Expanding Phaseolus coccineus Genomic Resources: De Novo Transcriptome Assembly and Analysis of Landraces ‘Gigantes’ and ‘Elephantes’ Reveals Rich Functional Variation Abstract Beans are one of the most important staple crops in the world. Runner bean (Phaseolus coccineus L.) is a small-scale agriculture crop compared to common bean (Phaseolusvulgaris). Beans have been introduced to Europe from the Central America to Europe and since then they have been scattered to different geographical regions. This has resulted in the generation of numerous local cultivars and landraces with distinguished characters and adaptive potential. To identify and characterize the underlying genomic variation of two very closely related runner bean cultivars, we performed RNA-Seq with de novo transcriptome assembly in two landraces of P. coccineus, ‘Gigantes’ and ‘Elephantes’ phenotypically distinct, differing in seed size and shape. The cleaned reads generated 37,379 and 37,774 transcripts for ‘Gigantes’ and ‘Elephantes,’ respectively. A total of 1896 DEGs were identified between the two cultivars, 1248 upregulated in ‘Elephantes’ and 648 upregulated in ‘Gigantes.’ A significant upregulation of defense-related genes was observed in ‘Elephantes,’ among those, numerous members of the AP2-EREBP, WRKY, NAC, and bHLH transcription factor families. In total, 3956 and 4322 SSRs were identified in ‘Gigantes’ and ‘Elephantes,’ respectively. Trinucleotide repeats were the most dominant repeat motif, accounting for 41.9% in ‘Gigantes’ and 40.1% in ‘Elephantes’ of the SSRs identified, followed by dinucleotide repeats (29.1% in both cultivars). Additionally, 19,281 putative SNPs were identified, among those 3161 were non-synonymous, thus having potential functional implications. High-confidence non-synonymous SNPs were successfully validated with an HRM assay, which can be directly adopted for P. coccineus molecular breeding. These results significantly expand the number of polymorphic markers within P. coccineus genus, enabling the robust identification of runner bean cultivars, the construction of high-resolution genetic maps, potentiating genome-wide association studies. They finally contribute to the genetic reservoir for the improvement of the closely related and intercrossable Phaseolus vulgaris.

NEMP1 Promotes Tamoxifen Resistance in Breast Cancer Cells Abstract Breast cancer (BC) is a worldwide malignant and a leading death cancer in women. Studies have shown that adjuvant tamoxifen reduces the recurrence rate and metastasis in BC. Even though tamoxifen has been used for the therapy of BC for decades, the resistance of it on BC cells could not be ignored. In this study, we first established a tamoxifen-resistant BC cell line and then demonstrated the overexpression of nuclear envelope integral membrane protein 1 (NEMP1) in the tamoxifen-resistant BC cells. Moreover, through a cell viability assay combined with depletion or overexpression technology, we addressed the important role of NEMP1 for the tamoxifen resistance in BC cells. Importantly, we further revealed that NEMP1 modulated tamoxifen resistance by regulating nuclear receptor coactivator 1 (NCOA1). In general, NEMP1 shows responsibility for the resistance of tamoxifen through regulating NCOA1 in BC cells. These results broaden the understanding of the tamoxifen resistance during the chemotherapy in BC and may provide new therapy method for BC.

Genome-Wide Identification and Comparative Expression Profile Analysis of the Long-Chain Acyl-CoA synthetase ( LACS ) Gene Family in Two Different Oil Content Cultivars of Brassica napus Abstract Long-chain acyl-CoA synthetase (LACS) is one of the key enzymes involved in fatty acid metabolism, including phospholipid biosynthesis, triacylglycerol (TAG) biosynthesis, and fatty acid β-oxidation in plants. However, the characterization of LACSs family in seed oil biosynthesis of Brassica napus (B. napus) remains unknown. In the present study, we performed a comprehensive genome-wide analysis of this gene family in B. napus, and 34 B. napus LACS genes (BnaLACSs) were identified. Phylogenetic analysis classified the BnaLACS proteins into four groups (A, B, C, and D), which were supported by highly conserved gene structures and consensus motifs. RNA-Sequencing (RNA-Seq) and qRT-PCR combined analysis revealed that 18 BnaLACSs (BnaLACS1-2, 1–3, 1–4, 1–9, 1–10, 2–1, 2–2, 4–1, 4–2, 6–1, 6–2, 6–4, 7–1, 7–2, 8–1, 8–2, 9–3, and 9–4) were highly expressed in developmental seeds. Comparative expression analysis between extremely high oil content (P1-HO) and low oil content (P2-LO) B. napus cultivars revealed that BnaLACS6-4, BnaLACS9-3, and BnaLACS9-4 may be involved in fatty acid synthesis in chloroplast, and BnaLACS1-10 and 4–1 may play a vital role in lipid biosynthesis in B. napus, which is important for further seed oil accumulation in oilseed rape. The present study provides important information for functional characterization of BnaLACSs in seed oil metabolism in B. napus.

Altered miR-21, miRNA-148a Expression in Relation to KRAS Mutation Status as Indicator of Adenoma-Carcinoma Transitional Pattern in Colorectal Adenoma and Carcinoma Lesions Abstract Sporadic colorectal cancer (CRC) is a fatal disease, mostly known as the silent killer, due to the fact that this disease is asymptomatic before diagnosis in advanced stage. Screening and the early detection of CRC and colorectal adenoma (CRA) by non-aggressive molecular biomarkers’ signature is useful for improvement of survival rate in CRC patients. To achieve such a goal, a better understanding of distinct molecular abnormalities as candidate biomarkers in CRC development is crucial. In this study, seventy-five archived FFPE CRC samples, including colorectal adenocarcinoma, adenomatous polyps (adenoma), and adjacent non-neoplastic mucosa were collected for the investigation by Sanger sequencing at the DNA level and by real-time PCR at the RNA level. The results of the KRAS mutational analysis have shown that the majority of somatic mutations in the KRAS affect only one codon, mainly codon 12(p.G12D) with low frequency in adenomas (13.3%) versus CRCs (36%). The results of dysregulated epigenetic changes of miR-21 clearly showed upregulation of expression in colorectal adenocarcinoma, compared to non-neoplastic mucosa, in colorectal adenoma vs non-neoplastic mucosa: (p < 0.001) and in CRC versus adenoma (p < 0.001); while miR-148a expression were significantly downregulated in CRC, compared to non-neoplastic mucosa, in colorectal adenoma vs non-neoplastic mucosa, and in adenoma vs CRC (p < 0.001). Our findings support the important role of miR-21 in stages I–II of CRC, and the KRAS G12D mutant, and differential miR-148a expression, in advanced stages of CRC.

Tissue-Specific Monoallelic Expression of Bovine AXL is Associated with DNA Methylation of Promoter DMR Abstract The AXL protein is a receptor tyrosine kinase and is often implicated in proliferation, migration and therapy resistance in various cancers. The AXL gene in humans is maternally expressed and paternally imprinted with differentially methylated regions (DMR) surrounding the promoter region. However, the imprinting status and epigenetic regulation of AXL gene in cattle remain unclear. Therefore, we explored the molecular structure along with the patterns of allelic expression and DNA methylation of the bovine AXL gene. First, the complete cDNA sequence of bovine AXL was gathered by Sanger method, from transcripts obtained from RT-PCR, 5′ and 3′ -RACE. In silico BLAST alignments showed that the longest mRNA sequence of bovine AXL consists of 19 exons and encodes a protein of 887 amino acids. We further analyzed the allelic expression of bovine AXL by employing single-nucleotide polymorphism (SNP)-based sequencing method. A SNP site (GenBank Accession no: rs210020651) found in exon 7 allowed us to distinguish the two parental alleles. Monoallelic expression of AXL was observed in four adult bovine tissues (heart, liver, spleen and fat), while biallelic expression was found in the other adult tissues such as the lung, kidney, muscle, brain and placenta. To determine whether the DNA methylation played a role in the tissue-specific imprinting of bovine AXL, we performed bisulfite sequencing of two regions: region 1 was a CpG island (CGI) in AXL promoter, mapping to 643 bp upstream of the transcription start site of AXL 5′-v1 transcripts, while region two was homologous to the region of human AXL DMR, with 10 CpG sites overlapping the first translation start site (TSS1) of bovine AXL. In region 2, DNA from both monoallelic and biallelic expressed tissues were mostly found to be completely unmethylated. However, tissue-specific differential methylation patterns were found in monoallelic expressed tissues such as the heart and liver while hypomethylation was noted in the promoter CpG island in biallelic expressed tissues such as the lung. These observations demonstrated that the tissue-specific monoallelic expression of bovine AXL is dependent on the DNA methylation of its promoter region.

Epigenetic Modifications in Head and Neck Cancer Abstract Head and neck squamous cell carcinoma (HNSCC) is the sixth most common human malignancy in the world, with high mortality and poor prognosis for patients. Among the risk factors are tobacco and alcohol intake, human papilloma virus, and also genetic and epigenetic modifications. Many studies show that epigenetic events play an important role in HNSCC development and progression, including DNA methylation, chromatin remodeling, histone posttranslational covalent modifications, and effects of non-coding RNA. Epigenetic modifications may influence silencing of tumor suppressor genes by promoter hypermethylation, regulate transcription by microRNAs and changes in chromatin structure, or induce genome instability through hypomethylation. Moreover, getting to better understand aberrant patterns of methylation may provide biomarkers for early detection and diagnosis, while knowledge about target genes of microRNAs may improve the therapy of HNSCC and extend overall survival. The aim of this review is to present recent studies which demonstrate the role of epigenetic regulation in the development of HNSCC.

Haplogroup Structure and Genetic Variation Analyses of 60 Mitochondrial DNA Markers in Southern Shaanxi Han Population Abstract Mitochondrial DNA (mtDNA) has been widely employed as one tool for the studies of human migration and phylogenetic evolution owing to the characteristics of its lack of recombination and matrilineal inheritance. In this study, we analyze genetic distributions of 60 mtDNA markers in 126 unrelated individuals of Southern Shaanxi Han population and classify their haplogroups. Genetic distribution comparisons between Southern Shaanxi Han and other populations from different continents are conducted based on the same mtDNA markers. The majority of 60 mtDNA markers are polymorphic in Southern Shaanxi Han population. The most common haplogroups observed in Southern Shaanxi Han population are B5, followed by D5, A, D4e, and N9a1′3. Obtained matching probability for these 60 mtDNA markers indicates that the panel could be used as a valuable tool in forensic caseworks. Results of genetic distances (Fst) and multidimensional scaling analysis show that Southern Shaanxi Han population has relatively close genetic relationships with other Han populations in different regions. In conclusion, the panel comprising 60 mtDNA markers could be utilized for forensic applications in Southern Shaanxi Han population.

Retraction Note to: Inferring Phylogenetic Relationships of Indian Citron ( Citrus medica L.) Based on rbcL and matK Sequences of Chloroplast DNA The Editor-in-Chief and the publisher have retracted this article [1] because of significant overlap with previously published articles [2–5]. Ajit Uchoi, Surendra Kumar Malik, Ravish Chaudhary, Susheel Kumar, M.R. Rohini, Digvender Pal, and Sezai Ercisli disagree with the retraction. The publisher was not able to get in contact with Rekha Chaudhury, she did not respond to any correspondence about this retraction.

Association of the Variant rs7561317 Downstream of the TMEM18 Gene with Overweight/Obesity and Related Anthropometric Traits in a Sample of Pakistani Population Abstract Obesity is a multifactorial disorder and requires favorable environment for its expression. However, some individuals are more prone to weight gain than others in an obesogenic environment. Thus, at individual level, who becomes overweight or obese is mostly determined by genetic factors. The current study was undertaken to explore for the first time the association of the TMEM18 rs7561317 variant with overweight/obesity and related anthropometric, metabolic, physical, and behavioral traits in a sample of Pakistani population with association between the rs7561317 and many traits was not investigated before in any population. The current study involved a total of 612 subjects including 306 overweight/obese and equal number of age- and sex-matched normal weight individuals. Obesity-related parameters were determined and the variant was genotyped by allelic discrimination assay. All the aforementioned associations were assessed by regression analyses adjusted for covariates and corrected for multiple comparisons. The results revealed a significant association of the TMEM18 rs7561317 with overweight/obese phenotype in more than one genetic model. Therefore, h-index (degree of dominance) was calculated, which indicated the recessive mode of inheritance for the above-said association. Similarly, a significant association of the rs7561317 with obesity-related anthropometric traits and clinical surrogate markers of visceral adiposity was observed. Thus, GG genotype of the rs7561317 was found to increase 1.74 times the risk of overweight/obesity in Pakistani population (OR = 1.74, 95% CI 1.210–2.496, p = 0.003) while low physical activity seemed to accentuate the TMEM18 rs7561317-associated risk of overweight/obesity (OR = 2.696, 95% CI 1.485–4.896, p = 0.004).

Expression of Concern: AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set