Stable Transcription Research Articles

Inheritance and ecological effects of exogenous genes from transgenic Brassica napus to Brassica juncea hybrids

●With the rapid development of new breeding techniques, the ecological impacts of transgenic plants receive wide concern again, particularly for potential gene flow from transgenic crops to their relatives. The transgene insertion position, number of gene copies, and flanking sequence of exogenous genes integrated into the recipient genome affect the genetic stability and fitness of offspring.●We employed hybrids F1 and F2, six backcross generations BC1-BC6 and BC1F1 from transgenic Brassica napus with Bacillus thuringiensis (Bt) cry1Ac gene and its wild relative B. juncea through hand pollination. We detected exogenous gene copies, mRNA transcription, and protein expression by ddPCR, qRT-PCR and ELISA, and the fitness of hybrid and backcross generations.●Exogenous genes followed Mendelian segregation expectations in hybrid and backcrossed generations, with stable gene copies, mRNA transcription and protein concentration of exogenous genes in offspring. Exogenous gene copies had no significant effects on plant fitness, but had positive effects on mRNA transcription and protein concentration that varied with growth stages in hybrid and backcross generations.●Our study demonstrated inheritance and ecological effects of exogenous genes from transgenic plants to wild relatives, which will help ecological risk management of biotechnological plants released in the nature.

Rewarding properties of L-Dopa in experimental parkinsonism are mediated by sensitized dopamine D1 receptors in the dorsal striatum.

Treatment of Parkinson's disease (PD) is based on the use of dopaminergic drugs, such as L-Dopa and dopamine receptor agonists. These substances counteract motor symptoms, but their administration is accompanied by motor and non-motor complications. Among these latter conditions a neurobehavioral disorder similar to drug abuse, known as dopamine dysregulation syndrome (DDS), is attracting increasing interest because of its profound negative impact on the patients' quality of life. Here we replicate DDS in a PD mouse model based on a bilateral injection of 6-hydroxydopamine (6-OHDA) into the dorsal striatum. Administration of L-Dopa induced locomotor sensitization and conditioned place preference in 6-OHDA lesion, but not in control mice, indicative of the acquisition of addictive-like properties following nigrostriatal dopamine depletion. These behavioral effects were accompanied by abnormal dopamine D1 receptor (D1R) signaling in the medium spiny neurons of the dorsal striatum, leading to hyperactivation of multiple signaling cascades and increased expression of ΔFosB, a stable transcription factor involved in addictive behavior. Systemic administration of the D1R antagonist, SCH23390, abolished these effects and the development of place preference, thereby counteracting the psychostimulant-like effect of L-Dopa. The rewarding properties of L-Dopa were also prevented by chemogenetic inactivation of D1R-expressing neurons in the dorsal striatum. Our results indicate the association between abnormal D1R-mediated transmission and DDS in PD and identify potential approaches for the treatment of this disorder.

Ligustilide Inhibits the PI3K/AKT Signalling Pathway and Suppresses Cholangiocarcinoma Cell Proliferation, Migration, and Invasion.

Angelica sinensis (Oliv.) Diels, a renowned traditional Chinese medicine, has gained widespread recognition for its antitumor properties. Further investigation is warranted to determine whether ligustilide (LIG), which is extracted from this plant, can effectively inhibit tumors. We delved into the impact of LIG on cholangiocarcinoma cells, aiming to unravel the mechanisms underlying its effects. Cholangiocarcinoma cells (HuccT1 and RBE) were exposed to varying concentrations of LIG (2, 5, 10, 15, 20 μg/mL) for 24, 48, and 72 h. After identifying differentially expressed genes, stable transcription strains were utilized to explore LIG's antitumor mechanism. The inhibitory effects of LIG (5 μg/mL, 48 h) were assessed by CCK-8, colony formation, wound healing, transwell migration, western blotting, and immunofluorescence. In vivo, experiments in NOG mice (Ac, Ac+LIG; five per group) evaluated LIG's antiproliferative efficacy (5 mg/kg, intraperitoneal injection, 18-day period). LIG significantly inhibited cell proliferation and migration with IC50 5.08 and 5.77 μg/mL in HuccT1 and RBE cell lines at 48h, increased the expression of E-cadherin while decreased N-cadherin and the protein of PI3K/AKT pathway. Silenced NDRG1 (N-Myc downstream- regulated gene 1) attenuated these effects. In vivo, the AC+LIG group (LIG, 5 mg/kg, qd, 18 d) exhibited smaller tumor volumes compared to the Ac group. The expression of Ki-67 was significantly downregulated in the AC+LIG group. For the first time, our study has revealed that LIG holds therapeutic potential for treating cholangiocarcinoma. These findings hold promise for advancing innovative therapeutic approaches in the treatment of cholangiocarcinoma. LIG may serve as a useful patent for treating CCA.

Patient-derived bladder cancer organoids show stable transcript expression along cultivation.

Bladder cancer (BC) is a prevalent malignancy with high recurrence rates. Patient-derived bladder cancer organoids (BCO) pose as a promising approach in both, disease modeling and individualized treatment screening. The aim of this study was to investigate the transcriptomic plasticity in BCOs as a function of cultivation times to define ideal time periods for the applications envisioned. Tumor samples of three patients with pathologically confirmed non-muscle invasive and muscle-invasive bladder cancer were included in this study and expanded as BCOs. RNA expression was investigated at different time periods of cells in culture using differential gene expression for overall transcript expression and quantitative real-time PCR (qRT-PCR) for pathological relevant markers. Differential gene expression of the BCO lines was investigated across passages 1-4, in passages 5-9 and above 9, respectively. Analysis of the entire transcriptome of the respective BCO lines revealed consistent profiles without significant alterations throughout the cultivation and expansion procedure. Notably, key transcripts like TP53, PIK3CA, BRCA1, among others, exhibited stable expression levels in the quantitative RNA analysis during the cultivation period. The robust transcriptome during BCO cultivation advocates for the use of earlier passages of BCOs in personalized medicine providing a time-efficient drug screening option to accelerate the counseling of patients' treatment options. Higher passages of BCOs still hold the potential in topics demanding for expanded cell masses such as medical device development and others.

Enhancers associated with unstable RNAs are rare in plants

Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (nascent) transcripts across diverse crops and other plants using capped small (cs)RNA sequencing. We discovered that unstable transcripts are rare in plants, unlike in vertebrates, and when present, often originate from promoters. In addition, many ‘distal’ elements in plants initiate tissue-specific stable transcripts and are likely bona fide promoters of as-yet-unannotated genes or non-coding RNAs, cautioning against using reference genome annotations to infer putative enhancer sites. To investigate enhancer function, we integrated data from self-transcribing active regulatory region (STARR) sequencing. We found that annotated promoters and other regions that initiate stable transcripts, but not those marked by unstable or bidirectional unstable transcripts, showed stronger enhancer activity in this assay. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements can encompass diverse structures and mechanisms in eukaryotes, including humans.

An ultrasensitive electrochemical biosensor based on logic transcription circuit-activated DNAzyme amplifier for flap endonuclease 1 activity detection

The accurate detection of flap endonuclease 1 (FEN1) activity is crucial for early cancer diagnosis and therapy. Herein, we have established a “target-substrate double-enhanced” DNA electrochemical biosensor by integrating a cleavage-ligation logic transcription circuit-activated DNAzyme amplifier with the transition-metal carbides-gold nanoparticles (MXene-Au) composites for the accurate detection of FEN1 activity. The FEN1 can be translated into a stable transcription hairpin DNA (TH), incorporating the catalytic strand of the DNAzyme via the logic transcription circuit. Then, the TH hybridizes with the substrate strand of DNAzyme and the DNAzyme amplifier can be activated, thus producing a significant quantity of single-stranded DNA (sDNA) and achieving the efficient amplification of the FEN1. Finally, the sDNA loaded with electroactive substances is immobilized on the capture DNA-anchored MXene-Au modified electrode, significantly enhancing the electrochemical signal intensity for highly sensitive FEN1 activity detection. The excellent selectivity and sensitivity of the proposed electrochemical biosensor can facilitate the accurate detection of FEN1 activity in biological samples and aid in screening FEN1-releated drugs. Additionally, three-input concatenated logic gates (AND-AND, INHIBIT-AND, and AND-OR) are constructed for FEN1 activity detection. Particularly, the AND-AND gate achieves logic detection of FEN1 activity in complex samples. Consequently, this bidirectionally enhanced electrochemical biosensor offers a novel analytical method for FEN1 activity detection, showing substantial promise for early diagnosis and drug discovery of FEN1-related disease.

Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli.

The phenomenon of de novo gene birth-the emergence of genes from non-genic sequences-has received considerable attention due to the widespread occurrence of genes that are unique to particular species or genomes. Most instances of de novo gene birth have been recognized through comparative analyses of genome sequences in eukaryotes, despite the abundance of novel, lineage-specific genes in bacteria and the relative ease with which bacteria can be studied in an experimental context. Here, we explore the genetic record of the Escherichia coli long-term evolution experiment (LTEE) for changes indicative of "proto-genic" phases of new gene birth in which non-genic sequences evolve stable transcription and/or translation. Over the time span of the LTEE, non-genic regions are frequently transcribed, translated and differentially expressed, with levels of transcription across low-expressed regions increasing in later generations of the experiment. Proto-genes formed downstream of new mutations result either from insertion element activity or chromosomal translocations that fused preexisting regulatory sequences to regions that were not expressed in the LTEE ancestor. Additionally, we identified instances of proto-gene emergence in which a previously unexpressed sequence was transcribed after formation of an upstream promoter, although such cases were rare compared to those caused by recruitment of preexisting promoters. Tracing the origin of the causative mutations, we discovered that most occurred early in the history of the LTEE, often within the first 20,000 generations, and became fixed soon after emergence. Our findings show that proto-genes emerge frequently within evolving populations, can persist stably, and can serve as potential substrates for new gene formation.

A system for assessing the effect of stress on the physiological state of a patient with sleep apnea

Problem statement. In modern society, the problems associated with sleep apnea are manifested against the background of public health. One of the reasons for this is social stress. Prolonged social stress forms stable transcription profiles when sleep apnea occurs, which has consequences for the patient in the form of various diseases. At the present stage, science is trying to understand which diagnostically significant indicators are modeled depending on the type of stress in the diagnosis of sleep apnea. Goal. To develop a system for assessing the physiological state of a patient with AS, depending on the type of stress, to support a doctor's decision on the diagnosis of the disease. Results. The principles of synthesis of the stress type assessment system in the diagnosis of AS are considered. Based on them, a model of a random process for assessing the effect of stress on the physiological state of a patient with sleep apnea, a method for determining the type of stress in sleep apnea, the combination of which can be defined as a solution to the scientific problem of improving the quality of life of patients with sleep apnea, is proposed. Practical significance. A decision support system for a doctor in assessing the physiological condition of a patient with sleep apnea.

Identification of Plasma hsa_circ_0001230 and hsa_circ_0023879 as Potential Novel Biomarkers for Focal Segmental Glomerulosclerosis and circRNA-miRNA-mRNA Network Analysis

Introduction: Focal segmental glomerulosclerosis (FSGS) is a common glomerulopathy with an unclear mechanism. The demand for FSGS clinical diagnostic biomarkers has not yet been met. Circular RNA (circRNA) is a novel non-coding RNA with multiple functions, but its diagnostic value for FSGS remains unexplored. This study aimed to identify circRNAs that could aid in early clinical diagnosis and to investigate their mechanisms in podocyte injury. Methods: The signature of plasma circRNAs for FSGS was identified by circRNA microarray. The existence of circRNAs was confirmed by quantitative real-time polymerase chain reaction (qRT-PCR), RNase R assay, and DNA sequencing. Plasma levels of circRNAs were evaluated by qRT-PCR. The diagnostic value was appraised by the receiver operating characteristic curve. The circRNA-miRNA-mRNA network was built with Cytoscape 7.3.2. Statistically significant differences were calculated by the Mann-Whitney U test. Results: A total of 493 circRNAs (165 upregulated, 328 downregulated) were differentially expressed in the plasma of FSGS patients (n = 3) and normal controls (n = 3). Eight candidate circRNAs were demonstrated to be circular and stable transcripts. Among them, hsa_circ_0001230 and hsa_circ_0023879 were significantly upregulated in FSGS patients (n = 29) compared to normal controls (n = 51). The areas under the curve value of hsa_circ_0001230 and hsa_circ_0023879 were 0.668 and 0.753, respectively, while that of the two-circRNA panel was 0.763. The RNA pull-down analysis revealed that hsa_circ_0001230 and hsa_circ_0023879 could sponge hsa-miR-106a. Additionally, hsa_circ_0001230 and hsa_circ_0023879 positively regulated hsa-miR-106a target genes phosphatase and tensin homolog (PTEN) and Bcl-2-like protein 11 (BCL2L11) in podocytes. Conclusion: hsa_circ_0001230 and hsa_circ_0023879 are novel blood biomarkers for FSGS. They may regulate podocyte apoptosis by competitively binding to hsa-miR-106a.

Principles of Creation of a Genetic Engineering Construction for Obtaining Humanized Transgenic Mice with <i>HLA-C*07:02:01:01</i>, as a Promote of Innovative Transgenic and Knockout Biomodels

Genetic differences in different populations influence the mechanism and efficacy of drugs. Biomodels that take into account the peculiarities of genetic polymorphism in different individuals allow to more fully investigate the molecular-genetic mechanisms of action of pharmacological agents, including immunobiological ones. Recombinant DNA encoding a hybrid MHC class I protein containing human ß2-microglobulin fused with antigen-presenting domains (α1 and α2 domains) of the HLA-C*07:02:01:01 molecule and α3 domain of the mouse H2-complex was created. The purified linearized DNA fragment containing the target construct flanked by regulatory fragments ensuring its stable transcription was used to obtain a new line of humanized transgenic mice. The principles of designing humanized transgenic mice by encoding a chimeric MHC class I protein containing antigen-presenting domains HLA-C*07:02:01:01 are similar to those for obtaining mice of the HLA-А*02:01:01 and HLA-B*18:01:01:02 humanized transgenic lines. These transgenic lines of laboratory mice are independent biomodels, and also be used as baselines for obtaining corresponding transgenic and knockout lines.

Uncovering the Role of an ABCA7 Frameshift Deletion in African American Alzheimer’s Disease Cellular Pathology

AbstractBackgroundThe ATP Binding Cassette Subfamily A Member 7 (ABCA7) gene is a risk factor for Alzheimer’s disease (AD). While ABCA7 has been implicated as a genetic determinant of AD across populations, the risk effect is the strongest in African Americans (AAs). We previously identified a common 44 base pair deletion in ABCA7 (p.Arg578Alafs) that is predicted to truncate the protein and is significantly associated with AD in AAs (frequency in cases = 15.2%, cognitively unimpaired (CU) = 9.74%, p = 1.41×10−5). Clinically, deletion homozygotes are similar to deletion heterozygotes, supporting dominant gain‐of‐function as a putative disease‐causing mechanism. We sought to determine if the deletion transcript is stable and if the truncated protein is expressed as steps to understanding the mechanism leading to AD risk.MethodRT‐PCR analysis of heterozygotes was conducted to assess the stability of the deletion transcript. FLAG‐tagged Arg578Alafs and wildtype ABCA7 vectors were constructed then overexpressed in HEK293APPsw cells. Western blot analysis of FLAG‐Arg578Alafs was performed to determine if the deletion produces a truncated protein. Induced pluripotent stem cell (iPSC) lines from six AA individuals with AD bearing the Arg578Alafs mutation (three heterozygous; three homozygous) were created in pair with isogenic CRISPR‐corrected control lines. These iPSC lines were validated for pluripotency, genomic stability, and lack of off‐target editing. The isogenic ABCA7 deletion and CRISPR‐corrected control iPSC lines will be differentiated into microglia and neurons and functionally assessed for cell type‐specific AD phenotypes.ResultInitial results comparing AD patients to CU individuals show that patient‐derived microglia have normal rates of phagocytosis but are impaired in the uptake and clearance of fibrillar Aβ. RT‐PCR analysis of the deletion in heterozygotes demonstrates that a stable RNA transcript is expressed from the ABCA7 deletion allele. Western blot analysis of overexpressed FLAG‐Arg578Alafs shows that the truncated protein is expressed, albeit at low levels compared to the wildtype protein.ConclusionThis ABCA7 deletion produces a stable transcript which appears to be translated into low levels of protein. This supports a potential gain of function as the disease risk mechanism. Studies in isogenic lines will further elucidate the functional effects of this ABCA7 deletion on AD pathology in AAs.

Treatment Free Remission (TFR) “for” Pregnancy. Overview and Outcome of Pregnancies Reported in the Italy-Tfr Registry

TFR is a consolidated practice and the goal to be reached for all CML patients. In Italy only a few centers participate in TFR clinical trials, while, in clinical practice, many patients discontinue TKIs for intolerance, pregnancy, or other reasons. A cohort of 467 Italian patients who underwent discontinuation outside of clinical trials were collected in the Italy TFR registry. This cohort showed a mean TFR rate of 73% at 12 months. Italy-TFR is an observational study, both retrospective and prospective, with the purpose of collecting data on patients with Ph+, chronic phase CML who discontinue TKIs in an off-protocol setting. Eligibility criteria include patients treated with TKI monotherapy or in association with other drugs (IFN, BCR:;ABL1 peptidic vaccine, and others) and those who discontinued therapy for any reason. Deep Molecular Response (DMR) defined as MR4 (BCR::ABL ratio ≤ 0.01% IS), MR4.5 (≤ 0.0032%) or MR5 (≤ 0.001%) was confirmed at least three times before TKI discontinuation. Data from patients discontinuing in less than DMR were collected and analyzed separately. Molecular responses were assessed by qPCR; tests were performed by the GIMEMA Laboratories Network (LabNet). TFR was assessed using the Kaplan-Meier method and 95% confidence interval, from the date of TKI discontinuation to the date when therapy was reinitiated. Patients discontinuing for pregnancy were analyzed in this sub-analysis. Thirty patients and 33 pregnancies (3 patients had 2 pregnancies) were entered from 8/32 participating centers. Main data are reported in Table 1. Median age at diagnosis was 28 years (range 19-36), and 35 years at pregnancy (range 29-41). Fifteen patients switched from 1st to 2 ndG TKI before pregnancy due to intolerance or resistance/unsatisfactory responses. Only one patient switched to another TKI to deepen the response before attempting a second pregnancy (imatinib to nilotinib). Not all patients at TKI interruption were in DMR, however, they were all treated with the last TKI for a median of 60 months (range 18-151), and exposed to any TKI for a median of 89 months (range 44-186). Specifically, 9/33 pregnancies started in MMR (≤0.1% transcript), 13 in MR4, 6 in MR4.5, and 5 in MR5. Three patients stopped TKI therapy before conception, two at 5 months and 1.5 months, respectively, before pregnancy. The third patient, in TFR after the first pregnancy, conceived a second child while still in TFR. These 3 patients were in TFR for 9, 9 and 5 years after treatment stoppage. During pregnancy 4 patients were treated after losing MMR. One patient, in MR5 with imatinib for 4 years rapidly lost MMR and was treated with a peptidic vaccine, maintaining complete cytogenetic remission until delivery; 2 patients were treated with IFN, and 1 restarted nilotinib at 23 weeks. All 33 pregnancies were carried to term, with unremarkable outcomes for mothers and babies. No CML progression was recorded. Breastfeeding was allowed for patients with stable transcript levels. With a median follow-up of 40 months, 11 patients were still in TFR (33%; 48% at 12 months), with no differences for patients treated with imatinib or a 2 ndG TKI. The lower number of patients maintaining TFR compared with the general population of patients studied can be explained by 3 main considerations. First, 9/33 pregnancies started in MMR, which is not a criteria that allows for discontinuation, the kinetics of transcript rise are often not correlated with molecular remission. Second, the biological clock in women can rush conception attempts before the appearance of a consolidated response (also resistant patients). Third, as demonstrated in the main study, older age is the only statistically significant positive prognostic factor, with a higher risk of relapse for younger patients. Indeed, all patients restarting treatment regained at least MMR within 3 months. Except for the patient described earlier, and a patient who had a suboptimal response to the 2nd line and switched to bosutinib 3rd line, patients recommenced the same TKI discontinued before pregnancy. There was no significant difference in TFR between patients who discontinued imatinib 1 st versus 2 nd lines (Fig.1) and also in patients who discontinued 2 ndG TKI frontline versus 2 nd line for intolerance/resistance unsatisfactory response. The Italy-TFR protocol is still enrolling in the prospective cohort and updating. We plan to include more cases and present an exhaustive analysis.

Evaluation of Different Gene Prediction Tools in Coccidioides immitis.

Gene prediction is required to obtain optimal biologically meaningful information from genomic sequences, but automated gene prediction software is imperfect. In this study, we compare the original annotation of the Coccidioides immitis RS genome (the reference strain of C. immitis) to annotations using the Funannotate and Augustus genome prediction pipelines. A total of 25% of the originally predicted genes (denoted CIMG) were not found in either the Funannotate or Augustus predictions. A comparison of Funannotate and Augustus predictions also found overlapping but not identical sets of genes. The predicted genes found only in the original annotation (referred to as CIMG-unique) were less likely to have a meaningful functional annotation and a lower number of orthologs and homologs in other fungi than all CIMG genes predicted by the original annotation. The CIMG-unique genes were also more likely to be lineage-specific and poorly expressed. In addition, the CIMG-unique genes were found in clusters and tended to be more frequently associated with transposable elements than all CIMG-predicted genes. The CIMG-unique genes were more likely to have experimentally determined transcription start sites that were further away from the originally predicted transcription start sites, and experimentally determined initial transcription was less likely to result in stable CIMG-unique transcripts. A sample of CIMG-unique genes that were relatively well expressed and differentially expressed in mycelia and spherules was inspected in a genome browser, and the structure of only about half of them was found to be supported by RNA-seq data. These data suggest that some of the CIMG-unique genes are not authentic gene predictions. Genes that were predicted only by the Funannotate pipeline were also less likely to have a meaningful functional annotation, be shorter, and express less well than all the genes predicted by Funannotate. C. immitis genes predicted by more than one annotation are more likely to have predicted functions, many orthologs and homologs, and be well expressed. Lineage-specific genes are relatively uncommon in this group. These data emphasize the importance and limitations of gene prediction software and suggest that improvements to the annotation of the C. immitis genome should be considered.

Loss of Arl6ip5 Gene Function Suppresses Thrombosis in Mice

Background: The genetic contributors to thrombosis have only been partly described. Heterozygous tissue factor pathway inhibitor deficiency ( Tfpi+/-) is a powerful negative genetic modifier of the homozygous FVL ( F5L/L) phenotype, demonstrating a nearly complete perinatal lethal genetic interaction in F5L/LTfpi+/- mice. To identifymutations suppressing lethal thrombosis, we used this F5L/LTfpi+/- phenotype for a sensitized genome wide ENU mutagenesis screen. We screened over 12,000 mice and generated a total of 31 thrombosis suppressor variant lines. We were able to identify ENU-induced mutations in 10 of these lines, each potentially representing an independent pathway for reducing thrombosis severity. One of the mutations that suppressed thrombosis in F5L/LTfpi+/- mice was a dominant loss of function mutation (i.e. mutation in a single allele) in the ADP Ribosylation Factor Like GTPase 6 Interacting Protein-5 ( Arl6ip5) gene. Interestingly, no direct role(s) of Arl6ip5 gene or protein in hemostasis have been reported. Therefore, the aim of our studies was to investigate the hypothesis that Arl6ip5 deficiency suppresses thrombosis by reducing blood coagulation and platelet reactivity in mice. Methods: We previously generated a mouse model of Arl6ip5 ( Arl6ip5 -) by genome editing, creating a 151 base pair deletion removing an exon 1 splice site. After backcrossing mice carrying the Arl6ip5 - allele to the wildtype C57BL/6J (B6) background, we performed Arl6ip5 +/-intercrosses to determine a potential difference in genotype frequency at weaning. To investigate whether the Arl6ip5 - allele was able to produce a stable mRNA transcript we performed RT-qPCR on whole liver, lung, heart, kidney, and brain samples derived from Arl6ip5 +/+ Arl6ip5 +/- and Arl6ip5 -/- mice. Furthermore, complete blood cell counts were analyzed using the Advia 2120 (N ≥ 10 for each group), and to investigate potential blood coagulation defects, Prothrombin Time (PT) (N ≥ 5 for each group) and activated Partial Thromboplastin Time (aPTT) (N ≥ 8 for each group) assays were performed on plasma from Arl6ip5 +/+ Arl6ip5 +/- and Arl6ip5 -/- mice with the operator blinded to the genotype. Similarly, we performed platelet function analyses on whole blood from Arl6ip5 +/+ Arl6ip5 +/- and Arl6ip5 -/- mice using the Roche Multiplate, with ADP and collagen as agonists (N ≥ 6 for each group). Results: Arl6ip5 +/- x Arl6ip5+/- crosses resulted in normal Mendelian proportions of progeny observed at weaning (N > 400). No Arl6ip5transcripts were present in any of the Arl6ip5 -/- tissue samples analyzed, whereas heterozygous mice had the expected 50% Arl6ip5 expression levels across all organs as compared to wildtype mice. A significant prolongation was observed in aPTT between Arl6ip5+/+ and Arl6ip5-/- animals (p<0.01). Although no differences in platelet counts between genotypes were observed, platelet aggregometry showed significant differences between wildtype Arl6ip5 +/+and Arl6ip5 -/-littermates for platelet aggregation, velocity, and area under the curve in response to ADP agonist (normalized to platelet counts, p<0.01). In addition, collagen-induced aggregometry also yielded significant differences in aggregation velocity. Conclusions: Our results support the hypothesis that Arl6ip5 deficiency contributes to thrombosis suppression by increasing the aPTT and reducing platelet reactivity. Since the PT in Arl6ip5 -/- mice is normal, we speculate that Arl6ip5 -/- is either directly or indirectly affecting one or more of the levels or activity of coagulation factors VIII, IX, XI and XII. Significant differences in ADP- and collagen-induced platelet aggregation between Arl6ip5 +/+wildtype littermates and Arl6ip5 -/- suggests that the lack of Arl6ip5affects an aggregation process common to both pathways. Additional analyses are being performed to refine these mechanisms. Understanding the mechanism by which Arl6ip5 deficiency suppresses thrombosis could provide insights into human thrombosis regulation.

Alpha Satellite DNA in Targeted Drug Therapy for Prostate Cancer.

Prostate cancer is the most common solid cancer in men and, despite the development of many new therapies, metastatic castration-resistant prostate cancer still remains a deadly disease. Therefore, novel concepts for the treatment of metastatic prostate cancer are needed. In our opinion, the role of the non-coding part of the genome, satellite DNA in particular, has been underestimated in relation to diseases such as cancer. Here, we hypothesise that this part of the genome should be considered as a potential target for the development of new drugs. Specifically, we propose a novel concept directed at the possible treatment of metastatic prostate cancer that is mostly based on epigenetics. Namely, metastatic prostate cancer is characterized by the strongly induced transcription of alpha satellite DNA located in pericentromeric heterochromatin and, according to our hypothesis, the stable controlled transcription of satellite DNA might be important in terms of the control of disease development. This can be primarily achieved through the epigenetic regulation of pericentromeric heterochromatin by using specific enzymes as well as their activators/inhibitors that could act as potential anti-prostate cancer drugs. We believe that our concept is innovative and should be considered in the potential treatment of prostate cancer in combination with other more conventional therapies.

Assessing Radish Health during Space Cultivation by Gene Transcription.

During the Advanced Plant Habitat experiment 2, radish plants were grown in two successive grow-outs on the International Space Station (ISS) for 27 days each. On days 10, 18, and 24, leaf punch (LP) samples were collected and frozen. At harvest, bulb tissue was sampled with oligo-dT functionalized Solid Phase Gene Extraction (SPGE) probes. The space samples were compared with samples from ground controls (GC) grown at the Kennedy Space Center (KSC) under the same conditions as on the ISS, with notably elevated CO2 (about 2500 ppm), and from lab plants grown under atmospheric CO2 but with light and temperature conditions similar to the KSC control. Genes corresponding to peroxidase (RPP), glucosinolate biosynthesis (GIS), protein binding (CBP), myrosinase (RMA), napin (RSN), and ubiquitin (UBQ) were measured by qPCR. LP from day 24 and bulb samples collected at harvest were compared with RNA-seq data from material that was harvested, frozen, and analyzed after return to Earth. The results showed stable transcription in LP samples in GC but decreasing values in ISS samples during both grow-outs, possibly indicative of stress. SPGE results were similar between GC and ISS samples. However, the RNA-seq analyses showed different transcription profiles than SPGE or LP results, possibly related to localized sampling. RNA-seq of leaf samples showed greater variety than LP data, possibly because of different sampling times. RSN and RPP showed the lowest transcription regardless of method. Temporal analyses showed relatively small changes during plant development in space and in ground controls. This is the first study that compares developmental changes in space-grown plants with ground controls based on a comparison between RNA-seq and qPCR analyses.

Overexpression of Pasteurella multocida OmpA induces transcriptional changes and its possible implications for the macrophage polarization

Pasteurella multocida (P. multocida) is a highly infectious, zoonotic pathogen. Outer membrane protein A (OmpA) is an important virulence component of the outer membrane of P. multocida. OmpA mediates bacterial biofilm formation, eukaryotic cell infection, and immunomodulation. It is unclear how OmpA affects the host immune response. We estimated the role of OmpA in the pathogenesis of P. multocida by investigating the effect of OmpA on the immune cell transcriptome. Changes in the transcriptome of rat alveolar macrophages (NR8383) upon overexpression of P. multocida OmpA were demonstrated. A model cell line for stable transcription of OmpA was constructed by infecting NR8383 cells with OmpA-expressing lentivirus. RNA was extracted from cells and sequenced on an Illumina HiSeq platform. Key gene analysis of genes in the RNA-seq dataset were performed using various bioinformatics methods, such as gene ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, Gene Set Enrichment Analysis, and Protein–Protein Interaction Analysis. Our findings revealed 1340 differentially expressed genes. Immune-related pathways that were significantly altered in rat alveolar macrophages under the effect of OmpA included focal adhesion, extracellular matrix and vascular endothelial growth factor signaling pathways, antigen processing and presentation, nucleotide oligomerization domain-like receptor and Toll-like receptor signaling pathways, and cytokine-cytokine receptor interaction. The key genes screened were Vegfa, Igf2r, Fabp5, P2rx1, C5ar1, Nedd4l, Gas6, Cxcl1, Pf4, Pdgfb, Thbs1, Col7a1, Vwf, Ccl9, and Arg1. Data of associated pathways and altered gene expression indicated that OmpA might cause the conversion of rat alveolar macrophages to M2-like. The related pathways and key genes can serve as a reference for OmpA of P. multitocida and host interaction mechanism studies.

Optimization of Constitutive Promoters Using a Promoter-Trapping Vector in Burkholderia pyrrocinia JK-SH007.

Selecting suitable promoters to drive gene overexpression can provide significant insight into the development of engineered bacteria. In this study, we analyzed the transcriptome data of Burkholderia pyrrocinia JK-SH007 and identified 54 highly expressed genes. The promoter sequences were located using genome-wide data and scored using the prokaryotic promoter prediction software BPROM to further screen out 18 promoter sequences. We also developed a promoter trap system based on two reporter proteins adapted for promoter optimization in B. pyrrocinia JK-SH007: firefly luciferase encoded by the luciferase gene set (Luc) and trimethoprim (TP)-resistant dihydrofolate reductase (TPr). Ultimately, eight constitutive promoters were successfully inserted into the probe vector and transformed into B. pyrrocinia JK-SH007. The transformants were successfully grown on Tp antibiotic plates, and firefly luciferase expression was determined by measuring the relative light unit (RLU). Five of the promoters (P4, P9, P10, P14, and P19) showed 1.01-2.51-fold higher activity than the control promoter λ phage transcriptional promoter (PRPL). The promoter activity was further validated via qPCR analysis, indicating that promoters P14 and P19 showed stable high transcription levels at all time points. Then, GFP and RFP proteins were overexpressed in JK-SH007. In addition, promoters P14 and P19 were successfully used to drive gene expression in Burkholderia multivorans WS-FJ9 and Escherichia coli S17-1. The two constitutive promoters can be used not only in B. pyrrocinia JK-SH007 itself to gene overexpression but also to expand the scope of application.

Multimodal single cell analysis infers widespread enhancer co-activity in a lymphoblastoid cell line

Non-coding regulatory elements such as enhancers are key in controlling the cell-type specificity and spatio-temporal expression of genes. To drive stable and precise gene transcription robust to genetic variation and environmental stress, genes are often targeted by multiple enhancers with redundant action. However, it is unknown whether enhancers targeting the same gene display simultaneous activity or whether some enhancer combinations are more often co-active than others. Here, we take advantage of recent developments in single cell technology that permit assessing chromatin status (scATAC-seq) and gene expression (scRNA-seq) in the same single cells to correlate gene expression to the activity of multiple enhancers. Measuring activity patterns across 24,844 human lymphoblastoid single cells, we find that the majority of enhancers associated with the same gene display significant correlation in their chromatin profiles. For 6944 expressed genes associated with enhancers, we predict 89,885 significant enhancer-enhancer associations between nearby enhancers. We find that associated enhancers share similar transcription factor binding profiles and that gene essentiality is linked with higher enhancer co-activity. We provide a set of predicted enhancer-enhancer associations based on correlation derived from a single cell line, which can be further investigated for functional relevance.

Immune-check blocking combination multiple cytokines shown curative potential in mice tumor model.

In order to ensure the stable transcription of target genes, we constructed a eukaryotic high expression vector carrying an immune-check inhibitor PD-1v and a variety of cytokines, and studied their effects on activating immune response to inhibit tumor growth. A novel eukaryotic expression plasmid vector named pT7AMPCE containing T7RNA polymerase, T7 promoter, internal ribosome entry site (IRES), and poly A tailing signal was constructed by T4 DNA ligase, on which homologous recombination was used to clone and construct the vector carrying PD-1v, IL-2/15, IL-12, GM-CSF, and GFP. In vitro transfection of CT26 cells was performed, and the protein expression of PD-1v, IL-12 and GM-CSF was detected by Western blot and ELISA after 48 h. Mice were subcutaneously inoculated with CT26-IRFP tumor cells in the rib abdomen, and the tumor tissues were injected with PD-1v, IL-2/15, IL-12, and GM-CSF recombinant plasmids for treatment during the experimental period. The efficacy of the treatment was evaluated by assay tumor size and survival time of tumor-bearing mice during the experiment. Expression levels of IFN-γ, TNF, IL-4, IL-2, and IL-5 in mouse blood were measured using the CBA method. Tumor tissues were extracted and immune cell infiltration in tumor tissues was detected by HE staining and the IHC method. The recombinant plasmids carrying PD-1v, IL-2/15, IL-12, and GM-CSF were successfully constructed, and the Western blot and ELISA results showed that PD-1v, IL-12, and GM-CSF were expressed in the supernatant of CT26 cells 48 h after in vitro cell transfection. The combined application of PD-1v, IL-2/15, IL-12, and GM-CSF recombinant plasmids significantly inhibited tumor growth in mice, and the tumor growth rate was significantly lower than that in the blank control group and GFP plasmid control group (p < 0.05). Cytometric bead array data suggested that the combination of PD-1v and various cytokines can effectively activate immune cells. HE and IHC analysis revealed plenty of immune cell infiltrates in the tumor tissue, and a large proportion of tumor cells showed the necrotic phenotype in the combination treatment group. The combination of immune check blockade and multiple cytokine therapy can significantly activate the body's immune response and inhibit tumor growth.