The functions and mechanisms of RNA modification in prostate: Current status and future perspectives.

The increasing incidence and mortality of prostate cancer worldwide significantly impact the life span of male patients, emphasizing the urgency of understanding its pathogenic mechanism and associated molecular changes that regulate tumor progression for effective prevention and treatment. RNA modification, an important post-transcriptional regulatory process, profoundly influences tumor cell growth and metabolism, shaping cell fate. Over 170 RNA modification methods are known, with prominent research focusing on N6-methyladenosine, N7-methylguanosine, N1-methyladenosine, 5-methylcytidine, pseudouridine, and N4-acetylcytidine modifications. These alterations intricately regulate coding and non-coding RNA post-transcriptionally, affecting the stability of RNA and protein expression levels. This article delves into the latest advancements and challenges associated with various RNA modifications in prostate cancer tumor cells, tumor microenvironment, and core signaling molecule androgen receptors. It aims to provide new research targets and avenues for molecular diagnosis, treatment strategies, and improvement of the prognosis in prostate cancer.

Resonant exchange of chiral Majorana Fermions modulated by two parallel quantum dots.

Resonant exchange of the chiral Majorana fermions (MFs) that is coupled to two parallel Majorana zero modes (MZMs) or two parallel quantum dots (QDs) is investigated. We find that, in the two QDs coupling case, the resonant exchange for the chiral MFs is analogous to that in the MZM coupling case. We further propose a circuit based on topological superconductor, which is formed by the proximity coupling of a quantum anomalous Hall insulator and a s-wave superconductor, to observe the resonant exchange of chiral MFs pairs. The numerical calculations show that the resonant transmission of the chiral MFs can be adjusted by varying the coupling parameters at superconductor phase differenceΔφ=π. It is particularly noteworthy that, by only modulating the coupling strength between the two QDs, the resonant exchange may be switched on or off. By adding another MZM, the non-Abelian braiding like operation can be realized. Therefore, our design scheme may provide another way for non-Abelian braiding operation of MFs and the findings may have potential application value in the realization of topological quantum computers.

A homozygous variant in INTS11 links mitosis and neurogenesis defects to a severe neurodevelopmental disorder.

The INTS11 endonuclease is crucial in modulating gene expression and has only recently been linked to human neurodevelopmental disorders (NDDs). However, how INTS11 participates in human development and disease remains unclear. Here, we identify a homozygous INTS11 variant in two siblings with a severe NDD. The variant impairs INTS11 catalytic activity, supported by its substrate's accumulation, and causes G2/M arrest in patient cells with length-dependent dysregulation of genes involved in mitosis and neural development, including the NDD gene CDKL5. The mutant knockin (KI) in induced pluripotent stem cells (iPSCs) disturbs their mitotic spindle organization and thus leads to slow proliferation and increased apoptosis, possibly through the decreased neurally functional CDKL5-induced extracellular signal-regulated kinase (ERK) pathway inhibition. The generation of neural progenitor cells (NPCs) from the mutant iPSCs is also delayed, with long transcript loss concerning neurogenesis. Our work reveals a mechanism underlying INTS11 dysfunction-caused human NDD and provides an iPSC model for this disease.

Comprehensive Analysis of Hemophilia A (CAHEA): Towards Full Characterization of the F8 Gene Variants by Long-Read Sequencing.

BACKGROUND: Hemophilia A (HA) is the most frequently occurring X-linked bleeding disorder caused by heterogeneous variants in the F8 gene, one of the largest genes known. Conventional molecular analysis of F8 requires a combination of assays, usually including long-range polymerase chain reaction (LR-PCR) or inverse-PCR for inversions, Sanger sequencing or next-generation sequencing for single-nucleotide variants (SNVs) and indels, and multiplex ligation-dependent probe amplification for large deletions or duplications. MATERIALS AND METHODS: This study aimed to develop a LR-PCR and long-read sequencing-based assay termed comprehensive analysis of hemophilia A (CAHEA) for full characterization of F8 variants. The performance of CAHEA was evaluated in 272 samples from 131 HA pedigrees with a wide spectrum of F8 variants by comparing to conventional molecular assays. RESULTS: CAHEA identified F8 variants in all the 131 pedigrees, including 35 intron 22-related gene rearrangements, 3 intron 1 inversion (Inv1), 85 SNVs and indels, 1 large insertion, and 7 large deletions. The accuracy of CAHEA was also confirmed in another set of 14 HA pedigrees. Compared with the conventional methods combined altogether, CAHEA assay demonstrated 100% sensitivity and specificity for identifying various types of F8 variants and had the advantages of directly determining the break regions/points of large inversions, insertions, and deletions, which enabled analyzing the mechanisms of recombination at the junction sites and pathogenicity of the variants. CONCLUSION: CAHEA represents a comprehensive assay toward full characterization of F8 variants including intron 22 and intron 1 inversions, SNVs/indels, and large insertions and deletions, greatly improving the genetic screening and diagnosis for HA.

Immune surveillance of brain metastatic cancer cells is mediated by IFITM1.

Brain metastasis, most commonly originating from lung cancer, increases cancer morbidity and mortality. Although metastatic colonization is the rate-limiting and most complex step of the metastatic cascade, the underlying mechanisms are poorly understood. Here, in vivo genome-wide CRISPR-Cas9 screening revealed that loss of interferon-induced transmembrane protein 1 (IFITM1) promotes brain colonization of human lung cancer cells. Incipient brain metastatic cancer cells with high expression of IFITM1 secrete microglia-activating complement component 3 and enhance the cytolytic activity of CD8+ T cells by increasing the expression and membrane localization of major histocompatibility complex class I. After activation, microglia (of the innate immune system) and cytotoxic CD8+ T lymphocytes (of the adaptive immune system) were found to jointly eliminate cancer cells by releasing interferon-gamma and inducing phagocytosis and T-cell-mediated killing. In human cancer clinical trials, immune checkpoint blockade therapy response was significantly correlated with IFITM1 expression, and IFITM1 enhanced the brain metastasis suppression efficacy of PD-1 blockade in mice. Our results exemplify a novel mechanism through which metastatic cancer cells overcome the innate and adaptive immune responses to colonize the brain, and suggest that a combination therapy increasing IFITM1 expression in metastatic cells with PD-1 blockade may be a promising strategy to reduce metastasis.

Developmental eye movement strategies for decoding facial expressions of emotion.

In our daily lives, we routinely look at the faces of others to try to understand how they are feeling. Few studies have examined the perceptual strategies that are used to recognize facial expressions of emotion, and none have attempted to isolate visual information use with eye movements throughout development. Therefore, we recorded the eye movements of children from 5 years of age up to adulthood during recognition of the six "basic emotions" to investigate when perceptual strategies for emotion recognition become mature (i.e., most adult-like). Using iMap4, we identified the eye movement fixation patterns for recognition of the six emotions across age groups in natural viewing and gaze-contingent (i.e., expanding spotlight) conditions. While univariate analyses failed to reveal significant differences in fixation patterns, more sensitive multivariate distance analyses revealed a U-shaped developmental trajectory with the eye movement strategies of the 17- to 18-year-old group most similar to adults for all expressions. A developmental dip in strategy similarity was found for each emotional expression revealing which age group had the most distinct eye movement strategy from the adult group: the 13- to 14-year-olds for sadness recognition; the 11- to 12-year-olds for fear, anger, surprise, and disgust; and the 7- to 8-year-olds for happiness. Recognition performance for happy, angry, and sad expressions did not differ significantly across age groups, but the eye movement strategies for these expressions diverged for each group. Therefore, a unique strategy was not a prerequisite for optimal recognition performance for these expressions. Our data provide novel insights into the developmental trajectories underlying facial expression recognition, a critical ability for adaptive social relations.

Endoscopic submucosal dissection for early cancers or precancerous lesions of the upper GI tract in cirrhotic patients with esophagogastric varices: 10-year experience from a large tertiary center in China.

BACKGROUND AND AIMS: Treatment strategies for early cancers or precancerous lesions of the upper GI tract in patients with cirrhosis and esophagogastric varices (EGVs) are complicated and risky. The aim of this study was to assess the efficacy and safety of endoscopic submucosal dissection (ESD) in the treatment of such patients and explore optimal treatment strategies. METHODS: We retrospectively enrolled 15 patients with cirrhosis and EGV who underwent ESD for early cancers or precancerous lesions of the upper GI tract from January 2012 to December 2021 at our center. Clinical features, endoscopic findings, treatment methods, adverse events, and follow-up data were analyzed. RESULTS: Of the 15 patients, 1 had a platelet count <30 × 1000/mm3. Five were untreated for EGV, 1 was treated after ESD, 6 were treated before ESD, 1 was treated before and during ESD, and 2 were treated during ESD. The R0 resection rate was 100%. Of the 16 mucosal lesions, 15 were endoscopic resection bleeding (ERB)-0 or ERB-c1, and 1 was ERB-c2. No patient experienced deterioration in liver function. The only adverse events were fever in 2 patients and postoperative bleeding in 2 patients. During a median follow-up of 27 months, 1 patient's esophageal high-grade dysplasia recurred at 19 months. No death resulted from the ESD procedure, liver function injury, or GI tumor itself. CONCLUSIONS: ESD is an effective and safe treatment for early cancers or precancerous lesions of the upper GI tract in patients with cirrhosis and EGV. The incidence of severe adverse events is very low due to the development of individualized clinical treatment strategies.

Investigation report on endoscopic management of esophagogastric variceal bleeding by Chinese endoscopists.

BACKGROUND: Esophagogastric variceal bleeding (EGVB) is a potentially life-threatening complication of portal hypertension. Endoscopic treatment combined with pharmacotherapy remains the mainstay in the management of acute variceal bleeding. AIM: This article intends to highlight the potential differences in the endoscopic management of EGVB in China. METHODS: A cross-sectional descriptive study was conducted. Endoscopists from 85 hospitals in 62 cities from 26 provinces were contacted by email. The items in questionnaire involved academic experience, screening, esophagogastric varices (EGV) classification, emergency treatment, and primary and secondary prophylaxis of EGVB by endoscopists with different lengths of experience. RESULTS: A total of 85 questionnaires were collected. There was no statistical difference in the selection of items (P < .05 indicated statistical significance). The majority of endoscopists (95.29%) offered EGV screening for patients with liver cirrhosis. The location, diameter, and risk factor classification was selected by 82.35% of endoscopists. Endoscopy + medication was preferred (42.35%) for the primary prophylaxis of moderate-to-severe EGVs. There was no statistical difference in emergency intervention time for active EGVB (P > .05). The response "patients receive emergency endoscopic intervention within 12 hours" was selected by 61.2% of the endoscopists. The preferred emergency treatment for EGVB was combination treatment (40%). Tissue adhesive embolization was selected for the treatment of gastric variceal bleeding by 74.12% of endoscopists; transjugular intrahepatic portosystemic stent shunt/percutaneous transhepatic variceal embolization were selected as remedial measures by 48.23% to 52.94% of endoscopists. In addition, 67.06% of endoscopists elected to perform secondary prophylaxis and treatment within 1 week after hemostasis. Endoscopy and endoscopy + medication were selected by 44.71% and 49.41% of endoscopists, respectively, for secondary prophylaxis. The choice of laboratory indicators did not differ with length of experience. CONCLUSIONS: There was no statistical difference in the endoscopic management of EGVB among Chinese endoscopists. The selection of diagnosis/treatment schemes was mainly based on guidelines and physician experience.

Comprehensive Analysis of Fragile X Syndrome: Full Characterization of the FMR1 Locus by Long-Read Sequencing.

BACKGROUND: Fragile X syndrome (FXS) is the most frequent cause of inherited X-linked intellectual disability. Conventional FXS genetic testing methods mainly focus on FMR1 CGG expansions and fail to identify AGG interruptions, rare intragenic variants, and large gene deletions. METHODS: A long-range PCR and long-read sequencing-based assay termed comprehensive analysis of FXS (CAFXS) was developed and evaluated in Coriell and clinical samples by comparing to Southern blot analysis and triplet repeat-primed PCR (TP-PCR). RESULTS: CAFXS accurately detected the number of CGG repeats in the range of 93 to at least 940 with mass fraction of 0.5% to 1% in the background of normal alleles, which was 2-4-fold analytically more sensitive than TP-PCR. All categories of mutations detected by control methods, including full mutations in 30 samples, were identified by CAFXS for all 62 clinical samples. CAFXS accurately determined AGG interruptions in all 133 alleles identified, even in mosaic alleles. CAFXS successfully identified 2 rare intragenic variants including the c.879A > C variant in exon 9 and a 697-bp microdeletion flanking upstream of CGG repeats, which disrupted primer annealing in TP-PCR assay. In addition, CAFXS directly determined the breakpoints of a 237.1-kb deletion and a 774.0-kb deletion encompassing the entire FMR1 gene in 2 samples. CONCLUSIONS: Long-read sequencing-based CAFXS represents a comprehensive assay for identifying FMR1 CGG expansions, AGG interruptions, rare intragenic variants, and large gene deletions, which greatly improves the genetic screening and diagnosis for FXS.

Comprehensive Analysis of Congenital Adrenal Hyperplasia Using Long-Read Sequencing.

BACKGROUND: Congenital adrenal hyperplasia (CAH) is an autosomal recessive disorder that has been included in newborn screening programs. Current approaches to gene testing for CAH are facing challenges because of the complexity of the CYP21A2 locus and genetic heterogeneity of the disease. METHODS: A comprehensive analysis of CAH (CACAH) combining long-range locus-specific PCR and long-read sequencing (LRS) was developed to perform full sequence analysis of 5 common CAH candidate genes, including CYP21A2, CYP11B1, CYP17A1, HSD3B2, and StAR. In a blind retrospective study, the clinical utility of CACAH was evaluated in 37 samples by comparing to standard CAH testing using multiplex ligation-dependent probe amplification (MLPA) plus Sanger sequencing. RESULTS: Of the 37 clinical samples, a total of 69 pathogenic variants were identified, comprising 65 CYP21A2 variants, 2 HSD3B2 variants, and 2 CYP17A1 variants. For CYP21A2, the most frequent variant was c.518T > A (29.2%), followed by c.293-13C/A > G (21.5%). Compared with the current CAH testing using MLPA plus Sanger sequencing, the CACAH assay showed 100% specificity and 100% sensitivity, and precisely determined the junction sites of deletions/insertions and cis-trans configuration of multiple variants without analyzing family samples. Moreover, CACAH identified a case carrying 2 copies of CYP21A1 with the c.1451_1452delinsC variant on the same chromosome, which was not confirmed by MLPA plus Sanger sequencing. CONCLUSION: LRS-based CACAH can determine all genotypes of CAH accurately and reliably in one assay, presenting a comprehensive approach for CAH genetic diagnosis and carrier screening.

Identification of four novel mutations in BTK from six Chinese families with X-linked agammaglobulinemia.

BACKGROUND: The defect of Bruton's tyrosine kinase (BTK) gene resulted in X-linked agammaglobulinemia (XLA), which is characterized by recurrent bacterial infections, immunodeficiency with low B-cell numbers and immunoglobulin. Diagnosis of XLA depends on clinical phenotype and genetic testing. METHODS: Six unrelated Chinese families with high suspicion of XLA were enrolled in this study. Potential pathogenic variants were detected and validated by Whole Exome Sequencing (WES) and Sanger Sequencing. Western blot, Quantitative PCR (qPCR) analysis and immunofluorescence analysis were used to evaluate the preliminary function of candidate BTK variants. RESULTS: A total of six variants were identified, four of which were not reported before. The novel missense mutation(c.1900 T > G) and deletion(c.897delG) were found that the mutant protein and mRNA expression levels have fallen by Western Blot and qPCR identification. We also constructed minigene expression vector to determine the deletion (c.1751-6_1755delttctagGGGTT) resulting a 35 bp skipping in exon 18. Meanwhile, the break point of gross deletion (Exon2-5) discovered based on WES was confirmed to be located at site ChX:101367539_101376531 through qPCR and Gap-PCR. CONCLUSION: This study makes definitive diagnosis for 6 families with suspected XLA and further expands the spectrum of BTK mutations, providing new information for the diagnosis of the disease.

Genome sequencing demonstrates high diagnostic yield in children with undiagnosed global developmental delay/intellectual disability: A prospective study.

Genome sequencing (GS) has been used in the diagnosis of global developmental delay (GDD)/intellectual disability (ID). However, the performance of GS in patients with inconclusive results from chromosomal microarray analysis (CMA) and exome sequencing (ES) is unknown. We recruited 100 pediatric GDD/ID patients from multiple sites in China from February 2018 to August 2020 for GS. Patients have received at least one genomic diagnostic test before enrollment. Reanalysis of their CMA/ES data was performed. The yield of GS was calculated and explanations for missed diagnoses by CMA/ES were investigated. Clinical utility was assessed by interviewing the parents by phone. The overall diagnostic yield of GS was 21%. Seven cases could have been solved with reanalysis of ES data. Thirteen families were missed by previous CMA/ES due to improper methodology. Two remained unsolved after ES reanalysis due to complex variants missed by ES, and a CNV in untranslated regions. Follow-up of the diagnosed families revealed that nine families experienced changes in clinical management, including identification of targeted treatments, cessation of unnecessary treatment, and considerations for family planning. GS demonstrated high diagnostic yield and clinical utility in this undiagnosed GDD/ID cohort, detecting a wide range of variant types of different sizes in a single workflow.

Two new stenosis detection methods of coronary angiograms.

PURPOSE: Coronary angiography is the "gold standard" for diagnosing coronary artery disease. At present, the methods for detecting and evaluating coronary artery stenosis cannot satisfy the clinical needs, e.g., there is no prior study of detecting stenoses in prespecified vessel segments, which is necessary in clinical practice. METHODS: Two vascular stenosis detection methods are proposed to assist the diagnosis. The first one is an automatic method, which can automatically extract the entire coronary artery tree and mark all the possible stenoses. The second one is an interactive method. With this method, the user can choose any vessel segment to do further analysis of its stenoses. RESULTS: Experiments show that the proposed methods are robust for angiograms with various vessel structures. The precision, sensitivity, and [Formula: see text] score of the automatic stenosis detection method are 0.821, 0.757, and 0.788, respectively. Further investigation proves that the interactive method can provide a more precise outcome of stenosis detection, and our quantitative analysis is closer to reality. CONCLUSION: The proposed automatic method and interactive method are effective and can complement each other in clinical practice. The first method can be used for preliminary screening, and the second method can be used for further quantitative analysis. We believe the proposed solution is more suitable for the clinical diagnosis of CAD.

Segmentation and Automatic Identification of Vasculature in Coronary Angiograms.

Coronary angiography is the "gold standard" for the diagnosis of coronary heart disease, of which vessel segmentation and identification technologies are paid much attention to. However, because of the characteristics of coronary angiograms, such as the complex and variable morphology of coronary artery structure and the noise caused by various factors, there are many difficulties in these studies. To conquer these problems, we design a preprocessing scheme including block-matching and 3D filtering, unsharp masking, contrast-limited adaptive histogram equalization, and multiscale image enhancement to improve the quality of the image and enhance the vascular structure. To achieve vessel segmentation, we use the C-V model to extract the vascular contour. Finally, we propose an improved adaptive tracking algorithm to realize automatic identification of the vascular skeleton. According to our experiments, the vascular structures can be successfully highlighted and the background is restrained by the preprocessing scheme, the continuous contour of the vessel is extracted accurately by the C-V model, and it is verified that the proposed tracking method has higher accuracy and stronger robustness compared with the existing adaptive tracking method.

Increase in diagnostic yield achieved for 174 whole-exome sequencing cases reanalyzed 1-2 years after initial analysis.

BACKGROUND: Some missed diagnoses have been presented in whole-exome sequencing (WES) analysis for cases with possible Mendelian diseases. To assess how much contributions of WES reanalysis might improve diagnostic yield, we reviewed the WES data of 174 undiagnosed cases. METHODS: We performed reanalysis with an updated bioinformatics pipeline involving better algorithms and updated databases so that CNVs and SNVs in intron regions and InDels within 10-50 bp can be detected. Upgraded variant interpretation processes, including updated software packages, databases and literature, expanded knowledge of genes and diseases, extended filtering conditions and phenotype reevaluation, were also implemented for reanalysis. Candidate variants were classified by ACMG guidelines and certified by Sanger sequencing, qPCR or MLPA. RESULTS: Fourteen additional cases received new diagnosis in the reanalysis. The results which became positive were sorted according to the following aspects: detection of CNVs; diagnosis by SNVs in intron regions or InDels within 10-50 bp; reclassification due to new reports of variants or gene-disease relationships; digenic inheritance leading to disease; disease caused by frequent variations in the general population; and accurate phenotype assessment enabling the establishment of the molecular diagnosis. CONCLUSION: Our study improved diagnosis yield through an optimized bioinformatics pipeline and variant interpretation strategy of WES and provided analysis experience learned from the WES reanalysis to reduce missed diagnoses.

Pressure and Temperature Dependencies of Rate Coefficients for the Reaction OH + NO2 + M → Products.

The OH + NO2 reaction is a critically important process for radical chain termination in the atmosphere with a major impact on the ozone budgets of the troposphere and stratosphere. Rate constants for the reaction of OH + NO2 + M → products have been measured under conditions relevant to the upper troposphere/lower stratosphere with a laser photolysis-laser-induced fluorescence (LP-LIF) technique augmented by in situ optical spectroscopy for quantification of [NO2]. The experiments are carried out over the temperature range of 230-293 K and the pressure range 50-750 Torr of N2 and air and as a function of [O2]. The observed rate coefficients in N2 agree with the newest experimental literature data sets and are within experimental uncertainty of current recommended literature values at 293 K but are systematically higher by up to 22% at 700 Torr and 230 K. The efficacy of different falloff parametrizations has been examined and compared to those in literature sources. The collisional quenching efficiency of O2 was found to be in excellent agreement with current literature sources, and rate coefficients determined in air at 293 and 245 K were observed to be within uncertainty of the rate coefficients measured in N2 bath gas. This work has improved confidence in the literature rate coefficients under conditions of the lower troposphere (∼760 Torr, 280-310 K) toward the stratosphere (10-100 Torr, 220-250 K).

Influence of the type of carrier on ferromagnetism in a Si semiconductor implanted with Cu ions.

Silicon semiconductor samples implanted with Cu ions and samples co-implanted with Cu- and N-ions were prepared by MEVVA and the Kaufman technique. None of the samples showed evidence of secondary phases. The initially n-type Si matrix, when implanted with Cu ions, changed to a p-type semiconductor, and the Cu ions existed as local Cu2+ cations in the p-type environment. As a result, none of the Cu-implanted samples were ferromagnetic at room temperature. The co-implanted samples, on the other hand, showed room-temperature ferromagnetism because the introduction of N ions made the carrier type change from p-type to n-type which is favorable for the appearance of Cu2+. First principles calculations were applied to understand the experimental phenomena. The formation energy was reduced by implanting N ions, and was decreased effectively with the increase in ratio of N to Cu ions. The density of states and spin density of states indicated that the hybridization of s, p and d electrons induced ferromagnetism at 0 K. Particularly, we proposed possible exchange interactions between the Cu2+-N-(N4+)-Cu2+ ions to explain the ferromagnetism mechanism.

A novel GJB1 mutation associated with X-linked Charcot-Marie-Tooth disease in a large Chinese family pedigree.

BACKGROUND: Charcot-Marie-Tooth (CMT) disease is a group of hereditary neuropathies with high phenotypic and genetic heterogeneity. In this study, we report a large family with X-linked CMT (CMTX) caused by a novel GJB1 mutation. METHODS: A family with the clinical diagnosis of CMTX was investigated. For mutation analysis, the coding region of GJB1 was sequenced using DNA from 15 family members. The identified GJB1 mutation was investigated by DHPLC in 120 normal controls. Mutation reanalysis was performed based on whole-exome sequencing (WES). Cell transfection studies were performed to characterize the function of the novel mutation. RESULTS: A missense mutation (c.605T>A) in GJB1 was detected in five patients and eight female carriers but not in two unaffected members of the family. The mutation was not found in 120 healthy controls and has not been previously reported. WES excluded other pathogenic mutations in the family. The pathogenicity of the mutation was confirmed by disrupting the membrane localization of the encoded proteins. CONCLUSION: Our findings demonstrate that a novel mutation (c.605T>A) in GJB1 is associated with CMTX and adds to the repertoire of GJB1 mutations related to CMTX.

Clinical utility of noninvasive prenatal screening for expanded chromosome disease syndromes.

PURPOSE: To assess the clinical performance of an expanded noninvasive prenatal screening (NIPS) test ("NIPS-Plus") for detection of both aneuploidy and genome-wide microdeletion/microduplication syndromes (MMS). METHODS: A total of 94,085 women with a singleton pregnancy were prospectively enrolled in the study. The cell-free plasma DNA was directly sequenced without intermediate amplification and fetal abnormalities identified using an improved copy-number variation (CNV) calling algorithm. RESULTS: A total of 1128 pregnancies (1.2%) were scored positive for clinically significant fetal chromosome abnormalities. This comprised 965 aneuploidies (1.026%) and 163 (0.174%) MMS. From follow-up tests, the positive predictive values (PPVs) for T21, T18, T13, rare trisomies, and sex chromosome aneuploidies were calculated as 95%, 82%, 46%, 29%, and 47%, respectively. For known MMS (n = 32), PPVs were 93% (DiGeorge), 68% (22q11.22 microduplication), 75% (Prader-Willi/Angleman), and 50% (Cri du Chat). For the remaining genome-wide MMS (n = 88), combined PPVs were 32% (CNVs ≥10 Mb) and 19% (CNVs <10 Mb). CONCLUSION: NIPS-Plus yielded high PPVs for common aneuploidies and DiGeorge syndrome, and moderate PPVs for other MMS. Our results present compelling evidence that NIPS-Plus can be used as a first-tier pregnancy screening method to improve detection rates of clinically significant fetal chromosome abnormalities.

Protocadherin γ-A7 is down-regulated in colorectal cancer and associated with the prognosis in patients with wild-type KRAS.

Many clustered protocadherin genes (PCDHs) within chromosome 5q31 are frequently down-regulated in colorectal cancer (CRC) due to the hypermethylation of this region, and some of them have been identified as tumor suppressors. However, the association between the expression of the clustered PCDHs and prognosis of CRC patients is still unclear. Here, we identified multiple PCDHs that were significantly down-regulated in CRC by analyzing the RNA-seq data of the Cancer Genome Atlas (TCGA) cohort. Among them, one γ-PCDH subfamily member, PCDHGA7, was found to be associated with overall survival in the patients with wild-type KRAS. Next, we experimentally validated the decrease of PCDHGA7 mRNA and protein levels in tumor tissues of 20 CRC patients by using quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry assay (IHC). To further investigate whether the expression of PCDHGA7 could predict clinical outcomes, an independent cohort of 138 patients, whose tumors carried wild-type KRAS, was enrolled. In-house tissue microarrays (TMAs) were developed to facilitate the protein detection, and prognostic significance was analyzed. The result showed low PCDHGA7 expression was associated with advanced TNM stage, high risk of tumor recurrence and short overall survival. In conclusion, this study demonstrates that PCDHGA7 is down-regulated in CRC, and its expression level is correlated with clinical outcomes in patients with wild-type KRAS. Our finding indicates PCDHGA7 could serve as a potential novel biomarker to predict prognosis by combining certain tumor genotypes in patients of CRC.