Upregulation Of Transcription Factors Research Articles

Spatial Transcriptomics Reveals Interaction of Injury-Derived Osteopontin with Mesothelial Cells in Serosal Scarring

Abstract Background Abdominal surgeries are often live-saving procedures. However, surgical interventions in the peritoneal cavity can cause the formation of post-surgical adhesions. These irreversible scar bands can trigger severe complications, such as chronic pelvic pain, small bowel obstruction, and infertility in women. Unfortunately, no effective treatment options for adhesion patients exist. On a cellular level, mesothelium-derived mesenchymal myofibroblasts have been identified as key pro-fibrotic players in adhesion formation. Aims Our aim is to study the molecular mechanisms of mesothelial cell recruitment in serosal repair and scarring, and thereby to identify potential targets for specific pharmacological anti-adhesion treatments. Methods We used a mesothelial cell reporter mouse system (Wt1CreERT2xRosa26tdTomato) and experimental injury models to study the differences of mesothelial cell recruitment to sites of adhesion formation in comparison to wound sites healing scar-free. To answer how injury zones affect the accumulation of mesothelial cells, we used untargeted spatial transcriptomics, identifying candidate molecules that were i) upregulated in adhesion formation sites, ii) not highly expressed in scar-free wound sites, and iii) had the potential to interact with mesothelial cells. Results We observed strong spatiotemporal correlation between accumulation of tdTomato+ cells and consecutive scarring. Spatial deconstruction of scar-specific signaling identified the candidate molecule Secreted phosphoprotein 1; an inflammatory zone-specific gene that encodes Osteopontin (OPN). After confirming increased OPN protein levels 7d post-surgery, we investigated its effect on adhesion formation using Spp1-/- mice. Indeed, Spp1-deficient mice showed significantly lower adhesion scores compared to control mice. Mechanistically, recombinant OPN had no chemotactic effect on primary human mesothelial cells, however triggered the upregulation of transcription factors associated with mesothelial-to-mesenchymal transition. Conclusion Together, these findings suggest a pivotal role for OPN in linking inflammation at injury sites with mesothelial cell recruitment in post-surgical serosal scarring. Therefore, OPN represents a potential target for novel pharmacological strategies to specifically inhibit scarring without affecting normal wound repair.

Transcriptional signatures of fentanyl use in the mouse ventral tegmental area.

Synthetic opioids such as fentanyl contribute to the vast majority of opioid-related overdose deaths, but fentanyl use remains broadly understudied. Like other substances with misuse potential, opioids cause lasting molecular adaptations to brain reward circuits, including neurons in the ventral tegmental area (VTA). The VTA contains numerous cell types that play diverse roles in opioid use and relapse; however, it is unknown how fentanyl experience alters the transcriptional landscape in specific subtypes. Here, we performed single nuclei RNA sequencing to study transcriptional programs in fentanyl-experienced mice. Male and female C57/BL6 mice self-administered intravenous fentanyl (1.5μg/kg/infusion) or saline for 10days. After 24 h abstinence, VTA nuclei were isolated and prepared for sequencing on the 10× platform. We identified different patterns of gene expression across cell types. In dopamine neurons, we found enrichment of genes involved in growth hormone signalling. In dopamine-glutamate-GABA combinatorial neurons, and some GABA neurons, we found enrichment of genes involved in Pi3k-Akt signalling. In glutamate neurons, we found enrichment of genes involved in cholinergic signalling. We identified transcriptional regulators for the differentially expressed genes in each neuron cluster, including downregulated transcriptional repressor Bcl6, and upregulated transcription factor Tcf4. We also compared the fentanyl-induced gene expression changes identified in mouse VTA with a published rat dataset in bulk VTA, and found overlap in genes related to GABAergic signalling and extracellular matrix interaction. Together, we provide a comprehensive picture of how fentanyl self-administration alters the transcriptional landscape of the mouse VTA that serves as the foundation for future mechanistic studies.

Abstract 1383: Investigation of biological role and cytokine axis of cancer-associated fibroblast (CAF) in lung cancer brain metastasis

Abstract Background: Brain metastases (BM) are among the most lethal forms of cancer globally. Lung cancer BM are frequently encountered and are associated with poor prognosis, decreased survival rates, and therapeutic resistances. Cancer-associated fibroblasts (CAFs) have emerged as important players of the brain metastases tumor microenvironment (TME). Mechanistic roles of brain metastases CAFs (hBM-CAFs) in tumorigenesis and therapeutic resistances remain unclear. Material and Methods: In the present study, the patient's BM surgical sample was subjected to primary culture to isolate CAF. The hBM-CAF induced EMT and stemness phenotype was investigated by western blot. Biological role of hBM-CAF in tumorigenesis was evaluated using indirect co-culture method in vitro. FACS analysis was performed to investigate the changes in cisplatin cytotoxicity and radiation susceptibility of lung cancer cell lines when co-cultured with hBM-CAF. CX3CL1 and IL26 expression was confirmed by ELISA along with transcriptomic analysis of hBM-CAF. Molecular events were validated by using neutralizing CX3CL1 and IL26. The tumorigenicity and response to chemotoxicity of lung cancer cells were examined by co-injecting them with hBM-CAF in a mouse xenograft model. Results: Our experiments demonstrated that hBM-CAFs significantly enhanced EMT and stemness phenotype by upregulating transcription factor SNAIL1, TWIST1, Slug and CD133, CD44 respectively in lung cancer cells. We also observed that hBM-CAFs decreased cisplatin cytotoxicity and enhanced radiation resistance, as measured by FACS analysis of apoptotic cells. In vivo experiments using xenograft mouse models revealed that co-injection of lung cancer cells with hBM-CAFs led to faster tumor growth and increased cisplatin resistance. Transcriptomic analysis of hBM-CAFs revealed a distinct genomic signature compared to normal fibroblast (hNFs), with significant overexpression of IL26 and CX3CL1 genes in the hBM-CAFs secretome, as validated by ELISA. Moreover, we found that lung cancer cells expressed high levels of the IL26 receptor IL10Rβ and ILR20α, and CX3CL1 receptor CX3CR1. Our hBM-CAF significantly upregulated JAK-STAT3 and Akt-mTOR pathway. Eventually, we have confirmed that neutralizing IL26 and CX3CL1 inhibit phosphorylation of JAK-STAT3 and Akt-mTOR respectively and revoked the IL26-CX3CL1 induced EMT and stemness phenotype of lung cancer cells. Conclusion: Patient derived hBM-CAF promote aggressive phenotype of lung cancer cells by upregulating EMT and stemness transcriptome factors. Overexpression of IL26 and CX3CL1 cytokine led to the therapeutic resistance through JAK-STAT3 and Akt-mTOR signaling pathway respectively. Targeting IL26-CX3CL1 might be a novel therapeutic efficacy for lung cancer brain metastasis patients. Citation Format: Nah Ihm Kim, SM Abdus Salam, Eshrat Jahan, Eun-Jeong Ahn, Tae-Young Jung, Jae-Hyuk Lee, Joon Haeng Rhee, Sung Sun Kim, Kyung-Hwa Lee, Kyung-Sub Moon. Investigation of biological role and cytokine axis of cancer-associated fibroblast (CAF) in lung cancer brain metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1383.

Human adenovirus type 3 restores pharmacologically inhibited exosomal cargo in lung carcinoma cells.

Introduction: Drug repurposing is fast growing and becoming an attractive approach for identifying novel targets, such as exosomes for cancer and antiviral therapy. Exosomes are a specialized class of extracellular vesicles that serve as functional mediators in intercellular communication and signaling that are important in normal physiological functions. A continuously growing body of evidence has established a correlation between the abnormal release of exosomes with various viral disease pathologies including cancer. Cells that are virus-infected release exosomes known to influence the process via the loading and transfer of viral components, such as miRNA, small (s) RNA, DNA, and proteins. Inhibition of exosome release may abate the spread and severity of viral infection, thus making exosomes an attractive target for antiviral therapies. We previously demonstrated the pharmacological inhibition of exosomes. Methods: Herein, we used a cell-based assay to determine the effect of Human adenovirus type 3 (HAdV3) on the exosome inhibition process by azole and Heparin derivatives. HAdV3-infected cells were treated with two concentrations of each inhibitor at different time points. Results: HAdV3 activities led to increased total sRNA, DNA, and exosome particle concentrations via particle tracking in the presence of Climbazole and Heparin relative to uninfected exosomes. In addition, there was an increased expression of classical markers such as ALG-2 interacting protein X (ALIX), and tetraspanin (CD63), (p < 0.05) and upregulated transcription factor interferon regulatory factor (IRF) 8 in the presence of HAdV3 after 24hours (h) of treatment. Whereas higher concentrations of Climbazole and Heparin sodium salt were found to inhibit total exosome protein (p < 0.001) and exo-RNA (p < 0.01) content even in the presence of HAdV3 relative to infected exosomes only. Activities of HAdV3 in the presence of selected inhibitors resulted in the positive regulation of exosome related DNA damage/repair signaling proteins. Blocking exosome secretion partially obstructed viral entry. Immunological studies revealed that HAdV3 fiber protein levels in A549 cells were reduced at all concentrations of Climbazole and Heparin and both multiplicities of infections (p < 0.001). Discussion: Our findings suggest that while HAdV may bolster inhibited exosome content and release when modulating certain activities of the endosomal pathway mediators, HAdV entry might be constrained by the activities of these pharmacological agents.

FOSL1 regulates hyperproliferation and NLRP3-mediated inflammation of psoriatic keratinocytes through the NF-kB signaling via transcriptionally activating TRAF3

Psoriasis is a common and immune-mediated skin disease related to keratinocytes hyperproliferation and inflammation. Fos-like antigen-1 (FOSL1) is an important transcription factor involved in various diseases. FOSL1 has been reported to be differentially expressed in psoriasis. However, the roles and mechanism of FOSL1 in psoriasis progression remain largely unknown. FOSL1 is an upregulated transcription factor in psoriasis and increased in M5-treated HaCaT cells. FOSL1 had a diagnostic value in psoriasis, and positively associated with PASI score, TNF-α and IL-6 levels in psoriasis patients. FOSL1 silencing attenuated M5-induced HaCaT cell hyperproliferation through decreasing cell viability and proliferative ability and increasing cell apoptosis. FOSL1 knockdown mitigated M5-induced NLRP3 inflammasome activation and it-mediated inflammatory cytokine (IL-6, IL-8 and CCL17) expression. TRAF3 expression was increased in psoriasis patients and M5-treated HaCaT cells. FOSL1 transcriptionally activating TRAF3 in HaCaT cells. TRAF3 overexpression reversed the suppressive effects of FOSL1 silencing on M5-induced hyperproliferation and NLRP3-mediated inflammation. FOSL1 knockdown attenuated M5-induced NF-κB signaling activation by reducing TRAF3. Activation of NF-κB signaling reversed the effects of FOSL1 knockdown on hyperproliferation and inflammation in M5-treated cells. FOSL1 silencing prevented M5-induced hyperproliferation and NLRP3-mediated inflammation of keratinocytes by inhibiting TRAF3-mediated NF-κB activity, indicating FOSL1 might act as a therapeutic target of psoriasis.

Study of Dandelion (Taraxacum mongolicum Hand.-Mazz.) Salt Response and Caffeic Acid Metabolism under Saline Stress by Transcriptome Analysis.

Utilizing salt-tolerant plants is a cost-effective strategy for agricultural production on salinized land. However, little is known about the mechanism of dandelion (Taraxacum mongolicum Hand.-Mazz.) in response to saline stress and caffeic acid biosynthesis. We investigated the morphological and physiological variations of two dandelions, namely, "BINPU2" (dandelion A) and "TANGHAI" (dandelion B) under gradient NaCl concentrations (0, 0.3%, 0.5%, 0.7%, and 0.9%), and analyzed potential mechanisms through a comparison analysis of transcriptomes in the two dandelions. Dandelion A had a high leaf weight; high ρ-coumaric acid, caffeic acid, ferulic acid, and caffeoyl shikimic acid contents; and high activities of POD and Pro. The maximum content of four kinds of phenolic acids mostly occurred in the 0.7% NaCl treatment. In this saline treatment, 2468 and 3238 differentially expressed genes (DEGs) in dandelion A and B were found, of which 1456 and 1369 DEGs in the two dandelions, respectively, showed up-regulation, indicating that more up-regulated DEGs in dandelion A may cause its high salt tolerance. Further, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that dandelion salt response and caffeic acid metabolism were mainly enriched in the phenylpropanoid biosynthesis pathway (ko00940) and response to ethylene (GO: 0009723). The caffeic acid biosynthesis pathway was reconstructed based on DEGs which were annotated to PAL, C4H, 4CL, HCT, C3'H, and CSE. Most of these genes showed a down-regulated mode, except for parts of DEGs of 4CL (TbA05G077650 and TbA07G073600), HCT (TbA03G009110, TbA03G009080, and novel.16880), and COMT (novel.13839). In addition, more up-regulated transcription factors (TFs) of ethylene TFs in dandelion A were found, but the TFs of ERF104, CEJ1, and ERF3 in the two dandelions under saline stress showed an opposite expression pattern. These up-regulated genes could enhance dandelion salt tolerance, and down-regulated DEGs in the caffeic acid biosynthesis pathway, especially CSE (TbA08G014310) and COMT (TbA04G07330), could be important candidate genes in the synthesis of caffeic acid under saline stress. The above findings revealed the potential mechanisms of salt response and caffeic acid metabolism in dandelion under saline stress, and provide references for salt-tolerant plant breeding and cultivation on saline-alkali land in the future.

LncRNA PART1 Attenuates Myocardial Ischemia-Reperfusion Injury by Regulating TFAP2C/DUSP5 Axis via miR-302a-3p.

Myocardial ischemia-reperfusion injury (MIRI) refers to the damage of cardiac function caused by restoration of blood flow perfusion in ischemic myocardium. However, long non-coding RNA prostate androgen regulated transcript 1 (PART1)'s role in MIRI remain unclear. Immunofluorescence detected LC3 expression. Intermolecular relationships were verified by dual luciferase reporter assay. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, flow cytometry and transferase-mediated dUTP nick-end labeling (TUNEL) assays analyzed cell viability and apoptosis. The release of lactate dehydrogenase was tested via enzyme-linked immunosorbent assay (ELISA). Left anterior descending coronary artery surgery induced a MIRI mouse model. Infarct area was detected by 2,3,5-triphenyltetrazolium chloride staining. Hematoxylin and eosin staining examined myocardial injury. ELISA evaluated myocardial marker (creatine kinase MB) level. PART1 was decreased in hypoxia/reoxygenation (H/R) induced AC16 cells and MIRI mice. PART1 upregulation attenuated the increased levels of Bax, beclin-1 and the ratio of LC3II/I, and enhanced the decrease of Bcl-2 and p62 expression in H/R-treated cells. PART1 upregulation alleviated H/R-triggered autophagy and apoptosis via miR-302a-3p. Mechanically, PART1 targeted miR-302a-3p to upregulate transcription factor activating enhancer-binding protein 2C (TFAP2C). TFAP2C silencing reversed the protected effects of miR-302a-3p inhibitor on H/R treated AC16 cells. We further established TFAP2C combined to dual-specificity phosphatase 5 (DUSP5) promoter and activated DUSP5. TFAP2C upregulation suppressed H/R-stimulated autophagy and apoptosis through upregulating DUSP5. Overexpressed PART1 reduced myocardial infarction area and attenuated MIRI in mice. PART1 improved the autophagy and apoptosis in H/R-exposed AC16 cells through miR-302a-3p/TFAP2C/DUSP5 axis, which might provide novel targets for MIRI treatment.

Integrated Transcriptomic and Metabolomic Analyses Identify Critical Genes and Metabolites Associated with Seed Vigor of Common Wheat.

Seed aging is a common physiological phenomenon during storage which has a great impact on seed quality. An in-depth analysis of the physiological and molecular mechanisms of wheat seed aging is of great significance for cultivating high-vigor wheat varieties. This study reveals the physiological mechanisms of wheat seed aging in two cultivars differing in seed vigor, combining metabolome and transcriptome analyses. Differences between cultivars were examined based on metabolomic differential analysis. Artificial aging had a significant impact on the metabolism of wheat seeds. A total of 7470 (3641 upregulated and 3829 downregulated) DEGs were detected between non-aging HT and LT seeds; however, 10,648 (4506 up and 6142 down) were detected between the two cultivars after aging treatment. Eleven, eight, and four key metabolic-related gene families were identified in the glycolysis/gluconeogenesis and TCA cycle pathways, starch and sucrose metabolism pathways, and galactose metabolism pathways, respectively. In addition, 111 up-regulated transcription factor genes and 85 down-regulated transcription factor genes were identified in the LT 48h group. A total of 548 metabolites were detected across all samples. Cultivar comparisons between the non-aged groups and aged groups revealed 46 (30 upregulated and 16 downregulated) and 62 (38 upregulated and 24 downregulated) DIMs, respectively. Network analysis of the metabolites indicated that glucarate O-phosphoric acid, L-methionine sulfoxide, isocitric acid, and Gln-Gly might be the most crucial DIMs between HT and LT. The main related metabolites were enriched in pathways such as glyoxylate and dicarboxylate metabolism, biosynthesis of secondary metabolites, fatty acid degradation, etc. However, metabolites that exhibited differences between cultivars were mainly enriched in carbon metabolism, the TCA cycle, etc. Through combined metabolome and transcriptome analyses, it was found that artificial aging significantly affected glycolysis/gluconeogenesis, pyruvate metabolism, and glyoxylate and dicarboxylate metabolism, which involved key genes such as ACS, F16P2, and PPDK1. We thus speculate that these genes may be crucial in regulating physiological changes in seeds during artificial aging. In addition, an analysis of cultivar differences identified pathways related to amino acid and polypeptide metabolism, such as cysteine and methionine metabolism, glutathione metabolism, and amino sugar and nucleotide sugar metabolism, involving key genes such as BCAT3, CHI1, GAUT1, and GAUT4, which may play pivotal roles in vigor differences between cultivars.

Exogenous abscisic acid and sugar induce a cascade of ripening events associated with anthocyanin accumulation in cultured Pinot Noir grape berries.

Fruit quality is dependent on various factors including flavour, texture and colour. These factors are determined by the ripening process, either climacteric or non-climacteric. In grape berry, which is non-climacteric, the process is signalled by a complex set of hormone changes. Abscisic acid (ABA) is one of the key hormones involved in ripening, while sugar availability also plays a significant role in certain ripening aspects such as anthocyanin production. To understand the relative influence of hormone and sugar signalling in situ can prove problematic due to the physiological and environmental (abiotic and biotic) factors at play in vineyards. Here we report on the use of in vitro detached berry culture to investigate the comparative significance of ABA and sugar in the regulation of Pinot noir berry anthocyanin production under controlled conditions. Using a factorial experimental design, pre-véraison berries were cultured on media with various concentrations of sucrose and ABA. After 15 days of in vitro culture, the berries were analysed for changes in metabolites, hormones and gene expression. Results illustrated a stimulatory effect of sucrose and ABA on enhancing berry colour and a corresponding increase in anthocyanins. Increased ABA concentration was able to boost anthocyanin production in berries when sucrose supply was low. The sucrose and ABA effects on berry anthocyanins were primarily manifested through the up-regulation of transcription factors and other genes in the phenylpropanoid pathway, while in other parts of the pathway a down-regulation of key proanthocyanindin transcription factors and genes corresponded to sharp reduction in berry proanthocyanidins, irrespective of sucrose supply. Similarly, increased ABA was correlated with a significant reduction in berry malic acid and associated regulatory genes. These findings suggest a predominance of berry ABA over berry sugar in coordinating the physiological and genetic regulation of anthocyanins and proanthocyanins in Pinot noir grape berries.

Combination of Decitabine and Etoposide Is Highly Effective in Treating p53-Mutated MDS/AML Via Activating Notch Signaling

The elderly MDS/AML patients, especially those with TP53 mutations, remain very difficult to treat and resistant to chemotherapy. A total of 105 elderly (age above 60 years) high risk MDS (n = 84, IPSS-R score &amp;gt; 4.5) or AML-MRC (n = 21) patients' records were collected from three medical centers across China and retrospectively analyzed. Decitabine and low dose etoposide was found to be superior to standard decitabine alone in MDS/AML patients with higher ORR (70.0% vs 52.7%) after two cycles of treatment, the longer median durations of ORR (24.0 months vs 12 months) and CR (38.0 months vs 24.0 months), and longer event-free survival (13 months vs 9 months, p = 0.023), without significant improvement in overall survival (20 months vs 15 months, p = 0.059). Other than the TP53 mutation, no other gene mutation (including NRAS, DNMT3A, TET2, EZH2, ASXL1, RUNX1) in the D+E group could reliably predict OS and EFS when compared to wild type phenotype. Patients with TP53 mutations showed higher response rate after two cycles of D+E therapy and had prolonged overall survival (Mutation vs WT: 31 months vs 9 months, p=0.012) and event-free survival (Mutation vs WT: 24 months vs 5 months, p = 0.022) compared with p53 wild type patients in D+E group from multivariate survival analyses. P53 mutated patients receiving D+E treatment also had significantly improved OS (31 months vs 12 months, p = 0.00) and EFS (24 months vs 8 months, p = 0.00) compared to patients receiving decitabine treatment. Moreover, we found decitabine and etoposide greatly reduced TP53 mutant AML tumor burden in the NSG mice xenografts (tumor burden: 92% reduction in p53-null xenograft mice, 65% reduction in p53-wild-type xenograft mice on day 20 after leukemia cells administration, p &amp;lt; 0.0001). It was found that TP53 mutant cells and p53 gene-editing MOLM13 cells showed terminal neutrophil differentiation in the combo of decitabine and etoposide, demonstrating the expected changes in cell-surface CD11b expression and neutrophil functional assays such as phagocytosis. Combo of decitabine and etoposide showed much higher percentage of differentiation marker expression compared to single drug decitabine or etoposide treatment. However, neither the p53 gene-edited THP-1 cells nor the TP53 wild type cell lines displayed markers of terminal differentiation, such as elevated CD11b expression or phagocytosis. Furthermore, the percentage of CD11b-positive cells increased significantly in p53-mutated primary cells while insignificantly in TP53 wild type cells. Decitabine and etoposide induced significant differentiation thus killing p53 mutated myeloid tumor cells and primary patients' cells in vitro. We also uncovered the underlying mechanism that why D+E could induce significant differentiation in TP53 Mutant while not in TP53 wild type myeloid tumors. Notch1 signaling pathway was activated after D+E treatment in TP53 Mutant myeloid tumors, which was consistently correlated with drug-induced myeloid differentiation. Notch1 knockout or Notch inhibitor incubation abrogated drug induced differentiation in TP53 Mutant myeloid tumors. The activation of the Notch1 signaling pathway has been observed to induce disease regression and decrease leukemia stem cells in AML mice as well as significant apoptosis in the AML patient sample. We also found D+E could upregulate transcription factor transcripts such as ETS1, ETS2, which could bind specifically to PSEN1 (PS1) promoter and activate its transcription directly. PS1 represent catalytic subunit of γ-secretase complexes and is responsible for Notch recognition. While in TP53 wild type AML cells, p53 might interact with p300. p300 acts as a coactivator of Ets1 and Ets2, competition for binding to p300 with p53 may confront p300 recruitment and repress ETS transcription activation directly, which might exert its effect on PS1 repression, thus inhibiting γ-secretase complex activity. In short, integrated p53 could repress PSEN1 transcription thus interfering gamma secretase complex activity, Notch recognition and cleavage as well as abrogating drug induced Notch activation and myeloid differentiation, which could be achieved in p53 mutated state. Combination of decitabine and etoposide regimen is also relatively safe and tolerable in elderly patients, which may open up a new path of therapy in the p53 mutated AML/MDS.

Erythroid Progenitor Cells in the Murine Bone Marrow: Parallels with Human Counterparts and Response to Acute Anemia

In mammals, the erythron consists of lineage-specific progenitor cells that transition to morphologically identifiable precursors that ultimately enucleate to become mature red blood cells. Early- and late-stage erythroid progenitors, BFU-E and CFU-E respectively, were originally defined by their capacity to generate colonies of erythroid cells in semisolid media. We have refined a flow cytometry-based strategy based on Pronk, et al. (2007) and Tusi, et al. (2018) that parallels similar strategies developed for human erythroid progenitor cells (Yan et al., 2021) to facilitate identification and isolation of progressive stages of primary murine erythroid progenitors, termed EP1 to EP4, in the bone marrow. Sorted erythroid progenitor (EP1 to EP4) populations were cultured in colony-forming assays. EP1 consists almost entirely of BFU-E, while EP4 was highly enriched in CFU-E, and the intermediate EP2 and EP3 populations progress from immature to more mature erythroid colony-forming progenitors. Global RNA-Seq studies were performed on three replicates of primary bone marrow EP1-4 from 9-12 week old outbred mice. EP1/2 and EP3/4 each shared the most similarities, consistent with the enrichment of BFU-E in the former and CFU-E in the latter. We also analyzed the global transcriptome of EP1-4 derived from in vitro culture of human CD34+ hematopoietic stem and progenitor cells to compare with the murine counterparts. Approximately two-thirds of differentially expressed genes displayed similar patterns as murine and human EP1 transition progressively to EP4. The largest transition in gene expression occurred between EP2 and EP3. Analysis of genes differentially expressed between EP2 and EP3 both in human and in mouse (adj. p-value &amp;lt;0.05, 361 down and 242 up) revealed marked downregulation of transcription factors expected from previous studies of erythroid progenitors (Gata2, Cd34), as well as those associated with multipotential, myeloid, and megakaryocyte lineages (Sp1 and Runx1). Upregulated transcription factors included prototypical factors associated with erythropoiesis (Klf1, Gata1 and Tal1), as well as Srebf1, a central regulator of cholesterol homeostasis. In both species the transition from EP2 to EP3 was characterized by downregulation of the gene ontology terms associated with myeloid and megakaryocyte development, and the upregulation of gene ontology terms associated with erythrocyte development, cell cycle, heme metabolism, and VLDL particle assembly. Interestingly, cholesterol content increases as EP1/2 transition to EP3/4 in both primary murine and human bone marrow. These data indicate a shared progression of erythroid progenitors can be proactively delineated in human and mouse systems. To better define the response of erythroid progenitors to stress, we established an acute anemia model in mice, reproducibly lowering the hematocrit by half via phlebotomy. Induction of acute anemia leads to a marked expansion of EP3 and EP4 at 48 hours both in the bone marrow and in the spleen. Additionally, these expanded EP3/4 populations were characterized by an increase percentage of the cells in S-phase. Principal component analysis of global transcriptomic studies of EP1-4 isolated from the marrow 48 hours after the induction of anemia revealed parallel differentiation programs when compared to their steady-state murine counterparts. 70% of the shared genes upregulated in the transition from EP2 to EP3 were upregulated to a greater extent in response to anemia. Upregulated genes, particularly in EP3/4, included known EPO-responsive genes (Pim1, Socs2, Tfrc, and Cited4), as well as hypoxia-associated genes. Interestingly, key cholesterol biosynthesis genes (Hmgcr, Hmgcs1, and Sqle) were also further upregulated in anemic versus steady-state EP3/4. This latter finding suggests that cholesterol homeostasis may play a key role in the erythroid progenitor response to stress. We conclude that late-stage erythroid progenitor (EP3/4) expansion is a specific and integral component of regenerative erythropoiesis. The identification and isolation of stage-specific murine erythroid progenitor cells that are highly analogous to their human counterparts will facilitate an improved understanding of normal and disordered erythropoiesis.

A comparative analysis of genes differentially expressed between rete testis cells and Sertoli cells of the mouse testis

The rete testis (RT) is a region of the mammalian testis that plays an important role in testicular physiology. The RT epithelium consists of cells sharing some well-known gene markers with supporting Sertoli cells (SCs). However, little is known about the differences in gene expression between these two cell populations. Here, we used fluorescence-activated cell sorting (FACS) to obtain pure cultures of neonatal RT cells and SCs and identified differentially expressed genes (DEGs) between these cell types using RNA sequencing (RNA-seq). We then compared our data with the RNA-seq data of other studies that examined RT cells and SCs of mice of different ages and generated a list of DEGs permanently upregulated in RT cells throughout testis development and in culture, which included 86 genes, and a list of 79 DEGs permanently upregulated in SCs. The analysis of studies on DMRT1 function revealed that nearly half of the permanent DEGs could be regulated by this SC upregulated transcription factor. We suggest that useful cell lineage markers and candidate genes for the specification of both RT cells and SCs may be present among these permanent DEGs.

NK-2 Homeobox Transcription Factor NKX2-3 Confers Differentiation Block in NPM1-Mutated in Acute Myeloid Leukaemia

Dysregulation of HOX homeobox family transcription factor (TF) gene expression is important in the pathogenesis of AML in particular in NPM1-mutated and MLL rearranged molecular subtypes. However, little is known about the role of NK2-homeobox (NKX2) family TF genes. NKX2 genes have critical roles in normal development of the central nervous system, thyroid, lung and pancreas. We observed high expression of NKX2-3 in patient AML samples and hypothesised the transcription factor might have a functional role in the disease. By qPCR, we found that NKX2-3 is highly expressed in normal HSCs but is rapidly down regulated as cells differentiate. In primary AML samples, it is highly expressed in 21-37% cases, including within the immunophenotypic LSC compartment, in particular in cases with NPM1 and/or FLT3-ITD mutations. Forced expression of NKX2-3 in normal murine KIT + bone marrow (BM) HSPCs transiently enhanced their clonogenic activity and impaired differentiation: NKX2-3-expressing HSPCs expressed higher levels of E2F or MYC target genes, and leukemia stem cell (LSC) maintenance genes. Congenic transplant experiments revealed that forced expression of NKX2-3 in normal BM HSPCs was sufficient to enhance multilineage engraftment across four months of follow up without inducing leukemia. In keeping with this, transplantation of Nkx2-3 -/- knockout BM cells led to significantly inferior engraftment compared with BM cells from litter mate control mice. Thus, while increased expression of Nkx2-3 enhances engraftment of normal stem cells in transplantation assays, loss of Nkx2-3 impairs it. Analysis of NKX2-3 high primary human AML cases demonstrated that HOXA9 was the most highly upregulated transcription factor gene compared with NKX2-3 low cases. We expressed both factors singly and together in murine KIT+ BM HSPCs: Hoxa9/NKX2-3 cells exhibited significantly higher clonogenic activity and reduced morphologic and immunophenotypic differentiation compared with Hoxa9/MTV cells. Congenic BM transplant experiments demonstrated that Hoxa9/NKX2-3 recipients developed leukemias significantly earlier than Hoxa9/MTV recipients (median 82 vs 155 days). BM morphology and immunophenotyping confirmed that Hoxa9/NKX2-3AMLs exhibited a greater degree of differentiation block than Hoxa9/MTV AMLs. Leukemia cells from Hoxa9/NKX2-3 recipients coordinately expressed higher levels of E2F or MYC target genes, and LSC maintenance genes. NKX2-3 KD to ~30% of control values reduced proliferation and induced morphologic and immunophenotypic differentiation in primary patient NPM1-mutated AML cells. NKX2-3 KD led to down regulation of E2F and MYC target genes and normal human CD34 + stem cell genes; and up regulation of myeloid differentiation genes. Using a CRISPR ribonucleofection approach to relocate NPM1c to the nucleus we confirmed that NKX2-3 expression in NPM1-mutant primary AML cells is sustained by mutant NPM1c. ChIPseq in NPM1-mutated primary patient and KO52 AML cells identified NKX2-3 binding peaks. As expected, DNA sequences under peak apices were strongly enriched for NKX2-3 binding motifs; there was also significant enrichment for RUNX and ETS family motifs, but not HOX/MEIS/PBX motifs. To identify genes potentially regulated by NKX2-3, genomic coordinates of strong binding peaks were mapped to the single nearest gene. Remarkably, among genes up regulated following NKX2-3 knockdown in primary human AML cells there was a highly significant enrichment of genes with putative regulatory elements bound by NKX2-3. Likewise, among genes down regulated in NKX2-3-expressing KIT+ murine HSPCs, there was a similar significant enrichment of genes with putative regulatory elements bound by NKX2-3. These data suggest that NKX2-3 functions as a transcription repressor at bound regulatory elements in primary AML cells. In summary, NKX2-3 is highly expressed in NPM1 &amp; FLT3 mutated molecular subtypes of AML and serves to enhance self-renewal and the level of differentiation block through binding to and repressing regulatory elements of myeloid differentiation genes.

Effects of Hypericin on Cultured Primary Normal Human Dermal Fibroblasts Under Increased Oxidative Stress

Introduction Wound healing is a dynamic process that begins with inflammation, proliferation, and cell migration of a variety of fibroblast cells. As a result, identifying possible compounds that may improve fibroblast cell wound healing capacity is crucial. Hypericin is a natural quinine that has been reported to possess a wide range of pharmacological profiles, including antioxidant and anti-inflammatory, activities. Herein we examined for the first time the effect of hypericin on normal human dermal fibroblasts (NHDFs) under oxidative stress. Methods NHDF were exposed to different concentrations of hypericin (0-20 μg/mL) for 24 h. For the oxidative stress evaluation, H2O2 was used as a stressor factor. Cell viability and proliferation levels were evaluated. Immunohistochemistry and flow cytometry were performed to assess cell apoptosis levels and with confocal microscopy we identified the mitochondrial superoxide production under oxidative stress and after the treatment with hypericin. Scratch assay was performed under oxidative stress to evaluate the efficacy of hypericin in wound closure. To gain an insight into the molecular mechanisms of hypericin bioactivity, we analyzed the relative expression levels of genes involved in oxidative response and in wound healing process. Results We found that the exposure of NHDF to hypericin under oxidative stress resulted in an increase in cell viability and ATP levels. We found a decrease in apoptosis and mitochondrial superoxide levels after treatment with hypericin. Moreover, treatment with hypericin reduced wound area and promoted wound closure. The levels of selected genes showed that hypericin upregulated the levels of antioxidants genes. Moreover, treatment with hypericin in wound under oxidative stress downregulated the levels of proinflammatory cytokines, and metalloproteinases; and upregulated transcription factors and extracellular matrix genes. Conclusion These findings indicated that hypericin possesses significant in vitro antioxidant activity on NHDF and provide new insights into its potential beneficial role in the management of diabetic ulcers.

RD29A and RD29B rearrange genetic and epigenetic markers in priming systemic defense responses against drought and salinity

Drought has become the most important limiting factor to crop productions. Research thus far has been devoted to identifying drought-responsive genes (DRGs) via breeding and engineering approaches. Still, these efforts have not resulted in a solution to combat drought’s effects because the ectopic expression of most DRGs causes adverse effects that reduce plant growth and yields. Lately, we discovered that two DRGs, Response to Desiccation (RD)29A and RD29B, induced by Paenibacillus polymyxa CR1, a plant growth-promoting rhizobacterium capable of priming drought tolerance and concurrently stimulating plant growth, play pivotal roles in defense responses against drought. In this study, we employ the ChlP and qRT-PCR analyses and further clarify that P. polymyxa CR1 reformats the chromatin/transcriptional memory of RD29s, positioned as upstream controllers that fine-tune the temporal dynamic of stress-regulating transcription factors (TFs) in elaborating induced systemic drought tolerance without growth penalties. Two genes coordinate the upregulation of NAC TFs, while feedback inhibiting CBF TFs, which regulate downstream DRG expressions. This supports that RD29s are unique, feasible transgene candidates for improving plants’ survival capacity in both optimal and drought conditions. However, the mode of action of RD29A and RD29B are partly independent, exerting distinct roles in disparate ecological states. When subjected to increasing NaCl concentrations, the KO mutant of RD29A (rd29a) displayed enhanced tolerance compared to WT and rd29b plants, proposing that RD29B, but not RD29A, a key player in conferring WT-like tolerance to salinity stress; further studies will be needed to optimize/maximize their applications in engineering for-profit drought and/or broad-spectrum stress tolerant crops.

Psilocybin, Depression, and Synaptogenesis: Insights into the Field’s Past, Present, and Future

Depression remains one the most commonly diagnosed mental health disorders in the United States. The Food and Drug Administration granted psilocybin breakthrough therapy status four years ago as a possible solution to this pervasive disorder. Since then, psilocybin, and hallucinogens in general, have produced promising results as alternatives to classical antidepressants. As more research confirms psilocybin’s potential therapeutic effect, research surrounding the mechanistic action of these 5-HT2A receptor agonists has increased as well. Hallucinogens have different downstream effects compared to non-hallucinogenic 5-HT2A receptor agonists, including the formation of a 5-HT2A receptor and metabotropic glutamate receptor complex. Psilocybin’s unique synaptogenic effect may play a role in its therapeutic effect for major depressive disorder; however, the underlying mechanism by which synaptogenesis is induced upon psilocybin administration has not been explored. Psilocybin’s distinctive upregulation of transcription factors, such as egr-2, c-fos, and brain-derived neurotrophic factors, and its connection with the TrkB signaling pathway, may be the answer to this unexplained mechanism.

The genetic variation in drought resistance in eighteen perennial ryegrass varieties and the underlying adaptation mechanisms

BackgroundDrought resistance is a complex characteristic closely related to the severity and duration of stress. Perennial ryegrass (Lolium perenne L.) has no distinct drought tolerance but often encounters drought stress seasonally. Although the response of perennial ryegrass to either extreme or moderate drought stress has been investigated, a comprehensive understanding of perennial ryegrass response to both conditions of drought stress is currently lacking.ResultsIn this study, we investigated the genetic variation in drought resistance in 18 perennial ryegrass varieties under both extreme and moderate drought conditions. The performance of these varieties exhibited obvious diversity, and the survival of perennial ryegrass under severe stress was not equal to good growth under moderate drought stress. ‘Sopin’, with superior performance under both stress conditions, was the best-performing variety. Transcriptome, physiological, and molecular analyses revealed that ‘Sopin’ adapted to drought stress through multiple sophisticated mechanisms. Under stress conditions, starch and sugar metabolic enzymes were highly expressed, while CslA was expressed at low levels in ‘Sopin’, promoting starch degradation and soluble sugar accumulation. The expression and activity of superoxide dismutase were significantly higher in ‘Sopin’, while the activity of peroxidase was lower, allowing for ‘Sopin’ to maintain a better balance between maintaining ROS signal transduction and alleviating oxidative damage. Furthermore, drought stress-related transcriptional and posttranscriptional regulatory mechanisms, including the upregulation of transcription factors, kinases, and E3 ubiquitin ligases, facilitate abscisic acid and stress signal transduction.ConclusionOur study provides insights into the resistance of perennial ryegrass to both extreme and moderate droughts and the underlying mechanisms by which perennial ryegrass adapts to drought conditions.

Single-cell transcriptome analysis and protein profiling reveal broad immune system activation in IgG4-related disease.

IgG4-related disease (IgG4-RD) is a systemic autoimmune disease with unclear pathogenesis. We performed single-cell RNA-seq and surface proteome analyses on 61,379 PBMCs from 9 treatment-naive IgG4-RD patients and 7 age- and sex-matched healthy controls. Integrative analyses were performed for altered gene expression in IgG4-RD, and flow cytometry and immunofluorescence were used for validation. We observed expansion of plasmablasts with enhanced protein processing and activation, which correlated with the number of involved organs in IgG4-RD. Increased proportions of CD4+ cytotoxic T lymphocytes (CTLs), CD8+ CTLs-GNLY (granulysin), and γδT cells with enhanced chemotaxis and cytotoxicity but with suppressed inhibitory receptors characterize IgG4-RD. Prominent infiltration of lymphocytes with distinct compositions were found in different organs of IgG4-RD patients. Transcription factors (TFs), including PRDM1/XBP1 and RUNX3, were upregulated in IgG4-RD, promoting the differentiation of plasmablasts and CTLs, respectively. Monocytes in IgG4-RD have stronger expression of genes related to cell adhesion and chemotaxis, which may give rise to profibrotic macrophages in lesions. The gene activation pattern in peripheral immune cells indicated activation of multiple interaction pathways between cell types, in part through chemokines or growth factors and their receptors. Specific upregulation of TFs and expansion of plasmablasts and CTLs may be involved in the pathogenesis of IgG4-RD, and each of these populations are candidate targets for therapeutic interventions in this disease.

ELF4 contributes to esophageal squamous cell carcinoma growth and metastasis by augmenting cancer stemness via FUT9.

Esophageal squamous cell carcinoma (ESCC) commonly has aggressive properties and a poor prognosis. Investigating the molecular mechanisms underlying the progression of ESCC is crucial for developing effective therapeutic strategies. Here, by performing transcriptome sequencing in ESCC and adjacent normal tissues, we find that E74-like transcription factor 4 (ELF4) is the main upregulated transcription factor in ESCC. The results of the immunohistochemistry show that ELF4 is overexpressed in ESCC tissues and is significantly correlated with cancer staging and prognosis. Furthermore, we demonstrate that ELF4 could promote cancer cell proliferation, migration, invasion, and stemness by in vivo assays. Through RNA-seq and ChIP assays, we find that the stemness-related gene fucosyltransferase 9 ( FUT9) is transcriptionally activated by ELF4. Meanwhile, ELF4 is verified to affect ESCC cancer stemness by regulating FUT9 expression. Overall, we first discover that the transcription factor ELF4 is overexpressed in ESCC and can promote ESCC progression by transcriptionally upregulating the stemness-related gene FUT9.

A Synthetic Poly(A) Tail Targeting Extracellular CIRP Inhibits Sepsis.

Sepsis is an infectious inflammatory disease that often results in acute lung injury (ALI). Cold-inducible RNA-binding protein (CIRP) is an intracellular RNA chaperon that binds to mRNA's poly(A) tail. However, CIRP can be released in sepsis, and extracellular CIRP (eCIRP) is a damage-associated molecular pattern, exaggerating inflammation, ALI, and mortality. In this study, we developed an engineered poly(A) mRNA mimic, AAAAAAAAAAAA, named A12, with 2'-O-methyl ribose modification and terminal phosphorothioate linkages to protect it from RNase degradation, exhibiting an increased half-life. A12 selectively and strongly interacted with the RNA-binding motif of eCIRP, thereby preventing eCIRP's binding to its receptor, TLR4. In vitro treatment with A12 significantly decreased eCIRP-induced macrophage MAPK and NF-κB activation and inflammatory transcription factor upregulation. A12 also attenuated proinflammatory cytokine production induced by eCIRP invitro and invivo in macrophages and mice, respectively. We revealed that treating cecal ligation and puncture-induced sepsis with A12 significantly reduced serum organ injury markers and cytokine levels and ALI, and it decreased bacterial loads in the blood and peritoneal fluid, ultimately improving their survival. Thus, A12's ability to attenuate the clinical models of sepsis sheds lights on inflammatory disease pathophysiology and prevention of the disease progress.