Integrating spatial and single-cell transcriptomics reveals tumor heterogeneity and intercellular networks in colorectal cancer.

Single cell RNA sequencing (scRNA-seq), a powerful tool for studying the tumor microenvironment (TME), does not preserve/provide spatial information on tissue morphology and cellular interactions. To understand the crosstalk between diverse cellular components in proximity in the TME, we performed scRNA-seq coupled with spatial transcriptomic (ST) assay to profile 41,700 cells from three colorectal cancer (CRC) tumor-normal-blood pairs. Standalone scRNA-seq analyses revealed eight major cell populations, including B cells, T cells, Monocytes, NK cells, Epithelial cells, Fibroblasts, Mast cells, Endothelial cells. After the identification of malignant cells from epithelial cells, we observed seven subtypes of malignant cells that reflect heterogeneous status in tumor, including tumor_CAV1, tumor_ATF3_JUN | FOS, tumor_ZEB2, tumor_VIM, tumor_WSB1, tumor_LXN, and tumor_PGM1. By transferring the cellular annotations obtained by scRNA-seq to ST spots, we annotated four regions in a cryosection from CRC patients, including tumor, stroma, immune infiltration, and colon epithelium regions. Furthermore, we observed intensive intercellular interactions between stroma and tumor regions which were extremely proximal in the cryosection. In particular, one pair of ligands and receptors (C5AR1 and RPS19) was inferred to play key roles in the crosstalk of stroma and tumor regions. For the tumor region, a typical feature of TMSB4X-high expression was identified, which could be a potential marker of CRC. The stroma region was found to be characterized by VIM-high expression, suggesting it fostered a stromal niche in the TME. Collectively, single cell and spatial analysis in our study reveal the tumor heterogeneity and molecular interactions in CRC TME, which provides insights into the mechanisms underlying CRC progression and may contribute to the development of anticancer therapies targeting on non-tumor components, such as the extracellular matrix (ECM) in CRC. The typical genes we identified may facilitate to new molecular subtypes of CRC.

Association of chronic hepatitis B infection with hepatic steatosis and injury in nonalcoholic fatty liver disease children.

BACKGROUND: The influence of chronic hepatitis B infection (CBI) on hepatic steatosis, necroinflammation, and fibrosis in nonalcoholic fatty liver disease (NAFLD) population was unclear. We aimed to investigate the effect of CBI on hepatic steatosis and assess the association between NAFLD co-existed CBI and hepatic injury in NAFLD pediatric population. METHODS: Consecutive hospitalized children with biopsy-proven NAFLD with or without CBI were included. Hepatic steatosis, necroinflammation and fibrosis were evaluated by NASH CRN system and/or METAVIR scoring system, appropriately. Using multivariate logistic analysis, we identified variables associated with hepatic steatosis and liver injury. RESULTS: Of 223 biopsy-proven NAFLD children, 161 were NAFLD without CBI, and 62 were NAFLD co-existed CBI. Grouped by mild, moderate and severe hepatic steatosis, there was an inverse association between CBI and the severity of hepatic steatosis [odd ratio (OR) 0.037, 95% confidence interval (CI) 0.014-0.098]. In addition, we explored the relationship between CBI and hepatic necroinflammation and fibrosis in NAFLD children. Hepatic necroinflammation and fibrosis, respectively, were divided into two groups according to severity. And CBI was positively associated with hepatic necroinflammation (OR 6.125, 95%CI 1.958-19.158). However, there was no statistically independent association between CBI and significant hepatic fibrosis. CONCLUSIONS: CBI was inverse associated with the grade of steatosis and positively associated with severe hepatic necroinflammation, and does not appear to affect significant hepatic fibrosis in pediatric NAFLD children.

Use total portosystemic shunt to rescue an emergency PNF with intractable hypotension: A case report.

RATIONALE: Living donor allogeneic liver transplantation is a surgical treatment for patients with end-stage liver disease, wherein a healthy liver is implanted in the patient, facilitating the recovery of the liver function in patients with end-stage liver disease. However, primary nonfunction (PNF) may occur as a result of this procedure. PATIENT CONCERNS: A case of an 65-year-old Asian male with a medical history of cirrhosis and hepatocellular carcinoma is described. Intractable hypotension occurred after open hepatic portal anastomosis, and large doses of vasoactive substances did not improve the condition. DIAGNOSIS: PNF was diagnosed during surgery and it caused intractable hypotension. INTERVENTIONS: we promptly used the total portosystemic shunt to achieve a successful rescue. OUTCOMES: The strengthening of perioperative management and active treatment allowed second liver transplantation and anhepatic phase of up to 10 hours, following which the patient was rescued. LESSONS: The lesson we have learned is that total portosystemic shunt composited with careful anesthesia management can rescue the event of PNF with intractable hypotension in liver transplantation surgery. At the same time, we give attention to blood pressure, electrocardiogram, albumin, calcium, potassium, acidosis, coagulopathy, anti-infection, and protection of vital organs is essential for successful retransplant outcomes.

Anti-phosphatidylserine/prothrombin complex antibodies (aPS/PT) increase the risk for thrombosis based on lupus anticoagulant positivity.

BACKGROUND: Lupus anticoagulants (LA) increase the risk of thrombotic and obstetric events in patients with antiphospholipid syndrome than in those with other antiphospholipid antibodies. Anti-phosphatidylserine/prothrombin (aPS/PT) complex antibodies are thought to cause LA positivity. Therefore, we aimed to explore whether aPS/PT antibodies could prolong phospholipid (PL)-dependent clotting time and increase the risk of thrombosis or pregnancy complications based on LA positivity. METHODS: We recruited 222 patients with positive LA and estimated their aPS/PT, anticardiolipin (aCL), anti-ß2-glycoprotein I (aß2GPI), and anti-ß2GPI domain I (anti-D1) antibody (IgM and IgG) titers and PL-dependent clotting time. RESULTS: PT was longer in aPS/PT IgG-positive patients than in aPS/PT IgM-negative patients (P < 0.001), while there was no significant difference between aPS/PT IgM-positive and IgM-negative patients (P = 0.100). Both SCT-S and dRVVT-S were prolonged in aPS/PT (IgG and IgM)-positive patients compared to aPS/PT-negative patients (P < 0.001, P = 0.010, P < 0.001, P = 0.002, respectively). Similarly, the associations between aPS/PT IgG or IgM antibody titers and SCT-S or dRVVT-S were significant. SCT-C and dRVVT-C did not show any significant differences. The incidence of thrombosis in the aPS/PT IgG-positive group was much higher than that in the IgG-negative group (P = 0.012). Likewise, the incidence of thrombosis was higher in the anti-D1- and aPS/PT IgG-positive patients than in the negative controls (40 % vs 14.3 %, χ2 = 3.934, P = 0.047). Furthermore, the aPS/PT IgG-positive group showed the strongest association with thrombosis [OR 2.584, 95 % CI (1.213, 5.505)]. CONCLUSION: The aPS/PT antibodies prolonged PL-dependent clotting time, especially SCT-S and dRVVT-S. In addition, the presence of aPS/PT IgG antibodies increased the risk of thrombosis in LA positivity.

Recombinant protein diannexin prevents preeclampsia-like symptoms in a pregnant mouse model via reducing the release of microparticles.

Preeclampsia (PE) is characterized by placenta-mediated pregnancy complication. The only effective treatment for PE is the delivery of the placenta. However, this treatment may cause preterm birth and neonatal death. Therefore, preventing PE is needed. The mechanism of PE involves abnormal placentation, which leads to the release of anti-angiogenic and inflammatory mediators into maternal circulation. These mediators contribute to systemic vascular dysfunction, inflammatory responses, and excessive thrombin generation. Microparticles (MPs) are reportedly involved in PE by promoting the thromboinflammatory response. This study describes a strategy to prevent PE by reducing MP release using the recombinant protein, diannexin. Results showed that the patients with PE had elevated MP number and procoagulant activity and increased NLRP3 inflammasome activation. Additionally, diannexin remarkably reduced the release of MPs from activated cells by binding to phosphatidylserine exposed on the surface of activated cells. Moreover, in vivo results showed that diannexin could prevent PE-like symptoms by decreasing MPs and NLRP3 inflammasome activation in pregnant mice. Furthermore, diannexin effectively inhibited trophoblast cell activation and NLRP3 inflammasome activation in vitro. These findings suggested that diannexin inhibited MP release and might be an effective therapeutic strategy for preventing PE.

CD155 in tumor progression and targeted therapy.

CD155, also known as the poliovirus receptor (PVR), has received considerable attention in recent years because of its intrinsic and extrinsic roles in tumor progression. Although barely expressed in host cells, CD155 is upregulated in tumor-infiltrating myeloid cells. High expression of CD155 in tumor cells across multiple cancer types is common and associated with poor patient outcomes. The intrinsic functions of CD155 in tumor cells promote tumor progression and metastasis, whereas its extrinsic immunoregulatory functions in the tumor microenvironment (TME) involve interaction with the upregulated inhibitory immune cell receptor and checkpoint TIGIT, suggesting that CD155 and CD155 pathways are promising tumor immunotherapy targets. Preclinical studies demonstrate that targeting CD155 and its receptor (anti-TIGIT) using a single treatment or in combination with anti-PD-1 can improve immune-mediated tumor control. However, there is still a limited understanding of CD155 and its associated targeting strategies, especially antibody and immune cell editing-related strategies of CD155 in cancer. Here, we review the role of CD155 in host and tumor cells in controlling tumor progression and discuss the potential of targeting CD155 for tumor therapy.

Deciphering the autophagy regulatory network via single-cell transcriptome analysis reveals a requirement for autophagy homeostasis in spermatogenesis.

Background: Autophagy has been implicated as a crucial component in spermatogenesis, and autophagy dysfunction can lead to reproductive disorders in animal models, including yeast, C. elegans and mice. However, the sophisticated transcriptional networks of autophagic genes throughout human spermatogenesis and their biological significance remain largely uncharacterized. Methods: We profiled the transcriptional signatures of autophagy-related genes during human spermatogenesis by assessing specimens from nine fertile controls (including two normal persons and seven obstructive azoospermia (OA) patients) and one nonobstructive azoospermia (NOA) patient using single-cell RNA sequencing (scRNA-seq) analysis. Dysregulation of autophagy was confirmed in two additional NOA patients by immunofluorescence staining. Gene knockdown was used to identify the role of Cst3 in autophagy during spermatogenesis. Results: Our data uncovered a unique, global stage-specific enrichment of autophagy-related genes. Human-mouse comparison analysis revealed that the stage-specific expression pattern of autophagy-related genes was highly conserved in mammals. More importantly, dysregulation of some clusters of autophagy-related genes was observed in NOA patients, suggesting the association of autophagy with male infertility. Cst3, a human-mouse conserved and autophagy-related gene that is actively expressed in spermatogonia and early spermatocytes, was found to regulate spermatogonial stem cell (SSC) maintenance and subsequent male germ cell development. Knockdown of Cst3 increased autophagic activity in mouse SSCs and subsequently suppressed the transcription of SSC core factors such as Oct4, Id1, and Nanos3, which could be efficiently rescued by manipulating autophagic activity. Conclusions: Our study provides comprehensive insights into the global transcriptional signatures of autophagy-related genes and confirms the importance of autophagy homeostasis in SSC maintenance and normal spermatogenesis, opening new avenues for further dissecting the significance of the autophagy regulatory network in spermatogenesis as well as male infertility.

Procoagulant platelets: Generation, characteristics, and therapeutic target.

Platelets play a pivotal role in hemostasis. Activated platelets are classified into two groups, according to their agonist response: aggregating and procoagulant platelets. Aggregating platelets consist of activated integrin αIIbß3 and stretch out pseudopods to further attract platelets to the site of injury by connecting with fibrinogen. They mainly gather in the core of the thrombus and perform a secretory function, such as releasing adenosine diphosphate (ADP). Procoagulant platelets promote the formation of thrombin and fibrin by interacting with coagulation factors and can thus be considered as the connector between primary and secondary hemostasis. In addition to their functions in blood coagulation, procoagulant platelets play a proinflammatory role by releasing platelet microparticles and inorganic polyphosphate. Considering these important functions of procoagulant platelets, this subpopulation warrants detailed study to analyze their potential in preventing human diseases. This review summarizes the generation and important characteristics of procoagulant platelets, as well as their potential for preventing the adverse effects associated with current antiplatelet therapies.

Evaluation of Urine NDRG1 as Noninvasive Biomarker for Bladder Cancer Diagnosis.

BACKGROUND: N-myc downstream regulated gene 1 (NDRG1) was involved in cell differentiation and was recently reported to exert various effects in tumorigenesis. The aim of this study was to assess its diagnostic value in urine as a useful marker for bladder cancer (BC). METHODS: In this study, we recruited 119 BC patients, 65 patients with non-cancerous bladder diseases, and 60 healthy volunteers as control. Their urine concentrations of NDRG1, nuclear matrix protein 22 (NMP22), and creatinine (Cr) were measured and relevant clinical information was retrieved from their medical history records. RESULTS: The expression of NDRG1/Cr and NMP22/Cr in urine were significantly higher in BC patients than those in non-cancerous bladder diseases (p = 0.009 and p = 0.023) and healthy controls (p = 0.005 and p = 0.002). The level of NDRG1/Cr was significantly associated with pathologic T stage (p < 0.001) and pathological grade (p < 0.001). The ROC of NDRG1/Cr to diagnose BC was 0.713 (95% CI, 0.630 - 0.797), with a sensitivity of 63.8% and a specificity of 73.4% at a cutoff of 76.3 ng/mg. NMP22/Cr was 0.705 (95% CI, 0.626 - 0.784), with a sensitivity of 64.2% and a specificity of 66.2% at a cutoff of 12.1 ng/mg. NDRG1/Cr in combination with NMP22/Cr shows a ROC of 0.719 (95% CI, 0.632 0.806) with a sensitivity of 64.9% and specificity of 75.9% Conclusions: Urine NDRG1 may be useful in a minimally invasive modality for determining bladder cancer. Predictive value of the two biomarkers was slightly higher than that of routine NMP22 parameter alone.

Seroepidemiology of TORCH antibodies in the reproductive-aged women in China.

TORCH, the acronym of Toxoplasma gondii (TOX), others, rubella virus (RUV), cytomegalovirus (CMV) and herpes simplex virus (HSV), is a major contributor to congenital infection. National population-based study on the seroepidemiology of TORCH in women is yet lacking, and it is still obscure whether TORCH infection in the women was associated with adverse pregnancy outcomes. A total of 48,406 asymptomatic women from eight hospitals in China which covered the most areas of mainland China were enrolled in this study, and 26,400 were simultaneously subjected to 7 detection tests for TORCH specific antibodies. Chemiluminescent immunoassay was performed to detect TORCH Immunoglobulin M (IgM) and/or Immunoglobulin G (IgG) antibodies, and IgG avidities of TOX and CMV IgM and IgG positive serum samples. The overall IgG prevalence of TOX, RUV, CMV and HSV-(1 + 2) in the reproductive-aged women was 1.71 %, 81.97 %, 95.09 % and 90.15 % respectively. The corresponding IgM prevalence of TOX, RUV and CMV was 0.30 %, 0.89 % and 0.52 %. Moreover, the rates of primary TOX and CMV infections were at least 0.08 % (21/26,400) and 0.03 % (7/26,400) in the studied population. The distributions of TORCH positive women in various age, season and region groups were different (P < 0.05). The CMV IgM-positive rate was higher in the pregnant women than those in non-pregnant women (P < 0.05). The higher past infection rates of RUV, CMV and HSV in women with bad obstetric history (BOH) imply that TORCH infections are associated with BOH. These data suggest that TORCH infections in the prenatal women, especially with BOH, are worthwhile to be screened by detections of specific IgG and IgM antibodies, and even IgG avidities.

RNAInter in 2020: RNA interactome repository with increased coverage and annotation.

Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA-RNA and RNA-protein interactions but also include RNA-DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the biological functions and molecular mechanisms of RNA, we updated RAID v2.0 to RNAInter (RNA Interactome Database), a repository for RNA-associated interactions that is freely accessible at http://www.rna-society.org/rnainter/ or http://www.rna-society.org/raid/. Compared to RAID v2.0, new features in RNAInter include (i) 8-fold more interaction data and 94 additional species; (ii) more definite annotations organized, including RNA editing/localization/modification/structure and homology interaction; (iii) advanced functions including fuzzy/batch search, interaction network and RNA dynamic expression and (iv) four embedded RNA interactome tools: RIscoper, IntaRNA, PRIdictor and DeepBind. Consequently, RNAInter contains >41 million RNA-associated interaction entries, involving more than 450 thousand unique molecules, including RNA, protein, DNA and compound. Overall, RNAInter provides a comprehensive RNA interactome resource for researchers and paves the way to investigate the regulatory landscape of cellular RNAs.

Exploration of invasive mechanisms via global ncRNA-associated virus-host crosstalk.

Viral infection is a complex pathogenesis and the underlying molecular mechanisms remain poorly understood. In this study, an integrated multiple resources analysis was performed and showed that the cellular ncRNAs and proteins targeted by viruses were primarily "hubs" and "bottlenecks" in the human ncRNA/protein-protein interaction. The common proteins targeted by both viral ncRNAs and proteins tended to skew toward higher degrees and betweenness compared with other proteins, showed significant enrichment in the cell death process. Specifically, >800 pairs of human cellular ncRNAs and viral ncRNAs that exhibited a high degree of functional homology were identified, representing potential ncRNA-mediated co-regulation patterns of viral invasion. Additionally, clustering analysis further revealed several distinct viral clusters with obvious functional divergence. Overall, this is the first attempt to systematically explore the invasive mechanism via global ncRNA-associated virus-host crosstalk. Our results provide useful information in comprehensively understanding the viral invasive mechanism.

Integrated Analysis of Brain Transcriptome Reveals Convergent Molecular Pathways in Autism Spectrum Disorder.

Autism spectrum disorder (ASD) is a set of complex neurodevelopmental disorders with etiology that remains elusive. Although there is a mounting body of investigation in different brain regions related to ASD, our knowledge about the common and distinct perturb condition between them is at the threshold of accumulation. In this study, based on protein-protein interactions, post-mortem transcriptome analysis was performed with corpus callosum (CC) and prefrontal cortex (PFC) samples from ASD individuals and controls. Co-expression network analysis revealed that a total of seven (four for CC set, three for PFC set) core dysfunctional modules strongly enriched for known ASD-risk genes. Three quarters of them in CC set (M4, M6, M29) significantly enriched for genes annotated by genetically associated variants in our previous whole genome sequencing data. We further determined transcriptional and post-transcriptional regulation subnetwork for each ASD-correlated module, including 47 pivot transcription factors, 130 pivot miRNAs, and 7 pivot lncRNAs. Moreover, there were significantly more interactions between CC-M4, -M6, and PFC-M2, mainly involved in synaptic functions and neuronal development. Our integrated multifactor analysis of ASD brain transcriptome profile illustrated underlying common and distinct molecular mechanisms and the module crosstalk between CC and PFC, helping to shed light on the molecular neuropathological underlying ASD.

Dissecting dynamic expression of autophagy-related genes during human fetal digestive tract development via single-cell RNA sequencing.

Macroautophagy/autophagy has been demonstrated to play an essential role in embryonic development. However, the role of autophagy during human fetal digestive tract development has not been investigated. Here, by using over 5,000 human embryonic digestive tract cells ranging from 6 weeks to 25 weeks, we explored the dynamic expression of autophagy-related genes at single-cell resolution, and found that the transcriptional activity of autophagy-related genes boosted remarkably and specifically in the early (between 6 and 9 weeks) stages. Interestingly, the small intestine cells at 9 weeks showed the most significant enrichment of autophagy-related genes than any other stages. In summary, our results for the first time revealed that autophagy may play an essential role in the development of the digestive tract, especially for the small intestine, in early human embryos. Abbreviations: GI: gastrointestinal; S-Intes: small intestine; t-SNE: t-distributed stochastic neighbor embedding.

Anti-domain 1 of beta2-glycoprotein I aids risk stratification in lupus anticoagulant-positive patients.

Lupus anticoagulant (LA) is considered a risk factor for thromboembolism (TE) and adverse pregnancy outcomes (APOs). However, quite a few patients diagnosed with LA positivity do not suffer these adverse events. Further testing of anticardiolipin (aCL), anti-beta2-glycoprotein I (anti-ß2GPI) or anti-domain 1 of ß2GPI (anti-D1) may help to assess the occurrence risk of TE and APOs. Therefore, we aimed to study how to stratify LA-positive patients. In our study, 167 LA-positive patients were consecutively enrolled from January 2015 to December 2016. Serum aCL and anti-ß2GPI (IgG, IgM and IgA) and anti-D1 IgG were simultaneously measured. Among these patients, 114 (68.3%) were followed for an average of 36.5 months for TE and APOs. The outcomes showed that 105 patients experienced TE and/or APOs, and 62 patients were LA carriers. Anti-D1 had good consistency with triple positivity (LA+, aCL+, anti-ß2GPI+) (kappa = 0.742). Elevated anti-D1 was related to increased risks for TE [odds ratio (OR) 29.87, 95% confidence interval (CI) 8.05-110.74] and APOs (OR 8.73, 95% CI 3.41-22.31). Area under curve showed that the diagnostic power of anti-D1 for TE and APOs was 0.856 (95% CI 0.743-0.970) and 0.682 (95% CI 0.599-0.765), respectively. Survival analysis revealed that patients with high anti-D1 titres had a high cumulative incidence of APOs (hazard ratio 4.66, 95% CI 1.46-14.87). In conclusion, anti-D1, based on good consistency with triple positivity in LA-positive patients, has a stronger association with TE and APOs and, to some degree, could predict pregnancy outcomes. Therefore, anti-D1 may aid risk stratification in LA-positive patients.

RIscoper: a tool for RNA-RNA interaction extraction from the literature.

MOTIVATION: Numerous experimental and computational studies in the biomedical literature have provided considerable amounts of data on diverse RNA-RNA interactions (RRIs). However, few text mining systems for RRIs information extraction are available. RESULTS: RNA Interactome Scoper (RIscoper) represents the first tool for full-scale RNA interactome scanning and was developed for extracting RRIs from the literature based on the N-gram model. Notably, a reliable RRI corpus was integrated in RIscoper, and more than 13 300 manually curated sentences with RRI information were recruited. RIscoper allows users to upload full texts or abstracts, and provides an online search tool that is connected with PubMed (PMID and keyword input), and these capabilities are useful for biologists. RIscoper has a strong performance (90.4% precision and 93.9% recall), integrates natural language processing techniques and has a reliable RRI corpus. AVAILABILITY AND IMPLEMENTATION: The standalone software and web server of RIscoper are freely available at www.rna-society.org/riscoper/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Trimester-specific coagulation and anticoagulation reference intervals for healthy pregnancy.

BACKGROUND: Due to the normal physiological need of pregnancy and childbirth, the haemostatic system of pregnant women is different from that of healthy non-pregnant women. The aim of this study was to establish trimester-specific reference intervals of coagulation screening tests and thrombophilia markers in pregnancies without complications of females with Han ethnicity from North China. METHODS: In total 744 Han healthy pregnant women (first trimester 207 cases, second trimester 222 cases and third trimester 315 cases) and 121 healthy non-pregnant women were recruited in North China. Eight tests-activated partial thromboplastin time (APTT), prothrombin time (PT), thrombin time (TT), fibrinogen (Fib), d-Dimer, antithrombin (AT), protein C (PC) and free protein S (fPS)-were processed on ACL TOP automated coagulation analyzer. The non-parametric 2.5th-97.5th percentiles reference intervals were calculated to establish trimester-specific reference intervals. RESULTS: The reference intervals for APTT, PT, TT, Fib, d-Dimer, AT, PC, and fPS at first trimester were 26.4-41.9s, 9.7-12.5s, 11.7-17.0s, 2.38-4.44g/L, 0.01-0.31µg/mL, 72-120%, 29-150%, 21-143%, respectively. At second trimester, the reference intervals were 24.4-35.8s, 8.5-13.2s, 10.0-16.0s, 2.40-5.97g/L, 0.05-0.73µg/mL, 68-125%, 20-138%, 24-155%, respectively. At third trimester, the reference intervals were 25.6-34.9s, 8.6-12.4s, 11.1-15.5s, 2.79-5.91g/L, 0.14-2.82µg/mL, 56-119%, 20-134%, 17-140%, respectively. From the first trimester to the third trimester, APTT, PT and TT presented shortened trends, Fib and d-Dimer presented increasing trends, AT, PC and fPS activity presented decreasing trends, respectively. CONCLUSIONS: The trimester-specific reference intervals of coagulation screening tests and thrombophilia markers in pregnancies without complications of females with Han ethnicity from North China are presented in this study, which may provide effective evidence for doctors to accurately diagnose and treat the disease during pregnancy.

Identifying reproducible cancer-associated highly expressed genes with important functional significances using multiple datasets.

Identifying differentially expressed (DE) genes between cancer and normal tissues is of basic importance for studying cancer mechanisms. However, current methods, such as the commonly used Significance Analysis of Microarrays (SAM), are biased to genes with low expression levels. Recently, we proposed an algorithm, named the pairwise difference (PD) algorithm, to identify highly expressed DE genes based on reproducibility evaluation of top-ranked expression differences between paired technical replicates of cells under two experimental conditions. In this study, we extended the application of the algorithm to the identification of DE genes between two types of tissue samples (biological replicates) based on several independent datasets or sub-datasets of a dataset, by constructing multiple paired average gene expression profiles for the two types of samples. Using multiple datasets for lung and esophageal cancers, we demonstrated that PD could identify many DE genes highly expressed in both cancer and normal tissues that tended to be missed by the commonly used SAM. These highly expressed DE genes, including many housekeeping genes, were significantly enriched in many conservative pathways, such as ribosome, proteasome, phagosome and TNF signaling pathways with important functional significances in oncogenesis.