cDNA Sequence Research Articles

AAV-based gene editing of type 1 collagen mutation to treat osteogenesis imperfecta

Osteogenesis imperfecta (OI) is a genetic disorder characterized by bone fragility, low bone mass, fractures, and extraskeletal manifestations. Since OI is commonly caused by single-nucleotide mutation(s) in the COL1A1 or COL1A2 genes encodingtype I collagens, we developed a genome-editing strategy to correct a Col1a2 mutation in an OIM mouse model resembling a severe dominant form of human type III OI. Using a recombinant adeno-associated virus (rAAV), we delivered CRISPR-Cas9 to bone-forming osteoblast-lineage cells in the skeleton. Homology-directed repair (HDR)-mediated gene editing efficiency in these cells was improved when CRISPR-Cas9 was coupled with a donor AAV vector containing a promoterless partial mouse Col1a2 complementary DNA sequence. This approach effectively reversed the dysregulation of osteogenic differentiation by a Col1a2 mutation invitro. Furthermore, systemic administration of dual rAAVs in OIM mice lowered bone matrix turnover rates by reducing osteoblast and osteoclast development while improving the cellular network of mechano-sensing osteocytes embedded in the bone matrix. This strategy significantly improved bone architecture/mass/mineralization, skeletal deformities, grip strength, and spontaneous fractures. Our study is the first demonstration that HDR-mediated gene editing via AAV-mediated delivery effectively corrects a collagen mutation in OI osteoblasts and reverses skeletal phenotypes in OIM mice.

PCR-Free, Label-Free, and Centrifugation-Free Diagnosis of Multiplex Antibiotic Resistance Genes by Combining mDNA-Au@Fe3O4 from Heating Dry and DNA Concatamers with G-Triplex.

Accurate identification of antibiotic resistance genes (ARGs) is crucial for improving treatment and controlling the spread of antibiotic-resistant bacteria (ARB). Herein, a novel PCR-free, centrifugation-free, and label-free magnetic fluorescent biosensor (MFB) was developed by combining polyA-medium DNA-polyT (mDNA, which contained a partial sequence of a target DNA), gold nanoparticle (AuNP)-anchored magnetic nanoparticle (Au@Fe3O4), complementary strand DNA (CS) of the target DNA, DNA concatamer with G-triplex (G3), and thioflavin T (ThT). Thereinto, Au@Fe3O4 nanoparticles were first capped by mDNA strands within 20 min using a simple hot drying method, and then CS was added and hybridized with mDNA on Au@Fe3O4. Second, a DNA concatamer was used to bind with CS on Au@Fe3O4. When an ARG was present in the sample, the CS would recognize it and release the DNA concatamer into solution by a toehold-mediated strand displacement reaction. Finally, under magnetic separation, the free DNA concatamers with G3 were taken out easily and bound with ThT, resulting in strong fluorescence signals. The fluorescence intensity of ThT was positively correlated with the concentration of the ARG. The whole analysis was accomplished within 1.5 h using 96-well plates. Remarkably, our MFB was universal; eight ARGs were detected by replacing the corresponding mDNA and CS in this study. To verify the practicability of our method, 12 clinically isolated strains were analyzed. The results of the MFB method were in good agreement with those of the quantitative real-time PCR method with an area under the curve of 0.92 (95% confidence interval: 0.8479 to 0.9932), sensitivity of 92.00%, and specificity of 91.55%. Above all, the MFB assay established here is simple, low-cost, and universal and has great potential for applications in the identification of ARGs.

The Neuropeptide HGAP Regulates Growth, Reproduction, Metamorphosis, Tissue Damage Repair, and Response against Starvation in Pacific Abalone

Introduction: Neuropeptides regulate vital physiological processes in multicellular organisms, including growth, reproduction, metamorphosis, and feeding. Recent transcriptome analyses have revealed neuropeptide genes with potential roles in vertebrate and invertebrate growth and reproduction. Among these genes, haliotid growth-associated peptide (HGAP) was identified as a novel gene in abalone. Methods: This study focused on HGAP in Pacific abalone (Haliotis discus hannai), where the complete cDNA sequence named Hdh-HGAP was identified and characterized. Samples from different experiments, such as metamorphosis, juvenile abalone growth, gonad development stages, muscle remodeling, and starvation, were collected for mRNA expression analysis. Results: The sequence spans 552 bp, encoding 96 amino acids with a molecular weight of 10.96 kDa. Expression analysis revealed that Hdh-HGAP exhibited higher levels in muscle tissue. Notably, during metamorphosis, Hdh-HGAP exhibited greater expression in the trochophore, veliger, and juvenile stages than in the cell division stages. Regarding growth patterns, Hdh-HGAP was highly expressed during rapid growth compared to stunted, minimal, and normal growth. In gonadal development, Hdh-HGAP mRNA reached its highest expression level during the ripening stage, indicating a potential role in gonadal cell proliferation and maturation. The in vivo effects of GnRH on gonad development and the expression of the Hdh-HGAP neuropeptide indicate its involvement in regulating reproduction in Pacific abalone. While tissue remodeling is primarily governed by immune genes, Hdh-HGAP was also upregulated during muscle tissue remodeling. Conversely, Hdh-HGAP was downregulated during prolonged starvation. Conclusion: This study marks the first comprehensive exploration of the Hdh-HGAP neuropeptide gene in Pacific abalone, shedding light on its involvement in growth, reproduction, metamorphosis, tissue remodeling, and response to starvation, although regulatory mechanisms are mostly unknown.

Deep intronic variant causes aberrant splicing of ATP7A in a family with a variable occipital horn syndrome phenotype

Genetic variants in ATP7A are associated with a spectrum of X-linked disorders. In descending order of severity, these are Menkes disease, occipital horn syndrome, and X-linked distal spinal muscular atrophy. After 30 years of diagnostic investigation, we identified a deep intronic ATP7A variant in four males from a family affected to variable degrees by a predominantly skeletal phenotype, featuring bowing of long bones, elbow joints with restricted mobility which dislocate frequently, coarse curly hair, chronic diarrhoea, and motor coordination difficulties. Analysis of whole genome sequencing data from the Genomics England 100,000 Genomes Project following clinical re-evaluation identified a deep intronic ATP7A variant, which was predicted by SpliceAI to have a modest splicing effect. Using a mini-gene splicing assay, we determined that the intronic variant results in aberrant splicing. Sanger sequencing of patient cDNA revealed ATP7A transcripts with exon 5 skipping, or inclusion of a novel intron 4 pseudoexon. In both instances, frameshift leading to premature termination are predicted. Quantification of ATP7A mRNA transcripts using a qPCR assay indicated that the majority of transcripts (86.1 %) have non-canonical splicing, with 68.0 % featuring exon 5 skipping, and 18.1 % featuring the novel pseudoexon. We suggest that the variability of the phenotypes within the affected males results from the stochastic effects of splicing. This deep intronic variant, resulting in aberrant ATP7A splicing, expands the understanding of intronic variation on the ATP7A-related disease spectrum.

A Missense Mutation in the Collagen Triple Helix of EDA Is Associated with X-Linked Recessive Hypohidrotic Ectodermal Dysplasia in Fleckvieh Cattle.

Mutations within the ectodysplasin A (EDA) gene have been associated with congenital hypotrichosis and anodontia (HAD/XHED) in humans, mice, dogs and cattle. We identified a three-generation family of Fleckvieh cattle with male calves exhibiting clinical and histopathological signs consistent with an X-linked recessive HAD (XHED). Whole genome and Sanger sequencing of cDNA showed a perfect association of the missense mutation g.85716041G>A (ss2019497443, rs1114816375) within the EDA gene with all three cases following an X-linked recessive inheritance, but normal EDAR and EDARADD. This mutation causes an exchange of glycine (G) with arginine (R) at amino acid position 227 (p.227G>R) in the second collagen triple helix repeat domain of EDA. The EDA variant was associated with a significant reduction and underdevelopment of hair follicles along with a reduced outgrowth of hairs, a complete loss of seromucous nasolabial and mucous tracheal and bronchial glands and a malformation of and reduction in number of teeth. Thermostability of EDA G227R was reduced, consistent with a relatively mild hair and tooth phenotype. However, incisors and canines were more severely affected in one of the calves, which correlated with the presence of a homozygous missense mutation of RNF111 (g.51306765T>G), a putative candidate gene possibly associated with tooth number in EDA-deficient Fleckvieh calves.

A Novel Kunitz-Type Serine Protease Inhibitor (HcKuSPI) is Involved in Antibacterial Defense in Innate Immunity and Participates in Shell Formation of Hyriopsis cumingii.

Serine protease inhibitors (SPIs) are abundantly reported for its inhibition against specific proteases involved in the immune responses, but SPI data related to calcareous shells are scarce. Previously, our research group has reported the proteome analysis of non-nucleated pearl powder, and a candidate matrix protein containing two Kunitz domains in the acid soluble fraction caught our attention. In the present study, the full-length cDNA sequence of HcKuSPI was obtained from Hyriopsis cumingii. HcKuSPI was specifically expressed in the mantle, with hybridization signals mainly concentrated to dorsal epithelial cells at the mantle edge and weak signals at the mantle pallium, suggesting HcKuSPI was involved in shell formation. HcKuSPI expression in the mantle was upregulated after Aeromonas hydrophila and Staphylococcus aureus challenge to extrapallial fluids (EPFs). A glutathione S transferase (GST)-HcKuSPI recombinant protein showed strong inhibitory activity against the proteases, trypsin and chymotrypsin. Moreover, HcKuSPI expression in an experimental group was significantly higher when compared with a control group during pellicle growth and crystal deposition in shell regeneration processes, while the organic shell framework of newborn prisms and nacre tablets was completely destroyed after HcKuSPI RNA interference (RNAi). Therefore, HcKuSPI secreted by the mantle may effectively neutralize excess proteases and bacterial proteases in the EPF during bacterial infection and could prevent matrix protein extracellular degradation by suppressing protease proteolytic activity, thereby ensuring a smooth shell biomineralization. In addition, GST-HcKuSPI was also crucial for crystal morphology regulation. These results have important implications for our understanding of the potential roles of SPIs during shell biomineralization.

Fluorine-doped carbon dots (F-CDs) adsorbing DNA via hydrophobic interaction play dual-role of quenching carrier and signal reference for ratiometric fluorescence strategy to detect microRNA

The expression levels of microRNAs (miRNA) can provide insights into the occurrence, progression, and treatment efficacy in tumors, highlighting the need for precise and easily controllable detection methodologies. The reasonable design of carbon dots enables the precise manipulation of luminescence and surface characteristics. Herein, fluorine doped carbon dots (F-CDs) were designed and prepared to establish a reasonable control of the interaction force between DNA and F-CDs. F-CDs were synthesized through a hydrothermal reaction involving tetrafluoroterephthalic acid and tetraethylene pentaamine, resulting in noteworthy optical and amphiphilic properties. F-CDs proficiently interact with single-stranded DNA (ssDNA) through hydrophobic interaction, leading to the quenching of dye labeled ssDNA, while maintaining self-fluorescence stability. The quenching mechanism was elucidated. The complementary DNA sequence induced nearly 100% desorption of ssDNA from F-CDs. Assisted by the target cycling signal amplification from duplex specific nuclease (DSN) and the self-fluorescence of F-CDs, an effective ratiometric strategy utilizing the adsorption system of F-CDs and probe DNA for let-7a was established for detecting let-7a, a critical miRNA in the assessment of tumor development. Under the optimized conditions, this method demonstrated high sensitivity and reproducibility in detecting let-7a with the linear range from 1.0 fM to 10.0 nM and a low limit of detection (LOD) of 3.0 fM. The recovery of let-7a in plasma and the evaluation of let-7a levels in seven cell types underscored the method's potential for efficient applications in monitoring of miRNA levels in real samples.

Full-Length Transcriptome and Gene Expression Analysis of Different Ovis aries Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis.

Sheep have historically been bred globally as a vital food source. To explore the transcriptome of adipose tissue and investigate key genes regulating adipose metabolism in sheep, adipose tissue samples were obtained from F1 Dorper × Hu sheep. High-throughput sequencing libraries for second- and third-generation sequencing were constructed using extracted total RNA. Functional annotation of differentially expressed genes and isoforms facilitated the identification of key regulatory genes and isoforms associated with sheep fat metabolism. SMRT-seq generated 919,259 high-accuracy cDNA sequences after filtering. Full-length sequences were corrected using RNA-seq sequences, and 699,680 high-quality full-length non-chimeric (FLNC) reads were obtained. Upon evaluating the ratio of total lengths based on FLNC sequencing, it was determined that 36,909 out of 56,316 multiple-exon isoforms met the criteria for full-length status. This indicates the identification of 330,375 full-length FLNC transcripts among the 370,114 multiple-exon FLNC transcripts. By comparing the reference genomes, 60,276 loci and 111,302 isoforms were identified. In addition, 43,423 new genes and 44,563 new isoforms were identified. The results identified 185 (3198), 394 (3592), and 83 (3286) differentially expressed genes (transcripts) between tail and subcutaneous, tail and visceral, and subcutaneous and visceral adipose tissues, respectively. Functional annotation and pathway analysis revealed the following observations. (1) Among the differentially expressed genes (DEGs) of TF and SF tissues, the downregulation of ACADL, ACSL6, and NC_056060.1.2536 was observed in SF, while FFAR4 exhibited upregulation. (2) Among the DEGs of TF and VF tissues, expressions of ACADL, ACSL6, COL1A1, COL1A2, and SCD were downregulated in VF, with upregulation of FFAR4. (3) Among SF and VF expressions of COL1A1, COL1A2, and NC_056060.1.2536 were downregulated in VF. Specific differentially expressed genes (ACADL, ACSL6, COL1A1, COL1A2, FFAR4, NC_056060.1.2536, and SCD) and transcripts (NC_056066.1.1866.16 and NC_056066.1.1866.22) were identified as relevant to fat metabolism. These results provide a dataset for further verification of the regulatory pathway associated with fat metabolism in sheep.

In vivo characterization of a podocyte-expressed short podocin isoform

The most common genetic causes of steroid-resistant nephrotic syndrome (SRNS) are mutations in the NPHS2 gene, which encodes the cholesterol-binding, lipid-raft associated protein podocin. Mass spectrometry and cDNA sequencing revealed the existence of a second shorter isoform in the human kidney in addition to the well-studied canonical full-length protein. Distinct subcellular localization of the shorter isoform that lacks part of the conserved PHB domain suggested a physiological role. Here, we analyzed whether this protein can substitute for the canonical full-length protein. The short isoform of podocin is not found in other organisms except humans. We therefore analysed a mouse line expressing the equivalent podocin isoform (podocinΔexon5) by CRISPR/Cas-mediated genome editing. We characterized the phenotype of these mice expressing podocinΔexon5 and used targeted mass spectrometry and qPCR to compare protein and mRNA levels of podocinwildtype and podocinΔexon5. After immunolabeling slit diaphragm components, STED microscopy was applied to visualize alterations of the podocytes’ foot process morphology.Mice homozygous for podocinΔexon5 were born heavily albuminuric and did not survive past the first 24 h after birth. Targeted mass spectrometry revealed massively decreased protein levels of podocinΔexon5, whereas mRNA abundance was not different from the canonical form of podocin. STED microscopy revealed the complete absence of podocin at the podocytes’ slit diaphragm and severe morphological alterations of podocyte foot processes. Mice heterozygous for podocinΔexon5 were phenotypically and morphologically unaffected despite decreased podocin and nephrin protein levels.The murine equivalent to the human short isoform of podocin cannot stabilize the lipid-protein complex at the podocyte slit diaphragm. Reduction of podocin levels at the site of the slit diaphragm complex has a detrimental effect on podocyte function and morphology. It is associated with decreased protein abundance of nephrin, the central component of the filtration-slit forming slit diaphragm protein complex.

Molecular characterization and functional analysis of peroxiredoxin 1 (Prx1) from roughskin sculpin (Trachidermus fasciatus).

Peroxiredoxin1(Prx1), also known as natural killer enhancing factor A (NKEF-A), is a crucial antioxidant involving in various cellular activities and immune response against bacterial and viral infection in fish. In the present study, a full-length Prx1 cDNA sequence (TfPrx1) was firstly cloned from roughskin sculpin (Trachidermus fasciatus), which was composed of 1044bp nucleotides encoding a peptide of 199 amino acids with a molecular weight of 22.35kDa and a theoretical pI of 6.42, respectively. The predicted peptide was a typical 2-cys Prx containing two conserved characteristic motifs 43FYPLDFTFVCPTEI56 and 170GEVCPA175 with the two conserved peroxidatic and resolving cysteine residuals forming disulfide bond. Quantitative real-time PCR analysis showed that TfPrx1 was ubiquitously expressed in all tested tissues with the highest expression in the intestine. It could be significantly induced following LPS injection and heavy metal exposure. Recombinant TfPrx1 (rTfPrx1) displayed insulin disulfide reduction and ROS-scavenging activity in a concentration-dependent manner, and further exhibited DNA and cytoprotective effects under oxidative stress. These results suggested that TfPrx1 protein may play an important role in fish immune protection from oxidative damage.

Identification, functional characterization and expression pattern of interferon-gamma (IFN-γ) and interferon-gamma receptor 1 (IFNGR1) in Nibea albiflora

Interferon-gamma (IFN-γ) is an inflammatory cytokine that plays a crucial role in regulating both innate and cell-mediated immune responses by binding to a receptor complex made up of IFNGR1 and IFNGR2. In this study, the complete cDNA of IFN-γ and IFNGR1 from Nibea albiflora were cloned and functionally characterized (named NaIFN-γ and NaIFNGR1), whose complete cDNA sequences were 1593 bp and 2792 bp, encoding 201 and 399 amino acids, respectively. Multiple sequence alignment and phylogenetic analysis showed that the concluded amino acids sequences of NaIFN-γ and NaIFNGR1 shared high identity with their teleost orthologues including the IFN-γ signature and nuclear localization signal (NLS) motif in NaIFN-γ and FN Ⅲ domain in NaIFNGR1. Real-time PCR showed that NaIFN-γ and NaIFNGR1 constitutively expressed in all tested tissues, such as the head-kidney, spleen, liver, kidney, gill, muscle, blood, and intestine with the highest expression of NaIFN-γ and NaIFNGR1 appearing in the liver and gill, respectively. After experiencing stimulation with Polyinosinic-polycytidylic acid (Poly (I:C)), Vibrio alginolyticus (V. alginolyticus) or Vibrio parahaemolyticus (V. parahaemolyticus), NaIFN-γ and NaIFNGR1 mRNA were up-regulated with the time-dependent model. Due to the presence of a nuclear localization signal (NLS), the subcellular localization revealed that NaIFN-γ dispersed throughout the cytoplasm and nucleus. NaIFNGR1, as a member of Cytokine receptor family B, was primarily expressed on the cell membrane. When NaIFN-γ and NaIFNGR1 were co-transfected, their fluorescence signals overlapped on the membrane of HEK 293T cells indicating the potential interaction between IFN-γ and IFNGR1. The GST-pull-down results further showed that NaIFN-γ could directly interact with the extracellular region of NaIFNGR1, further confirming the affinity between IFN-γ and IFNGR1. Taken together, the results firstly demonstrated that the NaIFN-γ ligand-receptor system existed in N.albiflora and played a pivotal part in N.albiflora's immune response against pathogenic bacterial infections, which contributed to the better understanding of the role of IFN-γ in the immunomodulatory mechanisms of teleost.

LncRNA VLDLR-AS1 Gene Expression in Colorectal Cancer in Patients from East Azerbaijan Province, Iran

Background: Colorectal cancer (CRC) is the third most common cancer that frequently spreads to other parts of the body, with a low chance of recovery and a high mortality rate. Long non-coding RNAs are considered significant prognostic and diagnostic indicators because they are dysregulated in various cancers and have distinctive expression patterns and high tissue- and cell-specificity. VLDLR-AS1 lncRNA deregulation has been associated with several malignancies. Objectives: This study aimed to evaluate the expression levels of VLDLR-AS1 in CRC. It was the first time this assessment was conducted. Methods: We studied 188 samples, including 94 tumor samples and 94 paired adjacent non-tumor tissues. Total RNA was extracted, and its quantity and purity were assessed. TaKaRa PrimeScript 1st Strand cDNA Synthesis Kit (Kusatsu, Japan) was used for the reaction. The StepOnePlus Real-Time PCR System (Applied Biosystems) was set up to assess the relative expression of VLDLR-AS1. Results: According to the qRT-PCR data, the VLDLR-AS1 expression levels in CRC tissues were significantly lower than in tumor margins (P < 0.0001). In addition, receiver operating characteristic curve analysis demonstrated that VLDLR-AS1 expression can discriminate between tumor and non-tumor samples with the sensitivity and specificity of 72.34% and 51.06%, respectively (P = 0.03, AUC = 0.6274). However, no significant association was found between the expression levels of VLDLR-AS1 and clinicopathological features in CRC patients. Conclusions: The results of this study indicated that VLDLR-AS1 lncRNA is significantly downregulated in the tumor tissues of CRC patients compared to healthy tumor margin tissues. This evidence shows the potential of this gene as a promising biomarker for the early detection of CRC development.

The Oxford Nanopore MinION as a Versatile Technology for the Diagnosis and Characterization of Emerging Plant Viruses.

The emergence of novel viral epidemics that could affect major crops represents a serious threat to global food security. The early and accurate identification of the causative viral agent is the most important step for a rapid and effective response to disease outbreaks. Over the last years, the Oxford Nanopore Technologies (ONT) MinION sequencer has been proposed as an effective diagnostic tool for the early detection and identification of emerging viruses in plants, providing many advantages compared with different high-throughput sequencing (HTS) technologies. Here, we provide a step-by-step protocol that we optimized to obtain the virome of "Lamon bean" plants (Phaseolus vulgaris L.), an agricultural product with Protected Geographical Indication (PGI) in North-East of Italy, which is frequently subjected to multiple infections caused by different RNA viruses. The conversion of viral RNA in ds-cDNA enabled the use of Genomic DNA Ligation Sequencing Kit and Native Barcoding DNA Kit, which have been originally developed for DNA sequencing. This allowed the simultaneous diagnosis of both DNA- and RNA-based pathogens, providing a more versatile alternative to the use of direct RNA and/or direct cDNA sequencing kits.

Identification and characterization of β3 integrin in Crassostrea hongkongensis

Crassostrea hongkongensis is a main oyster species farmed in South China Sea offshore area, and commonly suffers from vibriosis. Vibrio parahaemolyticus is one of the principal pathogens that causes the oyster vibriosis. The integrin from C. hongkongensis was studied for its function against V. parahaemolyticus in the current work. The full-length cDNA sequence was 3274 bp with an open reading frame (ORF) of 2397 bp that encoded a polypeptide of 798 amino acids. The polypeptide included typical domains of β integrin (such as INB domain, three EGF-like domains, and highly conserved NPX[Y/F] motif), and phylogenetically clustered with β3 integrins of other invertebrates, thereby, designated as ChIntβ3. The mRNA transcripts of ChIntβ3 were significantly higher in the heart, hemocytes, adductor muscle and hepatopancreas than those in gills and mantle of C. hongkongensis. Following stimulation with V. parahaemolyticus, the mRNA expression level of ChIntβ3 was significantly up-regulated in both hemocytes and hepatopancreas. The recombinant ChIntβ3 had significantly agglutinating activity on Escherichia coli, V. parahaemolyticus, Bacillus amyloliquefaciens, Pichia pastoris and the red blood cells of rabbit. In the one hand, the survival rate (83.33 ± 5.77%) of the oyster after V. parahaemolyticus infection at 30 days was significantly higher in the ChIntβ3 overexpression group than those in the physiological saline control group (26.67 ± 20.82%) (p < 0.01) and the overexpressed GFP group (26.67 ± 5.77%) (p < 0.01); in the other hand, the cumulative survival duration of C. hongkongensis was significantly shorter in the RNAi treatment group (197.6 ± 2.77 h) than that in the control group (247.2 ± 36.24 h) (p < 0.01). The results indicated that ChIntβ3 was involved in the recognition and clearance of V. parahaemolyticus through cell adhesion, and contributed to the further understanding of the function of ChIntβ3 against infection of pathogens.

Molecular Characteristics and Evolutionary Relationships of Toll-Like Receptor (TLR21) of Indonesian KUB-1 Chicken

In vertebrates, the immune system has several Toll-like receptors (TLRs) to recognize specific pathogen-associated molecular patterns (PAMPs). In aves, TLR21 is known to be a functional homolog of TLR9 in mammals. This study aimed to determine the molecular characteristics of TLR21 in KUB-1 chicken, a superior breed of Indonesian local chicken, and their evolutionary relationship. The TLR21 gene was obtained from the ovarian RNA extraction and synthesized into cDNA by reverse transcription. We found that the cDNA sequence of the TLR21 of KUB-1 chicken has a length of 3504 bp, including a 2823 bp open reading frame (ORF), which encodes a putative protein of 940 amino acids (aa). The deduced KUB-1 chicken TLR21 protein consisted of 720 aa in the extracellular domain containing 20 LRRs, 23 aa in the transmembrane region, and 141 aa of Toll‐IL‐1 receptor in the intracellular domain, and had a molecular weight of 107 kDa. The KUB-1 chicken TLR21 had homology of about 99%, 76%, and 43% with other TLR21 from other breeds of chicken, non-chicken poultry, and fish, respectively. Its molecular character was conserved throughout the evolution of TLR21 in chicken, so the KUB-1 chicken was not much different from the broiler. However, there has been an evolution in duck and goose, although the function is still the same. Evolutionarily, Gallus gallus_KUB-1 TLR21, which belongs to the TLR11 Family, has differentiated from fish TLR21 and formed a paraphyletic relationship with TLR21 in Anser cygnoides and Anas platyrhynchos.

Identification of WRKY gene family members in amaranth based on a transcriptome database and functional analysis of AtrWRKY42-2 in betalain metabolism.

WRKY TFs (WRKY transcription factors) contribute to the synthesis of secondary metabolites in plants. Betalains are natural pigments that do not coexist with anthocyanins within the same plant. Amaranthus tricolor ('Suxian No.1') is an important leaf vegetable rich in betalains. However, the WRKY family members in amaranth and their roles in betalain synthesis and metabolism are still unclear. To elucidate the molecular characteristics of the amaranth WRKY gene family and its role in betalain synthesis, WRKY gene family members were screened and identified using amaranth transcriptome data, and their physicochemical properties, conserved domains, phylogenetic relationships, and conserved motifs were analyzed using bioinformatics methods. In total, 72 WRKY family members were identified from the amaranth transcriptome. Three WRKY genes involved in betalain synthesis were screened in the phylogenetic analysis of WRKY TFs. RT-qPCR showed that the expression levels of these three genes in red amaranth 'Suxian No.1' were higher than those in green amaranth 'Suxian No.2' and also showed that the expression level of AtrWRKY42 gene short-spliced transcript AtrWRKY42-2 in Amaranth 'Suxian No.1' was higher than that of the complete sequence AtrWRKY42-1, so the short-spliced transcript AtrWRKY42-2 was mainly expressed in 'Suxian No.2' amaranth. Moreover, the total expression levels of AtrWRKY42-1 and AtrWRKY42-2 were down-regulated after GA3 treatment, so AtrWRKY42-2 was identified as a candidate gene. Therefore, the short splice variant AtrWRKY42-2 cDNA sequence, gDNA sequence, and promoter sequence of AtrWRKY42 were cloned, and the PRI 101-AN-AtrWRKY42-2-EGFP vector was constructed to evaluate subcellular localization, revealing that AtrWRKY42-2 is located in the nucleus. The overexpression vector pRI 101-AN-AtrWRKY42-2-EGFP and VIGS (virus-induced gene silencing) vector pTRV2-AtrWRKY42-2 were transferred into leaves of 'Suxian No.1' by an Agrobacterium-mediated method. The results showed that AtrWRKY42-2 overexpression could promote the expression of AtrCYP76AD1 and increase betalain synthesis. A yeast one-hybrid assay demonstrated that AtrWRKY42-2 could bind to the AtrCYP76AD1 promoter to regulate betalain synthesis. This study lays a foundation for further exploring the function of AtrWRKY42-2 in betalain metabolism.

Abstract A026: Synthesis and structure-activity studies of DNA- and RNA-binding nucleopeptides with a cell penetrating potential

Abstract In the field of modern biomedicine, significant progress has been made in countering or restoring faulty genes using exogenous nucleic acids or their mimetics (NAMs). This approach enables targeted and long-lasting therapeutic effects by circumventing the need of interventions at a protein level. Despite the boom of clinical approvals, the development of NAMs still faces crucial challenges, including susceptibility to metabolic breakdown, limited uptake by cells, self-aggregation, and the potential for immune reactions. In addition to employing advanced delivery strategies, alternative methods to address these issues involve modifying NAMs chemically or combining oligonucleotides (ONs) with cellular carriers, including cell-penetrating peptides. Against this background, herein we present the nucleopeptides (NPs) as a family of unexplored NAMs that bridge the gap between ONs and peptide structures. By incorporating two consecutive amino acids—one bearing a nucleobase on the side chain and the other remaining unaltered—we created a monomer that spans the length of a single nucleotide. This functional module possesses nucleobase recognition elements along with additional functional groups eligible to modulate physio-chemical properties. We investigated this class of macromolecules by preliminarily devising an efficient solid-phase peptide synthesis technique profitable for homo- and hetero-sequences and sparing the monomer assembly in solution. [1] The influence of the amino acid composition on target binding properties, metabolic stability, and cellular penetration, were assessed through the synthesis of a series of homothymine hexameric derivatives. This simplified model was also used to investigate the distance between the nucleobase and the backbone, the absolute configuration of the nucleobase- bearing element, and the polycationic/anionic nature of the unmodified amino acid. [2-4] We evaluated the recognition and the thermodynamic stability of NPs/DNA and NPs/RNA hetero-duplexes through circular dichroism and UV spectroscopy experiments, while we employed confocal microscopy with suitable FITC- labeled derivatives to determine the intracellular localization in target cells. [1,3] Our results suggested that NPs exhibit distinct binding properties towards complementary RNA and DNA sequences according to their aminoacidic composition, and are characterized by a higher affinity compared to ONs and PNAs, thus arising as promising cell penetrating NAMs. [1] Mercurio ME, Tomassi S, et al. J Org Chem. 2016, 81(23), 11612- 11625. [2] Tomassi S, Ieranò C, et al. Bioorg Med Chem. 2018, 26(9), 2539-2550. [3] Tomassi S, Montalban FF, et al. Symmetry 2019, 11(4), 567-582. [4] Tomassi S, Ieranò C, et al. Int J Mol Sci. 2022, 23(15), 8504-8518. Citation Format: Stefano Tomassi, Caterina Ieranò, Stefania Scala, Anna Messere, Salvatore Di Maro. Synthesis and structure-activity studies of DNA- and RNA-binding nucleopeptides with a cell penetrating potential [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A026.

Isoform characterisation &amp; splicing signatures of AD‐risk genes using long‐read sequencing

AbstractBackgroundAn increasing number of studies implicate a role for alternative splicing in development and neuropathology of Alzheimer’s disease (AD). However, it has been historically challenging to characterise splicing events, due to the inherent limitations of traditional RNA‐sequencing (RNA‐Seq) to capture full‐length transcripts critical for transcriptome assembly. In this study, we use two complementary targeted long‐read sequencing approaches, Pacific Biosciences (PacBio) isoform sequencing (Iso‐Seq) and Oxford Nanopore Technologies (ONT) nanopore cDNA sequencing, to profile the cortex of a mouse model of tau pathology (rTg4510) with ultra‐deep sequencing of a panel of 20 genes robustly implicated in AD.MethodTargeted PacBio Iso‐Seq and targeted ONT profiling were performed on RNA isolated from 24 female rTg4510 transgenic and wild‐type mice, aged 2, 4, 6 and 8 months. Following successful enrichment for target genes using custom‐designed probes (IDT), library preparation were performed for subsequent sequencing on Sequel and MinION. The panel of genes selected for enrichment included genes (i.e. App, Mapt, Snca) and dementia risk genes identified from GWAS analyses. Raw sequence data was processed using a customised bioinformatics, and full‐length reads were merged and annotated with our developed custom scripts (FICLE).ResultWe identify thousands of novel transcripts across the panel of 20 AD‐ and dementia‐associated genes. We reveal unprecedented diversity of alternatively‐spliced isoforms with widespread usage of alternative novel 5’ and 3’ splice sites. We further robust transcriptional and splicing differences in these AD‐risk genes associated with the development of tau pathology. Among these changes, we observed global up‐regulation of Trem2‐associated isoforms and isoform switches in Bin1, further supporting a role for the dysregulation of the immune response in the development of AD pathology.ConclusionThis represents the first study to comprehensively assess variable AS associated with the development of tau pathology using both PacBio Iso‐Seq and ONT nanopore sequencing. Our analyses confirm the importance of alternative RNA splicing in AD and identify evidence of differential transcript usage, even in the absence of gene‐level expression alterations. Further work will be undertaken to validate and functionally characterise these novel isoforms, and to extend these analyses to human post‐mortem AD brain samples.

Identification of luciferase cDNA of Neonothopanus sp. (Agaricales: Omphalotaceae)

Some fungi are capable of bioluminescence. One of the intriguing bioluminescent mushrooms is Neonothopanus. This mushroom has large fruity body and can produce light throughout their entire body. Light is produced by the reaction of luciferase enzyme to its substrate, luciferin. The information of Neonothopanus luciferase gene is still limited. The aim of this study is to characterize Neonothopanus sp. luciferase cDNA. Samples were collected in Pesisir Selatan West Sumatera. Total RNA and LuzF and LuzR primers were used to amplify 830 bp Neonothopanus sp luciferase cDNA. It was found that the query cover of the luciferase cDNA of Neonothopanus sp. to N. nambi is 93%, and 37% for N. gardnery. Neonothopanus sp and N. nambi have different nucleotides at position 320 – 369, while Neonothopanus sp and N. gardnery just have similar nucleotides at position 9 - 322 pb. Phylogenetic analysis shows bootstrap value of Neonothopanus sp cDNA sequences and Neonothopanus nambi 100% and 99.5% with N. gardneri. This suggests that Neonothopanus sp. luciferase cDNA is closely related to Neonothopanus nambi and N. gardneri.

Abstract A069: Generation of llama-derived phage display library specific to hepatocellular carcinoma tumor targets

Abstract Background: Primary liver cancer is the third leading cause of cancer-related deaths worldwide, with its incidence and mortality continuing to increase. Hepatocellular carcinoma (HCC) accounts for approximately 90% of these cases, and outcomes for most patients are poor. Unlike many cancer types, liver cancer cannot reliably be detected by 18F-fluorodeoxyglucose positron emission tomography (18F-FDG-PET) due to its limited tumor uptake. Curiously, despite the advent of precision oncology, no HCC-selective agents are clinically approved for the diagnosis or treatment of HCC in the United States. There are multiple tumor targets, including Glypican-3(GPC3) and Basigin (BSG) which are overexpressed on HCC tumors. GPC3 is a heparin sulfate proteoglycan expressed in 75% of HCC tumors, and rarely presented on other tissue types, making it a promising HCC-specific target. Similarly, BSG is a transmembrane glycoprotein that is expressed in 60% of HCC tumors, and is closely associated with tumor invasion, metastasis, and angiogenesis. Accordingly, radiopharmaceutical agents specific to GPC3 or BSG could allow for HCC-selective imaging and therapy. Methods:Using standard methods, a young, naïve llama was immunized four times with human and murine GPC3, along with BSG . Nanobody cDNA sequences were isolated from the B cells of the llama, amplified by PCR, cloned into phagemids, and transformed into E. Coli cells to create a nanobody library with over 10⁶ clones. Phage, displaying the nanobody protein, are then produced and used for immunopanning to enrich for specific nanobodies with affinity against each antigen. Using antigen-coated high binding tubes, phage particles displaying a specific nanobody will bind to the antigen and be eluted following stringent wash conditions, while non-specific phage particles are discarded. The eluted phage is then amplified, and a repeat round of phage display is performed. Enriched clones will then be screened by ELISA to identify high affinity binders. Lead candidate nanobodies are then sequenced and unique clones expressed to determine yield, stability, and purity. Once specific nanobodies are identified, additional biophysical characterization will be performed. Results: An antibody titer was performed by ELISA, demonstrating a successful immune response to all antigens. A phage display library was successfully created that is specific to human GPC3, murine GPC3 and BSG, with over 10⁶ clones. It is anticipated that after a few rounds of immunopanning, specific nanobodies will be identified. Conclusion: Thus far, a phage display library was created that is specific to mGPC3, hGPC3 and BSG. Immunopanning is currently underway to select out clones that are specific to the targeted antigens. Once enriched clones are isolated, orthogonal in vitro binding affinity assays, such as ELISA, flow cytometry and biolayer interferometry, will be used to measure specificity and strength of antigen binding. Subsequently, assessment of in vivo target binding will be performed using biodistribution studies and PET imaging. Citation Format: Divya Nambiar, Thomas J Esparza, Peter L Choyke, Freddy E Escorcia. Generation of llama-derived phage display library specific to hepatocellular carcinoma tumor targets [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A069.