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Both DNA damage response and methylation play a crucial role in antigen receptor recombination by creating a diverse repertoire in developing lymphocytes, but how their defects relate to T cell repertoire and phenotypic heterogeneity of immunodeficiency remains obscure. We studied the TCR repertoire in patients with the mutation in different genes (ATM, DNMT3B,ZBTB24,RAG1,DCLRE1C, andJAK3) and uncovered distinct characteristics of repertoire diversity. We propose that early aberrancies in thymus T cell development predispose to the heterogeneous phenotypes of the immunodeficiency spectrum. Shorter CDR3 lengths in ATM-deficient patients, resulting from a decreased number of nucleotide insertions during VDJ recombination in the pre-selected TCR repertoire, as well as the increment of CDR3 tyrosine residues, lead to the enrichment of pathology-associated TCRs, which may contribute to the phenotypes of ATM deficiency. Furthermore, patients withDNMT3BandZBTB24mutations who exhibit discrepant phenotypes present longer CDR3 lengths and reduced number of known pathology-associated TCRs.

Many aquatic invertebrates undergo an indirect development, a biphasic life cycle which encompasses the transformation of free-swimming larvae into benthic juveniles via settlement and metamorphosis. During this transition, metamorphic competence is a crucial developmental stage that allows larvae to swim and feed in the planktonic realm while retaining the ability to settle and metamorphose in response to environmental cues. Although there have been substantial efforts to decipher the molecular mechanisms underlying this event in several molluscan species, the conserved biological pathways that are crucial to enable this transition across species are not well understood. Here, we performed a comparative analysis of the developmental transcriptomes between bivalve Crassostrea gigas and gastropod Rapana venosa. We particularly explored the common gene expression signatures that may underlie their larval competence. We showed that, although the developmental transcriptomes differed remarkably between C. gigas and R. venosa, they likely shared a plethora of genes (n = 690) that exhibited similar expression signatures during their larval competence. Gene Ontology enrichment and expression analyses further indicated that competent larvae of both species exhibited up-regulation of pathways associated with response to stimuli, metal ion binding and transport, and neuronal development, but showed down-regulation of pathways that were mainly involved in cilium assembly and organ development. Using oyster and whelk as models, our study suggests that regulation of these conserved pathways is crucial for their subsequent settlement and metamorphosis and may represent a universal mechanism that enables the pelagic-to-benthic transition in a broader range of marine invertebrates.

Objectives. Recently, it has been demonstrated that patients with subtle preexisting cognitive impairment were susceptible to delayed neurocognitive recovery (DNR). This present study investigated whether preoperative alterations in gray matter volume, spontaneous activity, or functional connectivity (FC) were associated with DNR. Methods. This was a nested case-control study of older adults (≥60 years) undergoing noncardiac surgery. All patients received MRI scan at least 1 day prior to surgery. Cognitive function was assessed prior to surgery and at 7-14 days postsurgery. Preoperative gray matter volume, amplitude of low-frequency fluctuation (ALFF), and FC were compared between the DNR patients and non-DNR patients. The independent risk factors associated with DNR were identified using a multivariate logistic regression model. Results. Of the 74 patients who completed assessments, 16/74 (21.6%) had DNR following surgery. There were no differences in gray matter volume between the two groups. However, the DNR patients exhibited higher preoperative ALFF in the bilateral middle cingulate cortex (MCC) and left fusiform gyrus and lower preoperative FC between the bilateral MCC and left calcarine than the non-DNR patients. The multivariate logistic regression analysis showed that higher preoperative spontaneous activity in the bilateral MCC was independently associated with a higher risk of DNR (OR=3.11, 95% CI, 1.30-7.45; P=0.011). A longer education duration (OR=0.57, 95% CI, 0.41-0.81; P=0.001) and higher preoperative FC between the bilateral MCC and left calcarine (OR=0.40, 95% CI, 0.18-0.92; P=0.031) were independently correlated with a lower risk of DNR. Conclusions. Preoperative higher ALFF in the bilateral MCC and lower FC between the bilateral MCC and left calcarine were independently associated with the occurrence of DNR. The present fMRI study identified possible preoperative neuroimaging risk factors for DNR. This trial is registered with Chinese Clinical Trial Registry ChiCTR-DCD-15006096.

We designed a novel strategy to define codon usage bias (CUB) in 6 specific small cohorts of human genes. We calculated codon usage (CU) values in 29 non-disease-causing (NDC) and 31 disease-causing (DC) human genes which are highly expressed in 3 distinct tissues, kidney, muscle, and skin. We applied our strategy to the same selected genes annotated in 15 mammalian species. We obtained CUB hierarchical clusters for each gene cohort which showed tissue-specific and disease-specific CUB fingerprints. We showed that DC genes (especially those expressed in muscle) display a low CUB, well recognizable in codon hierarchical clustering. We defined the extremely biased codons as “zero codons” and found that their number is significantly higher in all DC genes, all tissues, and that this trend is conserved across mammals. Based on this calculation in different gene cohorts, we identified 5 codons which are more differentially used across genes and mammals, underlining that some genes have favorite synonymous codons in use. Since of the muscle genes clear clusters, and, among these, dystrophin gene surprisingly does not show any “zero codon” we adopted a novel approach to study CUB, we called “mapping-on-codons”. We positioned 2828 dystrophin missense and nonsense pathogenic variations on their respective codon, highlighting that its frequency and occurrence is not dependent on the CU values. We conclude our strategy consents to identify a hierarchical clustering of CU values in a gene cohort-specific fingerprints, with recognizable trend across mammals. In DC muscle genes also a disease-related fingerprint can be observed, allowing discrimination between DC and NDC genes. We propose that using our strategy which studies CU in specific gene cohorts, as rare disease genes, and tissue specific genes, may provide novel information about the CUB role in human and medical genetics, with implications on synonymous variations interpretation and codon optimization algorithms.

We compared relative synonymous codon usage (RSCU) across 15 species in 29 non-disease-causing (NDC) and 31 disease-causing (DC) kidney, muscle and skingenes. RSCU shows tissue-specific, evolutionarily conserved, and disease-specific fingerprints. The majority of DC genes display a lower codon usage bias (CUB) and show a different RSCU hierarchical clustering. Peculiarly, the DMD gene does not show any extreme CUB and still uses all synonymous codons. By “mapping-on-codons” its 2828 pathogenic variations, we found that missense and nonsense variations occurrence is CUB-independent. We conclude that DC and NDC genes have a specific RSCU behavior, underlined by a clear evolutionary trend, and a recognizable phenotype-related fingerprint. We suggest that studying CUB in rare-disease genes is a new and promising model to help understand its implications in gene evolution, mutational events, variations interpretation, and codon optimization for gene therapies.

The etiology of 80% of patients with primary antibody deficiency (PAD), the second most common type of human immune system disorder after human immunodeficiency virus infection, is yet unknown. Clinical/immunological phenotyping and exome sequencing of a cohort of 126 PAD patients (55.5% male, 95.2% childhood onset) born to predominantly consanguineous parents (82.5%) with unknown genetic defects were performed. The American College of Medical Genetics and Genomics criteria were used for validation of pathogenicity of the variants. This genetic approach and subsequent immunological investigations identified potential disease-causing variants in 86 patients (68.2%); however, 27 of these patients (31.4%) carried autosomal dominant (24.4%) and X-linked (7%) gene defects. This genetic approach led to the identification of new phenotypes in 19 known genes (38 patients) and the discovery of a new genetic defect (CD70 pathogenic variants in 2 patients). Medical implications of a definite genetic diagnosis were reported in ~50% of the patients. Due to misclassification of the conventional approach for targeted sequencing, employing next-generation sequencing as a preliminary step of molecular diagnostic approach to patients with PAD is crucial for management and treatment of the patients and their family members.

Pancreatic cancer remains a challenging disease with an overall cumulative 5-year survival rate around 6%. Though significant progress has been made in the availability of diagnostic techniques and treatment strategies, pancreatic cancer remains a disease of high mortality rate. Therefore, there is an urgent need for a better understanding of the molecular mechanisms that governs the oncogenesis and metastasis process of pancreatic cancer. In the present study, by using the Cancer Genome Atlas (TCGA) dataset analysis, we demonstrated that sorting nexin 6 (SNX6) serves as a biomarker for predicting prognosis of pancreatic cancer. In vitro studies demonstrated that silencing of SNX6 expression reduced cell proliferation, colony formation, invasion, and metastasis. Higher level of SNX6 helps maintain the mesenchymal properties, which renders migration and invasive capacities to pancreatic cancer cells. Moreover, in the process of TGF-β-induced epithelial to mesenchymal transition (EMT), the expression level of SNX6 was increased, and silencing of SNX6 expression could inhibit the TGF-β-induced EMT program. These results collectively uncovered a novel predictive marker for pancreatic cancer and provided the possible underlying molecular mechanism.

// Yun Wang 1, * , Abir Garraoui 2, 3, * , Liuzhi Zeng 4, * , Mingying Lai 1 , Fen He 1 , Huaizhou Wang 5 , Chongyi Jiang 2 , Yulan Chen 2 , Lanlan Dai 2 , Ning Fan 1 , Huanming Yang 2, 6 , Jianguo Zhang 2, 7 and Xuyang Liu 1 1 Shenzhen Key Laboratory of Ophthalmology, Shenzhen Eye Hospital, Shenzhen University, Shenzhen, China 2 BGI-Shenzhen, Shenzhen, China 3 Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia 4 The First People's Hospital of Chengdu, Chengdu, China 5 Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Ophthalmology & Visual Sciences Key Laboratory, Capital Medical University, Beijing, China 6 James D. Watson Institute of Genome Sciences, Hangzhou, China 7 Shenzhen Key Laboratory of Neurogenomics, BGI-Shenzhen, Shenzhen, China * These authors have contributed equally to this work Correspondence to: Xuyang Liu, email: xliu1213@126.com Jiangguo Zhang, email: Jianguozhang@genomics.cn Keywords: Bardet-Biedl syndrome, retinitis pigmentosa, FBN3 , whole exome sequencing Received: March 27, 2017 Accepted: August 29, 2017 Published: September 30, 2017 ABSTRACT Purpose: This study was designed to evaluate the molecular genetics of a Chinese family with Bardet-Biedl syndrome (BBS). Methods: All the family members underwent medical history evaluation, ophthalmologic and physical examinations. Whole exome sequencing was performed on two affected individuals and their parents. All variants were verified in all family members by PCR amplification and Sanger sequencing. Results: Patients in this family were diagnosed as Bardet-Biedl syndrome, with an inheritance pattern of autosomal recessive. Compound heterozygous mutations of the FBN3 gene (c.3616G>A and c.6037C>T) were identified by whole exome sequencing. Results from Sanger sequencing showed co-segregation of these compound heterozygous mutations in the FBN3 gene with BBS disease in the family. Conclusion: Novel compound heterozygous mutations c.3616G>A and c.6037C>T of FBN3 were identified in all affected individuals but not in the unaffected family members. This is the first time to the best of our knowledge, that the FBN3 gene is involved in the pathogenesis of BBS. This study will expand our understanding about the gene spectrum related to this genetically heterogeneous disorder.

Adipocyte infiltration in pancreatic cancer (PC) has been demonstrated to be independently associated with PC risk and an active contributor to tumor progression. However, to date, little is known about these unique pancreatic tumor-surrounding adipocytes, or their response to cancer cells. The present study utilized an in vitro indirect coculture model in which the phenotypic changes of adipocytes following exposure to PC cells were directly observed. RNA-sequencing was performed on 3T3-L1 adipocytes cultured with or without Panc-1 cancer cells, and significant changes were identified at the transcriptional level. In terms of delipidation and the impaired function of glucose and lipid metabolism, coculture with tumor cells resulted in an altered metabolic phenotype in mature adipocytes. In co-cultured adipocytes, the appearance of fibroblast-like cells was observed, and the mesenchymal cell differentiation pathway was enriched following the integrated analysis into the transcriptome. In addition, reverse transcription-quantitative PCR analyses of co-cultured adipocytes revealed a loss in gene expression of mature adipocyte markers, and a gain in gene expression of fibroblast-specific markers. It was also confirmed that newly generated cancer-associated adipocytes could facilitate the invasive capacities of the tumor, and may contribute to PC stromal remodeling. The present study supports a novel concept that reprogramming of stromal adipocytes orchestrated by PC cells may generate cancer-associated adipocytes with activated phenotypes, which may ultimately drive pancreatic tumor progression.

// Sujie Ni 1, * , Hongwei Wang 1, 2, * , Xiaolin Zhu 3 , Chunhua Wan 4 , Junfei Xu 5 , Chen Lu 6 , Li Xiao 6 , Jiaqi He 2 , Chongyi Jiang 2 , Wei Wang 2 , Zhixian He 5 1 Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong University, Nantong 226001, China 2 Bilary and Pancreatic Center, Huadong Hospital of Fudan University, Fudan University, Shanghai 200040, China 3 Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong University, Nantong 226001, China 4 Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226001, China 5 Department of General Surgery, Affiliated Hospital of Nantong University, Nantong University, Nantong 226001, China 6 Department of Pathology, Huadong Hospital of Fudan University, Fudan University, Shanghai 200040, China * These authors have contributed equally to this work Correspondence to: Zhixian He, email: hezhixian@ntu.edu.cn Wei Wang, email: hdwangwei@fudan.edu.cn Keywords: CBX7, pancreatic cancer, prognosis, tumor suppression, PTEN Received: April 23, 2016 Accepted: November 21, 2016 Published: December 20, 2016 ABSTRACT Chromobox protein homolog 7 (CBX7), one of the polycomb group (PcG) proteins, is a transcriptional repressor involved in the regulation of cell proliferation and senescence. In the present study, we showed that CBX7 negatively regulates the proliferation, viability, chemoresistance, and migration of pancreatic cancer cells. Overexpression of CBX7 significantly inhibited the proliferation of pancreatic cancer cells in vitro and in vivo . Depletion of CBX7 facilitated their growth. CBX7 also impaired the viability and chemoresistance of pancreatic cancer cells. Transwell assays showed that CBX7 reduces the migratory capacity of pancreatic cancer cells. Of note, CBX7 reduced PTEN/Akt signaling in pancreatic cancer cells by increasing PTEN transcription, suggesting involvement of PTEN/Akt pathway in the tumor suppressive activity of CBX7. In addition, immunohistochemical analysis the CBX7 and PTEN expression in 74 surgically resected pancreatic ductal adenocarcinoma (PDAC) specimens revealed that CBX7 expression is significantly downregulated in pancreatic ductal adenocarcinoma, compared to normal pancreatic tissues. Reduced expression of CBX7 and PTEN was associated with increased malignancy grade in pancreatic adenocarcinoma, whereas maintenance of CBX7 and PTEN expression showed a trend toward a longer survival. These findings suggest CBX7 is an important tumor suppressor that negatively modulates PTEN/Akt signaling during pancreatic tumorigenesis.

Additional file 2: Figure S1. Representative USG image of mice eyes. Both males and females eyes of every examined group are presented.

Zinc finger 644 (Zfp644 in mouse, ZNF644 in human) gene is a transcription factor whose mutation S672G is considered a potential genetic factor of inherited high myopia. ZNF644 interacts with G9a/GLP complex, which functions as a H3K9 methyltransferase to silence transcription. In this study, we generated mouse models to unravel the mechanisms leading to symptoms associated with high myopia. Employing TALEN technology, two mice mutants were generated, either with the disease-carrying mutation (Zfp644S673G) or with a truncated form of Zfp644 (Zfp644Δ8). Eye morphology and visual functions were analysed in both mutants, revealing a significant difference in a vitreous chamber depth and lens diameter, however the physiological function of retina was preserved as found under the high-myopia conditions. Our findings prove that ZNF644/Zfp644 is involved in the development of high-myopia, indicating that mutations such as, Zfp644S673G and Zfp644Δ8 are causative for changes connected with the disease. The developed models represent a valuable tool to investigate the molecular basis of myopia pathogenesis and its potential treatment. Electronic supplementary material The online version of this article (10.1186/s13578-019-0280-4) contains supplementary material, which is available to authorized users.

The etiology of 80% of patients with primary antibody deficiency (PAD), the second most common type of human immune system disorder after human immunodeficiency virus infection, is yet unknown.Clinical/immunological phenotyping and exome sequencing of a cohort of 126 PAD patients (55.5% male, 95.2% childhood onset) born to predominantly consanguineous parents (82.5%) with unknown genetic defects were performed. The American College of Medical Genetics and Genomics criteria were used for validation of pathogenicity of the variants.This genetic approach and subsequent immunological investigations identified potential disease-causing variants in 86 patients (68.2%); however, 27 of these patients (31.4%) carried autosomal dominant (24.4%) and X-linked (7%) gene defects. This genetic approach led to the identification of new phenotypes in 19 known genes (38 patients) and the discovery of a new genetic defect (CD70 pathogenic variants in 2 patients). Medical implications of a definite genetic diagnosis were reported in ~50% of the patients.Due to misclassification of the conventional approach for targeted sequencing, employing next-generation sequencing as a preliminary step of molecular diagnostic approach to patients with PAD is crucial for management and treatment of the patients and their family members.

Background: Congenital cataract is a common cause of childhood vision impairment or blindness with genetic and clinical heterogeneity. The aim of this study was to identify the disease-associated gene in a Chinese family with congenital cataract. Methods: A four-generation Chinese family with three enrolled patients suffering from congenital cataract was studied. Detailed family history and clinical data of all the members were collected and recorded. Exome sequencing was applied in the proband to screen potential genetic variants, and then Sanger sequencing was used to verify the variant within the family. Results: A heterozygous variant, c.3673G > A (p.V1225M), in the periaxin gene ( PRX ) was identified in three patients and two asymptomatic individuals of the family. The variant was absent in the other three unaffected family members and in 3290 ethnically matched in-house controls from BGI-Shenzhen. Conclusions: By utilizing both exome sequencing and Sanger sequencing, we identified a missense variant in the PRX gene that is possibly associated with disease in this family. Our finding may broaden the spectrum of genes associated with congenital cataract, and may provide insights into lens development, pathogenic mechanism, future clinical genetic diagnosis and therapy of congenital cataract.