Functional characterization of a rare pathogenic variant c.875G > A, p.(Cys292Tyr) in COMP.

BACKGROUND: The protein encoded by the cartilage oligomeric matrix protein (COMP) gene is a noncollagenous extracellular matrix (ECM) protein that is important for chondrocyte formation and growth. Variations in the COMP gene cause pseudoachondroplasia (PSACH), which is mainly characterized by short-limbed dwarfing in the clinic. AIMS: To characterize the function of a rare pathogenic variant in the COMP gene (c.875G > A, p.Cys292Tyr). MATERIALS & METHODS: We performed 3D structural analysis, in vitro expression analysis, and immunofluorescence to characterize the effects of the variant on protein structure, expression, and cellular localization respectively. RESULTS: Variation modeling showed that the interactions between amino acids were changed after the variation, and there were 31 changes in the secondary structure of mutant COMP (MT-COMP). Western blot showed that the intracellular quantity of MT-COMP was higher than the wild-type COMP (WT-COMP). Cellular immunofluorescence results showed that WT-COMP was less abundant and homogenously distributed in cells, while the MT-COMP accumulated in the cytoplasm. DISCUSSION: Herein, we report a variant of COMP in a Chinese family with PSACH. We have shown that the rare missense variant, COMP c.875G > A, previously reported in ClinVar and identified in our patient, results in excessive accumulation of mutant protein in the cytoplasm, and is therefore pathogenic. CONCLUSION: Through in silico and experimental analyses, we provide evidence that COMP c.875G > A is the likely cause of PSACH in a Chinese family.

[Analysis of C2ORF71 gene variant in a Chinese patient with retinitis pigmentosa].

OBJECTIVE: To explore the genetic basis for a Chinese patient with retinitis pigmentosa (RP). METHODS: Whole exome sequencing (WES) was carried out to screen potential variant in the proband. Candidate variants were determined by taking consideration of clinical phenotype. Sanger sequencing was used to verify the variant in the proband and his parents. RESULTS: The proband was found to harbor compound heterozygous variants of c.8G>A (p.Cys3Tyr) and c.958_959insA (p.Arg320Glnfs*29) in the C2ORF71 gene, which has derived from his father and mother, respectively. Both variants were unreported previously. Based on the ACMG guidelines, they were predicted to be likely pathogenic and pathogenic, respectively. CONCLUSION: The novel compound heterozygous variants of the C2ORF71 gene probably underlay the pathogenesis of RP in the proband. Above finding has enriched the spectrum of C2ORF71 gene mutations and facilitated genetic counseling for the family.

PIWIL1 suppresses circadian rhythms through GSK3ß-induced phosphorylation and degradation of CLOCK and BMAL1 in cancer cells.

Circadian rhythms are maintained by series of circadian clock proteins, and post-translation modifications of clock proteins significantly contribute to regulating circadian clock. However, the underlying upstream mechanism of circadian genes that are responsible for circadian rhythms in cancer cells remains unknown. PIWIL1 participates in many physiological processes and current discoveries have shown that PIWIL1 is involved in tumorigenesis in various cancers. Here we report that PIWIL1 can suppress circadian rhythms in cancer cells. Mechanistically, by promoting SRC interacting with PI3K, PIWIL1 can activate PI3K-AKT signalling pathway to phosphorylate and inactivate GSK3ß, repressing GSK3ß-induced phosphorylation and ubiquitination of CLOCK and BMAL1. Simultaneously, together with CLOCK/BMAL1 complex, PIWIL1 can bind with E-BOX region to suppress transcriptional activities of clock-controlled genes promoters. Collectively, our findings first demonstrate that PIWIL1 negatively regulates circadian rhythms via two pathways, providing molecular connection between dysfunction of circadian rhythms and tumorigenesis.

PIWIL2 stabilizes ß-catenin to promote cell cycle and proliferation in tumor cells.

PIWIL2 belongs to the PIWI protein subfamily and is widely expressed in a variety of tumors. Previous studies have shown that PIWIL2 has the characteristics of oncogene. Recently we reported that PIWIL2 suppresses GSK3ß activity to regulate circadian rhythms through SRC-PI3K-AKT pathway. As GSK3ß is a key part of the ß-catenin destruction complex, it plays a vital role in regulating the degradation of ß-catenin. Besides, the activated ß-catenin/CyclinD1 pathway is involved in the proliferation of tumor cells. It is intriguing to investigate whether PIWIL2 regulates ß-catenin and downstream pathway. In this study, we found that PIWIL2 suppressed GSK3ß induced phosphorylation and ubiquitination of ß-catenin, and thus increased ß-catenin accumulation in the nucleus. By up-regulating ß-catenin and CyclinD1, PIWIL2 can promote cell cycle and proliferation in tumor cells. Taken together, our results revealed a novel function of PIWIL2 in regulating ß-catenin/CyclinD1 pathway in tumor cells, providing a new perspective for PIWIL2 as an oncogene.

DNA demethylation facilitates the specific transcription of the mouse X-linked Tsga8 gene in round spermatids†.

Some X-linked genes necessary for spermiogenesis are specifically activated in the postmeiotic germ cells. However, the regulatory mechanism about this activation is not clearly understood. Here, we examined the potential mechanism controlling the transcriptional activation of the mouse testis specific gene A8 (Tsga8) gene in round spermatids. We observed that the Tsga8 expression was negatively correlated with the methylation level of the CpG sites in its core promoter. During spermatogenesis, the Tsga8 promoter was methylated in spermatogonia, and then demethylated in spermatocytes. The demethylation status of Tsga8 promoter was maintained through the postmeiotic germ cells, providing a potentially active chromatin for Tsga8 transcription. In vitro investigation showed that the E12 and Spz1 transcription factors can enhance the Tsga8 promoter activity by binding to the unmethylated E-box motif within the Tsga8 promoter. Additionally, the core Tsga8 promoter drove green fluorescent protein (GFP) expression in the germ cells of Tsga8-GFP transgenic mice, and the GFP expression pattern was similar to that of endogenous Tsga8. Moreover, the DNA methylation profile of the Tsga8-promoter-driven transgene was consistent with that of the endogenous Tsga8 promoter, indicating the existence of a similar epigenetic modification for the Tsga8 promoter to ensure its spatiotemporal expression in vivo. Taken together, this study reports the details of a regulatory mechanism that includes DNA methylation and transcription factors to mediate the postmeiotic expression of an X-linked gene.

[Mutation analysis of a family affected with isolated proteinuria].

OBJECTIVE: To analyze the clinical characteristics and genetic features of a family affected with isolated proteinuria. METHODS: Clinical data of the family was collected. Mutations of 191 renal disease-related genes in the proband were screened with next generation sequencing (NGS). Sanger sequencing was used to verify suspected mutations in his family members and 100 healthy controls. The impact of the mutation was predicted with online software SIFT. Frequency of the mutation was searched in databases including 1000 Genomic Project, ESP and ExAC. RESULTS: NGS and Sanger sequencing showed that the proband harbored compound heterozygous mutations of ADCK4 gene including c.748C>G (p.Asp250His) and c.1041G>T (p.Cys347*), which were respectively inherited from his mother and father whom were both non-symptomatic. CONCLUSION: The proband may have ADCK4-associated glomerulopathy due to the compound heterozygous mutations of the ADCK4 gene.

Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.

Circadian clock and Smad2/3/4-mediated Nodal signaling regulate multiple physiological and pathological processes. However, it remains unknown whether Clock directly cross-talks with Nodal signaling and how this would regulate embryonic development. Here we show that Clock1a coordinated mesoderm development and primitive hematopoiesis in zebrafish embryos by directly up-regulating Nodal-Smad3 signaling. We found that Clock1a is expressed both maternally and zygotically throughout early zebrafish development. We also noted that Clock1a alterations produce embryonic defects with shortened body length, lack of the ventral tail fin, or partial defect of the eyes. Clock1a regulates the expression of the mesodermal markers ntl, gsc, and eve1 and of the hematopoietic markers scl, lmo2, and fli1a Biochemical analyses revealed that Clock1a stimulates Nodal signaling by increasing expression of Smad2/3/4. Mechanistically, Clock1a activates the smad3a promoter via its E-box1 element (CAGATG). Taken together, these findings provide mechanistic insight into the role of Clock1a in the regulation of mesoderm development and primitive hematopoiesis via modulation of Nodal-Smad3 signaling and indicate that Smad3a is directly controlled by the circadian clock in zebrafish.

[Identification of proteins interacting with the circadian clock protein PER1 in tumors using bacterial two-hybrid system technique].

OBJECTIVE: To identify protein-protein interaction partners of PER1 (period circadian protein homolog 1), key component of the molecular oscillation system of the circadian rhythm in tumors using bacterial two-hybrid system technique. METHODS: Human cervical carcinoma cell Hela library was adopted. Recombinant bait plasmid pBT-PER1 and pTRG cDNA plasmid library were cotransformed into the two-hybrid system reporter strain cultured in a special selective medium. Target clones were screened. After isolating the positive clones, the target clones were sequenced and analyzed. RESULTS: Fourteen protein coding genes were identified, 4 of which were found to contain whole coding regions of genes, which included optic atrophy 3 protein (OPA3) associated with mitochondrial dynamics and homo sapiens cutA divalent cation tolerance homolog of E. coli (CUTA) associated with copper metabolism. There were also cellular events related proteins and proteins which are involved in biochemical reaction and signal transduction-related proteins. CONCLUSION: Identification of potential interacting proteins with PER1 in tumors may provide us new insights into the functions of the circadian clock protein PER1 during tumorigenesis.

PKM2 is a potential prognostic biomarker and related to immune infiltration in lung cancer.

Pyruvate kinase M2 (PKM2), a subtype of pyruvate kinase, plays a crucial role as a key enzyme in the final step of glycolysis. It is involved in regulating the tumor microenvironment and accelerating tumor progression. However, the relationship between PKM2 expression and the prognosis and immune infiltration remains unclear in lung cancer. In this study, we analyzed PKM2 expression in pan-cancer, and investigated its association with prognosis and immune cell infiltration of lung cancer by using multiple online databases, including Gent2, Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), PrognoScan, Kaplan-Meier plotter, and The Human Protein Atlas (HPA). The results showed that PKM2 expression is elevated in tumor tissues compared with the adjacent normal tissues of most cancers, including lung cancer. Prognostic analysis indicated that high expression of PKM2 was associated with poorer prognosis in overall lung cancer patients, especially in lung adenocarcinoma (LUAD). Notably, PKM2 exhibited a strong correlation with B cells and CD4+ T cells in LUAD; and with B cells, CD8+ T cells, CD4+ cells, and macrophages in lung squamous cell carcinoma (LUSC). Furthermore, PKM2 expression displayed a significant negative correlation with the expression of immune cell markers in both LUAD and LUSC. These findings suggested that PKM2 could serve as a promising prognostic biomarker for lung cancer and provided insights into its essential role in modulating the immune cell infiltration.

A novel NPHS2 mutation (c.865A > G) identified in a Chinese family with steroid-resistant nephrotic syndrome alters subcellular localization of nephrin.

BACKGROUND: NPHS2 is the causative gene of nephrotic syndrome type 2 (MIM 600995) which often clinically manifests as steroid-resistant nephrotic syndrome (SRNS). The NPHS2 gene encodes a slit diaphragm (SD) associated protein podocin. OBJECTIVE: This study reported a novel disease-causing mutation of NPHS2 in a Chinese family with SRNS. We also investigated the pathogenic mechanism of the variants in this family. METHOD: A Chinese family with SRNS was recruited. Whole exome sequencing was performed to screen for disease-causing mutation. Sanger sequencing was used to confirm the results. In vitro functional experiments including immunoblotting, co-immunoprecipitation and double immunofluorescence staining were performed to explore the pathogenic mechanisms of mutations. RESULTS: In this family, compound heterozygous mutations of NPHS2 (c.467dupT and c.865A > G) were identified and segregated with the disease. The maternal c.865A > G was a novel variant, leading to amino acid substitution (p.K289E). In vitro functional assays indicated that c.467dupT (p.L156FfsX11) mutant lost interaction with nephrin. Both K289E and L156FfsX11 mutants showed sharply diminished plasma membrane localization. Furthermore, abnormal distribution of podocin mutants also altered the cell membrane localization of nephrin. CONCLUSION: We reported a family with SRNS caused by compound heterozygous mutations of NPHS2 (c.467dupT and c.865A > G). c.865A > G (p.K289E) in NPHS2 was a novel causative variant associated with SRNS. Both variants in this family not only affected the normal cell membrane localization of podocin, but also altered the cell membrane localization of nephrin which is the major architectural protein of SD.

[Identification and expression analysis of Macaca mulatta piwil4 gene].

To investigate the structure and expression pattern of rhesus monkey PIWIL4 protein, homologous comparison and reverse transcription PCR (RT-PCR) were carried out to identify rhesus monkey piwil4. The expression of piwil4 mRNA was tested in rhesus monkey heart, brain, colon, epididymis and testis, and the result showed that piwil4 mRNA was expressed in these rhesus monkey tissues. Bioinformatic analysis suggested that the rhesus PIWIL4 protein shared 97% identity in amino acids and the same domains such as PAZ and Piwi with the human PIWIL4 (HIWI2) protein. The immunohistochemical result indicated that PIWIL4 proteins had the same localization in adult testes of the two species, but the distribution of these proteins was altered dynamically at different developmental stages in rhesus monkey testes. PIWIL4 protein was expressed in the nucleus of convoluted seminiferous tubules in infant monkey testes, whereas it was expressed in the cytoplasm of adult monkey testes. The results suggest that piwil4 gene play a similar role in rhesus and human, and different localizations of PIWIL4 protein in infant monkey and adult monkey testes suggest that it functions differently at different developmental stages.

PIWIL2 interacting with IKK to regulate autophagy and apoptosis in esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies and cause of death from cancer in China. Previous studies showed that autophagy and apoptosis inhibition are critical for the survival of ESCC cells. However, the underlying mechanisms remain to be clarified. Recently, we found that PIWIL2, a novel cancer testis protein, is highly expressed in ESCC and associated with high T-stage and poor 5-year survival rate in patients. Our further study showed that PIWIL2 can directly bind to IKK and promote its phosphorylation, leading to phosphorylation of IκB and subsequently nuclear translocation of NF-κB for apoptosis inhibition. Meanwhile, PIWIL2 competitively inhibits binding of IKK to TSC1, and thus deactivate mTORC1 pathway which suppresses ULK1 phosphorylation and initiation of autophagy. The mouse xenograft model suggested that PIWIL2 can promote ESCC growth in an IKK-dependent manner. This present work firstly revealed that PIWIL2 can play a role in regulating autophagy and apoptosis, and is associated with poor prognosis in ESCC patients, providing novel insights into the roles of PIWIL2 in tumorigenesis.

Compound heterozygous KCNV2 variants contribute to cone dystrophy with supernormal rod responses in a Chinese family.

BACKGROUND: Cone dystrophy with supernormal rod response (CDSRR) is an autosomal recessive retinal disorder characterized by myopia, dyschromatopsia, nyctalopia, photophobia, and nystagmus. CDSRR is caused by mutations in KCNV2, the gene encoding for an electrically silent Kv subunit (Kvs) named Kv8.2. METHODS: A Chinese CDSRR family was recruited. Complete ophthalmology clinical examinations were performed to clarify the phenotype. Genetic examination was underwent using whole exome sequencing (WES). In addition, a candidate gene was validated by Sanger sequencing. Expression analysis in vitro including immunoblotting, quantitative real-time PCR (qRT-PCR), and co-immunoprecipitation experiments was performed to investigate the pathogenic mechanism of the identified gene variants. RESULTS: WES identified two KCNV2 heterozygous mutations from the proband. Sanger sequencing validated that the patient's parents had, respectively, carried those two mutations. Further in vitro functional experiments indicated that the mutated alleles had led the Kv8.2 proteins to fail in expressing and interacting with the Kv2.1 protein, respectively. CONCLUSIONS: This study expanded the KCNV2 mutation spectrum. It can also be deduced that CDSRR has a broad heterogeneity. It is further confirmed that the inability expression of Kv8.2 proteins and the failure of Kv8.2 proteins to interact with Kv2.1 may have accounted for the etiology of CDSRR based on previous studies and this study.

Sp1 plays an important role in regulating the transcription of ZNF313.

The ZNF313 gene has the highest transcription level in fertile male testes and may be related to human spermatogenesis. The deletion-mutated plasmids of ZNF313 promoter were constructed and transfected into HEK293 cells. The result showed that the fragment from nt -157 to +8 has a basal transcriptional activity. A functional Sp1 binding site was identified by site-directed mutation test and mithramycin A treatment. A 447-bp based at +233 to -213 exhibits a characteristic CpG island, which overlaps with the promoter region. Our work suggests that ZNF313 is controlled at the transcriptional level, and a common mechanism controlling the basal transcription of ZNF313 gene exists.

Piwi-like 2 mediates fibroblast growth factor signaling during gastrulation of zebrafish embryo.

Piwi (P-element-induced wimpy testis) proteins have been shown to play important roles in maintenance of germ line stem cells, germ cell proliferation and differentiation, and control of Piwi-interacting RNAs (PiRNAs). PiRNAs comprise a broad class of small noncoding RNAs that function as an endogenous defense system against transposable elements. Fibroblast growth factor (Fgf) signals, mediated partly by no tail gene (ntl), are responsible for patterning embryo and mesoderm formation. To understand the function of Piwi proteins, we used zebrafish as a model system. In zebrafish, piwi-like 2 gene (piwil2) is also required for germ cell differentiation and meiosis. Here we report that piwil2 knockdown is able to inhibit the expression of fibroblast growth factor 8a (fgf8a). In contrast, injection with piwil2 mRNA enhances fgf8a expression. Knockdown of piwil2 reduces the inductive effect of fgf8a on dorsalized phenotype, in which embryos extend to an oval shape at the end of epiboly stage. Coinjection with fgf8a and piwil2 mRNAs led to more seriously dorsalized phenotype than coinjection with fgf8a mRNA and piwil2-cMO. In addition, knockdown of piwil2 inhibits the inductive effect of fgf8a on ntl, whereas overexpression of piwil2 enhances the inductive effect of fgf8a on ntl. We also demonstrate that piwil2 positively regulates ntl expression at bud stage, while piwil2 negatively regulates ntl expression at 24 hours post-fertilization. Thus, the functional consequences of piwil2 expression vary during early development of zebrafish embryo. Taken together, we suggest that zebrafish piwil2 is a mediator of Fgf signals in gastrula period.

[Initial study on zili functions to the development of the germ layers during zebrafish early embryogenesis].

OBJECTIVE: To study the role for piwil2 gene (zili) in the development of the ectoderm, mesoderm and endoderm during early embryogenesis of zebrafish. METHODS: zili morpholino antisense oligonucleotide and 5 mis-pair control morpholino were used in this study. zili was cloned into expression vector. zili mRNA was synthesized in vitro. The antisense RNA probes of gsc, evel and sox17 were synthesized. zili-MO, zili-cMO and zili mRNA was microinjected into one-cell embryos, respectively. Whole-mount in situ hybridization was used to monitor the expressions of marker genes. RESULTS: Microinjection of zili-MO, which knocked down the expression of zili, downregulated the expression of the ectodermal and mesodermal marker gene gsc, promoting the expression of the ectodermal marker gene evel and resulting in the decrease of endodermal cell expressed sox17. The overexpression of zili, promoting the expression of gsc, inhibiting the expression of eve1 and resulting in the decrease of endodermal cell expressed sox17 were observed after microinjection of zili-mRNA. CONCLUSION: zili might have some effect on the formation of the ectoderm, mesoderm and endoderm during early embryogenesis and might be important for normal embryonic development.

Identification of two rare mutations c.1318G>A and c.6438+2T>G in a Chinese DMD family as genetic markers.

BACKGROUND: Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive disorder with no effective treatment, which underscores the importance of avoiding the birth of children with DMD by identifying pathogenic mutations and obtaining an accurate prenatal diagnosis. OBJECTIVE: The objective of this study was to analyze the genetic defect of a Chinese family where all male patients have died of DMD. METHODS: Multiplex ligation dependent probe analysis (MLPA) and next-generation sequencing (NGS) were employed to detect DMD mutations. The candidate mutations were then validated by Sanger sequencing. In vitro splicing assay was further conducted to examine the potential effect of the novel DMD splice site mutation on splicing. RESULTS: We found that two rare DMD mutations c.1318G>A and c.6438+2T>G passed from generation to generation among female carriers and they may be used as genetic markers in the Chinese DMD family. In vitro splicing assay further revealed that the novel classical splice site mutation c.6438+2T>G gave rise to a new donor splice site, which resulted in a frame shift of the transcripts and a premature termination at position 2159 in exon 45 (p.Y2144Nfs*16). CONCLUSION: We found that two co-inherited mutations passed from generation to generation in female carriers and they may be used as genetic markers in the Chinese DMD family. Our findings not only expanded the DMD mutation spectrum, but also provided an important basis for identifying of female carriers and avoiding the birth of affected male children in this DMD family.

DAZL binds to 3'UTR of Tex19.1 mRNAs and regulates Tex19.1 expression.

Spermatogenesis is a complex process subject to strict controls at both levels of transcription and translation. It has been proposed that DAZL protein binds to RNA in the cytoplasm of germ cells and controls spermatogenesis. In male mice, loss of Dazl results in numerous defects throughout the mitotic and meiotic process of germ cell development. Tex19.1 also plays an important role during spermatogenesis and Tex19.1(-/-) knockout males exhibit impaired spermatogenesis. Mouse DAZL protein can bind to 3'UTR of mTex19.1 mRNAs and may repress mTex19.1 expression at the translational level. These have been confirmed by both electrophoretic mobility shift assay and translation assay in Zebrafish embryo detecting the luciferase activity. Taken together these data suggest that mDazl may regulate mTex19.1 expression through binding to 3'UTR of mTex19.1 mRNAs in germ cells.

Microarray profiling of microRNAs expressed in testis tissues of developing primates.

PURPOSE: MicroRNAs (miRNAs) are small non-coding RNA molecules that have been identified as potent regulators of gene expression. Recent studies indicate that miRNAs are involved in mammalian spermatogenesis but the mechanism of regulation is largely unknown. METHODS: miRNA microarray was employed to compare miRNA expression profiles of testis tissues from immature rhesus monkey (Sample IR), mature rhesus monkey (Sample MR), and mature human (Sample MH). Real-time RT-PCR was used to confirm the changed miRNAs. RESULTS: Twenty-six miRNAs were shared by samples IR/MR and IR/MH with differential expression patterns greater than three-fold difference. PicTar and TargetScan prediction tools predicted a number of target mRNAs, and some of these target genes predicted by miRNAs have been shown to associate with spermatogenesis. CONCLUSIONS: Our results indicate that miRNAs are extensively involved in spermatogenesis and provide additional information for further studies of spermatogenetic mechanisms.

RAE1 promotes BMAL1 shuttling and regulates degradation and activity of CLOCK: BMAL1 heterodimer.

Circadian rhythm is an autoregulatory rhythm, which is sustained by various mechanisms. The nucleocytoplasmic shuttling of BMAL1 is essential for CLOCK translocation between cytoplasm and nucleus and maintenance of the correct pace of the circadian clock. Here we showed that RAE1 and NUP98 can promote the degradation of BMAL1 and CLOCK. Knockdown of RAE1 and NUP98 suppressed BMAL1 shuttling, leading to cytoplasm accumulation of CLOCK. Furthermore, Chip assay showed that knockdown of RAE1 and NUP98 can enhance the interaction between CLOCK: BMAL1 and E-box region in the promoters of Per2 and Cry1 while reducing its transcription activation activity. Our present study firstly revealed that RAE1 and NUP98 are critical regulators for BMAL1 shuttling.