperm concentration and motility but with a strict normal morphology had a higher prevalence of varicocele than men undergoing IUI (20.7%) and IVF (18.1%). In IUI, the odds ratios (ORs) for pregnancy and live birth were significantly lower for couples in men diagnosed with grades 1 or 2 varicocele as compared to those for men with grade 3 varicocele. In IVF, ORs for live birth where men were diagnosed with grades 1 or 2 varicocele were also lower than those for men with grade 3,whereas a higher miscarriage rate was found when men had grades 1 or 2 varicocele than when men had grade 3. However, for ICSI, no significant outcomes were found in grades 1, 2 or 3 varicocele versus the no varicocele group. Conclusions: The increasing grade of varicocele was negatively associated with sperm parameters and can alter the outcome of further IUI/IVF.

Possible misdiagnosis of 46,XX testicular disorders of sex development in infertile males.

Objectives: The 46,XX disorders of sex development (DSD) is a rare genetic cause of male infertility and possible misdiagnosis of this condition has never been reported. We aim to investigate clinical characteristics and laboratory results of infertile males with possibly misdiagnosed 46,XX DSD. Methods: Between January 2008 and December 2017, a retrospective case series study was performed involving sixteen 46,XX DSD males without azoospermia factor (AZF) deletion. Demographics, clinical features, laboratory results and assisted reproductive technology (ART) outcomes of these patients were depicted, and the underlying accurate diagnosis was also discussed. Results: The mean age was 30.06 ± 5.40 years old. Thirteen patients (81.25%) merely obtained secondary school education. Gynaecomastia occurred in one case, and cryptorchidism appeared in two cases. Testicular volumes were equal to 15 mL on two sides in one patient who had severe asthenozoospermia. Thirteen patients (81.25%) had bilateral atrophic testes which were below 5 mL. The majority of patients were observed with elevated levels of gonadotropic hormones and decreased testosterone values. Neither AZF region nor sex-determining region Y gene was absent among all patients. Twelve patients had normal ejaculatory function, whereas four were diagnosed with ejaculatory dysfunction. Eleven patients (68.75%) were diagnosed with azoospermia. Testicular sperm aspiration was performed in six subjects (37.50%). The pathological results showed that Leydig cell hyperplasia with spermatic failure was found in each case, and no sperm was found in testicular tissue. ART with donor sperm was conducted in 15 patients. Live birth was achieved in three cases through artificial insemination by donor and in one case using in-vitro fertilization by donor. Conclusions: Chromosomal analysis rarely yields 46,XX karyotype combined with no deletion of AZF in infertile males. Under this condition, molecular analysis should be conducted to avoid potential misdiagnosis and false interpretation of other findings.

Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes.

BACKGROUND: The amount of RNA per cell, namely the transcriptome size, may vary under many biological conditions including tumor. If the transcriptome size of two cells is different, direct comparison of the expression measurements on the same amount of total RNA for two samples can only identify genes with changes in the relative mRNA abundances, i.e., cellular mRNA concentration, rather than genes with changes in the absolute mRNA abundances. RESULTS: Our recently proposed RankCompV2 algorithm identify differentially expressed genes (DEGs) through comparing the relative expression orderings (REOs) of disease samples with that of normal samples. We reasoned that both the mRNA concentration and the absolute abundances of these DEGs must have changes in disease samples. In simulation experiments, this method showed excellent performance for identifying DEGs between normal and disease samples with different transcriptome sizes. Through analyzing data for ten cancer types, we found that a significantly higher proportion of the DEGs with absolute mRNA abundance changes overlapped or directly interacted with known cancer driver genes and anti-cancer drug targets than that of the DEGs only with mRNA concentration changes alone identified by the traditional methods. The DEGs with increased absolute mRNA abundances were enriched in DNA damage-related pathways, while DEGs with decreased absolute mRNA abundances were enriched in immune and metabolism associated pathways. CONCLUSIONS: Both the mRNA concentration and the absolute abundances of the DEGs identified through REOs comparison change in disease samples in comparison with normal samples. In cancers these genes might play more important upstream roles in carcinogenesis.

Thyroid hormone regulates hematopoiesis via the TR-KLF9 axis.

Congenital hypothyroidism (CH) is one of the most prevalent endocrine diseases, for which the underlying mechanisms remain unknown; it is often accompanied by anemia and immunodeficiency in patients. Here, we created a severe CH model together with anemia and T lymphopenia to mimic the clinical features of hypothyroid patients by ethylnitrosourea (ENU) mutagenesis in Bama miniature pigs. A novel recessive c.1226A>G transition of the dual oxidase 2 (DUOX2) gene was identified as the causative mutation. This mutation hindered the production of hydrogen peroxide (H2O2) and thus contributed to thyroid hormone (TH) synthesis failure. Transcriptome sequencing analysis of the thymuses showed that Krüppel-like factor 9 (KLF9) was predominantly downregulated in hypothyroid mutants. KLF9 was verified to be directly regulated by TH in a TH receptor (TR)-dependent manner both in vivo and in vitro. Furthermore, knockdown of klf9 in zebrafish embryos impaired hematopoietic development including erythroid maturation and T lymphopoiesis. Our findings suggest that the TR-KLF9 axis is responsible for the hematopoietic dysfunction and might be exploited for the development of novel therapeutic interventions for thyroid diseases.