The interactome of Cryptococcus neoformans Rmt5 reveals multiple regulatory points in fungal cell biology and pathogenesis

Protein arginine methylation is a key post-translational modification in eukaryotes that modulates core cellular processes, including translation, morphology, transcription, and RNA fate. However, this has not been explored in Cryptococcus neoformans, a human-pathogenic basidiomycetous encapsulated fungus. We characterized the five protein arginine methyltransferases in C. neoformans and highlight Rmt5 as critical regulator of cryptococcal morphology and virulence. An rmt5∆ mutant was defective in thermotolerance, had a remodeled cell wall, and exhibited enhanced growth in an elevated carbon dioxide atmosphere and in chemically induced hypoxia. We revealed that Rmt5 interacts with post-transcriptional gene regulators, such as RNA-binding proteins and translation factors. Further investigation of the rmt5∆ mutant showed that Rmt5 is critical for the homeostasis of eIF2α and its phosphorylation state following 3-amino-1,2,4-triazole-induced ribosome stalling. RNA sequencing of one rmt5∆ clone revealed stable chromosome 9 aneuploidy that was ameliorated by complementation but did not impact the rmt5∆ phenotype. As a result of these diverse interactions and functions, loss of RMT5 enhanced phagocytosis by murine macrophages and attenuated disease progression in mice. Taken together, our findings link arginine methylation to critical cryptococcal cellular processes that impact pathogenesis, including post-transcriptional gene regulation by RNA- binding proteins.

HDAC6 Interacts With Poly (GA) and Modulates its Accumulation in c9FTD/ALS

The aberrant translation of a repeat expansion in chromosome 9 open reading frame 72 (C9orf72), the most common cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), results in the accumulation of toxic dipeptide repeat (DPR) proteins in the central nervous system We have found that, among the sense DPR proteins, HDAC6 specifically interacts with the poly (GA) and co-localizes with inclusions in both patient tissue and a mouse model of this disease (c9FTD/ALS). Overexpression of HDAC6 increased poly (GA) levels in cultured cells independently of HDAC6 deacetylase activity, suggesting that HDAC6 can modulate poly (GA) pathology through a mechanism that depends upon their physical interaction. Moreover, decreasing HDAC6 expression by stereotaxic injection of antisense oligonucleotides significantly reduced the number of poly (GA) inclusions in c9FTD/ALS mice. These findings suggest that pharmacologically reducing HDAC6 levels could be of therapeutic value in c9FTD/ALS.

SWI/SNF-Related SMARCA2 Gene Mutation Associated with Nicolaides–Baraitser's Syndrome: Follow-up Study

Nicolaides–Baraitser's syndrome is a rare, dominantly inherited well-delineated syndrome caused by mutations in the SMARCA2 gene which is located on the small arm of chromosome 9. In this study, a de novo missense variant, which was identified in a 3-year-old boy by whole exome sequencing is reported. The de novo heterozygous V1198M missense variant in SMARCA2 gene in exon 25 is novel. Identifying the condition is crucial for the long-term management and family counseling. Follow-up over 4 years revealed improvements in overall performance.

Analysis of the Link between rs4977574 Single Nucleotide Polymorphism of the Long Non-Coding RNA ANRIL Gene and Prostate Cancer Development

The purpose of the study was to investigate the possible association between ANRIL gene rs4977574-polymorphism and prostate cancer occurrence among men of the Ukrainian population. Materials and methods. A total of 250 males were enrolled in the study. Of these, the experimental group included 184 prostate cancer patients, and the control group included 66 men without a history of malignant tumors. Genotyping of the ANRIL rs4977574 locus was performed by real-time polymerase chain reaction. The reaction was performed on a Quant Studio 5 DX Real-Time instrument (Applied Biosystems, USA) in the presence of TaqMan assays (TaqMan®SNP Assay C_31720978_30). The genotyping results were statistically processed using the SPSS software package (version 17.0). Values of p less than 0.05 were considered as statistically significant. Results and discussion. ANRIL (Antisense Non-coding RNA in the INK4 Locus), also known as CDKN2B-AS1, is a long non-coding RNA (3.8-kb) transcribed from the short arm of the human chromosome 9 (p21.3). ANRIL transcripts promote their main molecular effects through interaction with proteins of Polycomb repressive complex 1 and Polycomb repressive complex 2. Ultimately, this leads to epigenetic cis-inactivation of the tumor growth suppressor genes located in the Chr9p21 region: CDKN2A/p16INK4A, CDKN2A/p14ARF, CDKN2B/p15INK4B. Recent experimental studies have demonstrated the involvement of ANRIL in the development of malignant tumors of different localization. At the same time, there is almost no information about the role of the gene polymorphisms of this RNA in the occurrence of prostate cancer. The possible link between ANRIL gene polymorphism and prostate cancer risk in the Ukrainian population is not fully understood. It was found that the control men and prostate cancer patients did not differ significantly in the frequency of rs4977574-genotypes (p = 0.886). No significant difference was found during the corresponding comparison separately among persons with normal weight, overweight, without, and with the habit of smoking (p >0.05). Analysis of the association of different rs4977574 genotypes of the ANRIL gene with the risk of prostate cancer using logistic regression also did not show a reliable relationship under different models of inheritance, both before and after adjustment for age, body mass index and smoking (p >0.05). Conclusion. Thus, for the first time, we performed an analysis of the relation between ANRIL gene polymorphism and the development of malignant tumors of the genitourinary system in the Ukrainian population. The results showed that the polymorphic locus rs4977574 is not associated with the risk of prostate cancer

No Evidence of Abnormal Expression of Beta-Catenin and Bcl-2 Proteins in Pilomatricoma as One Clinical Feature of Tetrasomy 9p Syndrome

Background. Little is currently known about the genetics of pilomatricoma. A number of studies have reported some evidence that this disease may have a genetic association with mutations of CTNNB1 gene or expression of the beta-catenin protein. In this study, we reviewed literatures involving 30 patients with various genetic syndromes that have been linked to pilomatricoma and found that somatic mutations of the CTNNB1 gene were reported in 67% of patients. Pilomatricoma has been reported in patients with chromosome 9 rearrangements, including 4 patients with tetrasomy 9p syndrome and one patient with partial trisomy 9. In addition to beta-catenin, the expression of bcl2 was observed in pilomatricoma. Objectives. To report an additional case of tetrasomy 9p syndrome with concurrent pilomatricoma and to examine whether abnormal protein expressions of the CTNNB1 and/or BCL2 genes were present. Methods. Cytogenetic analysis was carried out on peripheral blood, biopsied skin, and pilomatricoma tissue obtained from a patient with tetrasomy 9p syndrome. Immunohistochemical staining was performed on the pilomatricoma tissue, using beta-catenin and bcl2 monoclonal antibodies. Results. SNP microarray revealed nonmosaic gain of the short arm of chromosome 9. A nonmosaic isodicentric chromosome 9 was identified in the peripheral blood but this rearranged chromosome was detected in only 8.3% of the skin fibroblasts. Chromosomal abnormalities were not detected in the pilomatricoma nor expression of beta-catenin or bcl2 proteins in our patient. Conclusion. Pilomatricoma could be a new clinical feature associated with tetrasomy 9p syndrome; however, we found no evidence of tetrasomy 9p or abnormal beta-catenin or bcl2 proteins of the CTNNB1 and BCL2 genes in our pilomatricoma patient.

Rare Case of Pericentric Inversion, Inv(9)(p13q34) of the Der(9)t(9;22)(q34;q11) in A Patient with Chronic Myeloid Leukemia – A Case Report

As we know, the Philadelphia chromosome (Ph) is a highly specific marker for chronic myeloid leukemia (CML). This hematological disease is characterised by the formation of the BCR/ABL1 fusion gene, usually with typical translocation pattern including 9q34 and 22q11. In this paper we describe a 55 years old female patient with typical clinical and haematological signs of CML and a chromosome 9 differing from that which normally participates in translocation t(9;22). The karyotype of this Ph positive patient is characterised by pericentric inv(9)(p13q34) of the der(9)t(9;22)(q34;q11). Reverse transcriptase-polymerase chain reaction revealed a e14a2 type of BCR/ABL1 fusion transcript. As a consequence of this unusual translocation, FISH also found the separation of the ABL1/BCR1 fusion gene on chromosome 9. On reviewing the literature, to date only 10 Ph-positive leukemia patients have been noticed to have pericentric inversion inv(9)(p22q34)der(9)t(9;22)(q34;q11). No one case has been described with pericentric inversion inv(9)(p13q34) of the der(9)t(9;22)(q34;q11). This indicate that pericentric inv(9)(p13q34) of the der(9)t(9;22)(q34;q11) is a novel, rare, chromosomal abnormality in Ph-positive CML.

Molecular Delineation of De Novo Small Supernumerary Marker Chromosomes in Prenatal Diagnosis, A Retrospective Study

Background To define the genotype-phenotype correlation of small supernumerary marker chromosomes (sSMCs) and conduct precise genetic counseling, we retrospectively searched and reviewed de novo sSMC cases detected during prenatal diagnosis at The First Affiliated Hospital of Zhengzhou University. Chromosome karyotypes of 20,314 cases of amniotic fluid from pregnant women were performed. For 16 samples with de novo sSMCs, 10 were subjected to single-nucleotide polymorphism (SNP) array or low-coverage massively parallel copy number variation sequencing (CNV-seq) analysis. Results Among the 10 sSMC cases, two sSMCs derived from chromosome 9, and three sSMCs derived from chromosomes 12, 18 and 22. The remaining 5 cases were not identified by SNP array or CNV-seq because they lacked euchromatin or had a low proportion of mosaicism. Four of them with a karyotype of 47,XN,+mar presented normal molecular cytogenetic results (seq[hg19] 46,XN), and the remaining patient with a karyotype of 46,XN,+mar presented with Turner syndrome (seq[hg19] 45,X). Five sSMC samples were mosaics of all 16 cases. Conclusion Considering the variable origins of sSMCs, further genetic testing of sSMCs should be performed by SNP array or CNV-seq. Detailed molecular characterization would allow precise genetic counseling for prenatal diagnosis.

The Genetic Control of Polyacetylenes Involved in Bitterness of Carrots (Daucus Carota L.): Identification of QTLs and Candidate Genes From the Plant Fatty Acid Metabolism

Background Falcarinol-type polyacetylenes (PAs) such as falcarinol (FaOH) and falcarindiol (FaDOH) are produced by several Apiaceae vegetables such as carrot, parsnip, celeriac and parsley. They are known for numerous biological functions and contribute to the undesirable bitter off-taste of carrots and their products. Despite their interesting biological functions, the genetic basis of their structural diversity and function is widely unknown. A better understanding of the genetics of the PA levels present in carrot roots might support breeding of carrot cultivars with tailored PA levels for food production or nutraceuticals. Results A large carrot F2 progeny derived from a cross of a cultivated inbred line with an inbred line derived from a Daucus carota ssp. commutatus accession rich in PAs was used for linkage mapping and quantitative trait locus (QTL) analysis. Ten QTLs for FaOH and FaDOH levels in roots were identified in the carrot genome. Major QTLs for FaOH and FaDOH with high LOD values of up to 40 were identified on chromosomes 4 and 9. To discover putative candidate genes from the plant fatty acid metabolism, we examined an extended version of the inventory of the carrot FATTY ACID DESATURASE2 (FAD2) gene family. Additionally, we used the carrot genome sequence for a first inventory of ECERIFERUM1 (CER1) genes possibly involved in PA biosynthesis. We identified genomic regions on different carrot chromosomes around the found QTLs, that contain several FAD2 and CER1 genes within their 2-LOD confidence intervals. With regard to the major QTLs on chromosome 9 three putative CER1 decarbonylase gene models are proposed as candidate genes. Conclusion The present study increases the current knowledge on the genetics of PA accumulation in carrot roots. Our finding, that carrot candidate genes from the fatty acid metabolism are significantly associated with major QTLs for both major PAs, will facilitate future functional gene studies and a further dissection of the genetic factors controlling PA accumulation. Characterization of such candidate genes will have a positive impact on carrot breeding programs aimed at both lowering or increasing PA concentrations in carrot roots.

Identification, Analysis, and Confirmation of Seed Storability-Related Loci in Dongxiang Wild Rice (Oryza rufipogon Griff.)

Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) has strong seed storability and identifying its elite gene resources may facilitate genetic improvements in rice seed storability. In this study, we developed two backcross inbred lines (BILs) populations, with DXWR as a common donor parent and two rice varieties (F6 and R974) as recipient parents. Bulked segregant analysis via whole genome sequencing (BSA-seq) was used to identify seed storability-related loci in the DXWR and F6 population. Two main genomic regions containing 18,550,000–20,870,000 bp on chromosome 4 and 7,860,000–9,780,000 bp on chromosome 9 were identified as candidate loci of DXWR seed storability; these overlapped partially with seed storability-related quantitative trait loci (QTLs) discovered in previous studies, suggesting that these loci may provide important regions for isolating the responsible genes. In total, 448 annotated genes were predicted within the identified regions, of which 274 and 82 had nonsynonymous and frameshift mutations, respectively. We detected extensive metabolic activities and cellular processes during seed storability and confirmed the effects of the seed storability-related candidate loci using four BILs from DXWR and R974. These results may facilitate the cloning of DXWR seed storability-related genes, thereby elucidating rice seed storability and its improvement potential.