title: StrokeofGenus: RNA-seq in five tissues of the hibernating 13-lined ground squirrel

city: Baltimore

first: Kurt

last: Weir

address: 733 North Broadway

institute: Johns Hopkins School of Medicine

summary: Identify shifts in gene expression relevant to torpor phenotypes and recovery following torpor in five tissues of the 13-lined ground squirrel. Sampled tissues and time points overlap with prior hibernation RNA-seq studies in 13-lined ground squirrel and other species, allowing for the analysis of conserved gene expression patterns in torpor.

overall_design: RNA-seq from the Cortex, Hypothalamus, Retina, Retinal pigment epithelium (RPE), and Liver of 13-lined ground squirrel taken at five points surrounding and during hibernation: euthermia, prehibernation (RT torpor), torpor,  three days post torpor euthermia, and fourteen days post torpor euthermia. Tissue was collected from three specimens for each time point, though two liver samples for the prehibernation time point and two RPE sample samples for the euthermia time point failed quality checks and were not sequenced.

first: Ben

last: Sadjak

first: Les

last: Kallestad

first: Joseph

last: Carroll

first: Krzysztof

last: Palczewsk

first: Seth

last: Blackshaw


title: KIF1A promotes neuroendocrine differentiation in prostate cancer by regulating the OGT-mediated O-GlcNAcylation

status: Public on Oct 23 2024

city: Jinan

first: Qianqian

last: Zhou

state: Shandong Province

address: 44 Wenhua Xi Rd.

country: China

institute: Shandong University

type: Expression profiling by high throughput sequencing

summary: Background: Treatment-related neuroendocrine prostate cancer (t-NEPC) is a highly aggressive form of prostate cancer (PCa). Understanding the molecular mechanisms driving t-NEPC may provide valuable therapeutic strategies. Methods: we performed a pan-cancer differential mRNA abundance analysis of neuroendocrine tumors (NET) and non-NETs using integrated datasets to identify potential driver genes in NEPC. Gain- and loss-of-function studies were performed in PCa cell lines and subcutaneous xenografts in mouse to characterize the role of Kinesin-like protein (KIF1A) in neuroendocrine (NE) differentiation. Western blot, qRT-PCR, immunoprecipitation (IP), nuclear and cytoplasmic protein extraction, CO-IP and immunofluorescence were performed to study the regulation of KIF1A to OGT. Results: We identified that KIF1A overexpression is highly correlated to NE differentiation. NE differentiation features in PCa, including NE marker gene expression, stemness and EMT, were impaired by KIF1A knockdown and promoted by KIF1A overexpression. Targeting KIF1A inhibited the growth of NE-differentiated PCa cells in vitro and in vivo. Mechanistically, KIF1A bound with OGT and regulated its protein expression and O-linked N-acetylglucosamine transferase activity. OGT nuclear translocation induced by elevated KIF1A inhibited OGT ubiquitin-proteasome pathway degradation in the cytoplasm and promoted intranuclear O-GlcNAcylation of β-catenin and OCT4. More importantly, our data revealed that OGT is critical for KIF1A induced NE differentiation and aggressive growth. Conclusion: KIF1A promotes NE differentiation through modeling OGT O-GlcNAcylation in PCa. Targeting KIF1A - OGT may impede the development of NEPC for a group of PCa patients with elevated KIF1A expression.

overall_design: LNCaP-AI cells were established by culturing LNCaP cells in phenol red-free RPMI1640 medium containing 10% charcoal-stripped FBS (CSS) for  6 months.Parental LNCaP cells were cultured in RPMI1640 medium containing 10% FBS  for 6 months.

first: Jiawei

last: Fu

first: Bo

last: Han


title: Systematic transcriptome and molecular docking analyses reveals that Cirsium japonicum mitigates allergic nasal inflammation through regulation of NRF2-mediated mucin production in an allergic rhinitis mouse model

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

summary: Allergic rhinitis (AR) is a typical allergic disease mediated by immunoglobulin E (IgE), which greatly affects the quality of life and is more sensitive to change of seasons due to various nasal symptoms. AR worsening symptoms can lead to more dangerous diseases, there is an urgent need to develop safe and effective treatments. Cirsium japonicum (CSJ) is a plant that has been used in traditional medicine due to its various efficacy and safety; so far, the effects and major mechanisms of CSJ on AR have not been reported. Therefore, the purpose of this study was to investigate the possible targets of CSJ for AR treatment and its underlying mechanisms. An ovalbumin (OVA)-induced AR mouse model was established and the therapeutic effects of CSJ were evaluated. CSJ reduced the production level of OVA-specific IgE, histamine, and Th2 cytokines in serum, and significantly alleviated the typical symptoms of AR and the level of inflammation in the nasal mucosa. In addition, we used transcriptome analysis in AR models to identify that O-linked glycosylation of mucins, MUC5AC, and NRF2 are key targets for CSJ related to AR. Then, we identified the active ingredients of CSJ for AR, and verified that the active core compounds of CSJ, cryptochromogenic acid and cirsimarin, could bind closely to potential key targets, NRF2-KEAP1, and MUC5AC using molecular docking analysis. In conclusion, our results suggest that CSJ may be a more effective candidate drug for the treatment of AR with dual function to regulate both NRF2 pathway and MUC5AC expression.

overall_design: To investigate the gene expression signatures of Cirsium japonicum (CSJ), we performed whole transcriptome sequencing (WTS) in an OVA-induced AR mouse model treated with two increasing doses of CSJ.

first: Taesoo

last: Kim

first: YunHee

first: Bo-Jeong

last: Pyun


title: T cell infiltration as a novel therapeutic target in aged traumatic brain injury

city: Chicago

first: Jennie

last: Chen

address: 240 E Huron St

country: USA

institute: Northwestern University

type: Non-coding RNA profiling by high throughput sequencing

summary: Patients aged 65 years and older account for an increasing proportion of those who suffer from traumatic brain injury (TBI). Aged TBI patients experience increased morbidity and mortality compared to young TBI patients. Our prior data demonstrated that anti-CD49d antibody (aCD49d Ab), an FDA-approved drug that blocks α4 integrin, abrogates infiltration of CD8+ T-cells into the injured brain, improves survival, and attenuates neurocognitive deficits. Yet, the molecular mechanisms underlying the therapeutic effects of aCD49d Ab remained unexplored. Here, we aimed to uncover how aCD49d Ab treatment alters local cellular responses in the aged mouse brain. Consequently, we found that mice incur age-associated toxic cytokine and chemokine responses long-term post-TBI. aCD49d Ab attenuates this response along with a T helper (Th)1/Th17 immunological shift and remediation of CD8+ T cell cytotoxicity. Further, aCD49d Ab further produces a neuroprotective Th2 response and restores age-associated CD8+ T cell senescence. Our results demonstrate that targeting infiltrating CD8+ T cells with aCD49d Ab is a promising therapeutic strategy for treating TBI in aged individuals.

overall_design: Aged versus young mice were subject to controlled cortical impact of traumatic brain injury followed by receving aCD49d Ab versus isotype treatmemt. Treatment was repeated every two weeks. At two months post TBI, brain cell isolated from aged versus young mouse underwent CD45+ FACS followed by 10x single cell RNA sequencing and TCR sequencing


title: Effect of iPSC-derived megakaryocytes and platelets on gene expression of HUVEC

city: Chiba-shi

first: Kentaro

last: Kosaka

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

country: Japan

institute: Chiba University Graduate School of Medicine

summary: Platelet-rich plasma (PRP), which is prepared by concentrating platelets in autologous blood, shows efficacy in chronic skin wounds via multiple growth factors. However, it exhibits heterogeneity across patients, leading to unstable therapeutic efficacy. Human induced pluripotent stem cell-derived megakaryocytes and platelets (iMPs) are capable of providing a stable supply, holding promise as materials for novel therapies. Thus, we evaluated the effect of iMPs on wound healing in vitro. iMPs specifically released FGF2 and exhibited superior enhancement on HUVEC proliferation compared to PRP. RNA-seq revealed that iMPs induce polarization to stalk cells and enhance ANGPTL4 gene expression in HUVECs. These mechanisms were suggested to provide the superior effects of iMPs.

overall_design: RNA-sequencing (RNA-Seq)

first: Sudip

middle: K

last: Paul

first: Masaki

last: Fukuyo

first: Bahityar

last: Rahmutulla

first: Atsushi

last: Kaneda

first: Naoya

last: Takayama


title: The global phosphorylation landscape of mouse oocytes during meiotic maturation

city: Nanjing

first: Jiashuo

last: Li

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

summary: To explore the impact of BTG4-T145/S146/S147 mutations on the degradation of transcripts in MII-stage oocytes, we injected wild-type BTG4 mRNA (BTG4wt) and mutant BTG4 mRNA (BTG4tm) into GV-stage oocytes. These oocytes were matured in vitro to the MII stage, after which samples of MII-stage oocytes were collected for library construction and subsequent second-generation transcriptome sequencing.

overall_design: Transcriptome profiling by high throughput sequencing

first: Hongzheng

last: Sun

first: Longsen

first: Yueshuai

last: Guo

first: Qiang

last: Wang


title: Morphological and Genetic Characterization of Fruit Abscission Zone in Muscadine

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: Muscadines face limitations to fresh market production due to high manual labor costs. Mechanical harvesting holds promise for reducing the costs associated with muscadine production but requires cultivars with easily detached berries at maturity. This study aimed to determine muscadine fruit and pedicel characteristics influencing fruit detachment force and to unravel the genes, hormones, and regulatory networks governing muscadine abscission. We characterized the fruit detachment force of muscadine berries across eighteen genotypes and at four developmental stages. Following this, we performed a transcriptome analysis using the mature pedicel tissue of two genotypes, a genotype with high fruit detachment force at maturity and a genotype with low fruit detachment force at maturity, to identify differentially expressed and uniquely expressed genes contributing to fruit detachment. We found that pedicel length, pedicel-fruit junction area, and fruit diameter were all positively correlated with fruit detachment force. This study also identifies novel candidate genes, transcription factor families, and pathways associated with muscadine fruit abscission. These findings provide valuable knowledge on the progression of fruit abscission and insights for reducing fruit detachment force, particularly in developing machine-harvestable muscadine cultivars and fostering sustainability and efficiency in muscadine production.

overall_design: By studying grape physical characteristics such as abscission zone morphology, fruit and pedicel characteristics, and fruit detachment force in conjunction with a transcriptomic analysis, we offer a comprehensive approach to studying muscadine abscission on a level that has not been previously reported in any grape species. This study identifies several muscadine genotypes with the potential for mechanical harvesting.

first: Alana

last: Brinley

first: Patrick

last: Conner

first: Fahong

last: Yi

first: Ali

last: Sarkhosn

first: Tie

last: Liu


title: Gene expression changes in 786-O cells in response to Everolimus, SGI-1027, or their combination.

city: Xia Men

first: Yu

last: Luo

address: zhenhai Road

institute: the fiirst affiliated hospital of Xiamen University

summary: Renal cell carcinoma (RCC) is one of the most common malignant tumors of urinary system. The Food and Drug Administration (FDA) has approved everolimus for the treatment of advanced RCC, but r everolimus resistance limits its application in clinic. We here reported the DNA methyltransferase 1 (DNMT1) inhibitor SGI-1027 as an inducer of methuosis, a type of cell death form independent of apoptosis. Additionally, SGI-1027 and everolimus worked in concert to suppress the proliferation, migration, and invasion of renal cancer cells while also inducing apoptosis and GSDME-dependent pyroptosis. In vitro transplanted tumor mice models, everolimus combined with SGI-1027 played a significant inhibitory effect on the growth of renal cancer tumors with good tolerance. The objective of this study is to explore the mechanism of the synergistic effect of everolimus and SGI-1027. We demonstrated through analysis of transcriptome high-throughput sequencing data that lysosomes were strongly linked with the synergistic effect of everolimus and SGI-1027 at the transcriptional level, which provides a new strategy for everolimus resistance and the treatment of advanced RCC.

overall_design:
To investigated the synergistic effect of everolimus and SGI-1027, 786-O cells were treated with 10uM everolimus, 1.5uM SGI-1027, 5uM everolimus combined with 1.5uM SGI-1027, or vehicle (DMSO) for 24 hours. Each processing group contains three replicates.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 786-O cells in each group.
Comparative gene expression profiling analysis of RNA-seq data for Individual drug treated groups and vehicle (DMSO) group.

first: Bing

last: Guan

first: Tao


title: Transcriptome response of granulosa cells to seasonal heat stress in beef cows

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: Investigation of cellular responses to thermal heat stress can lead to identifying novel targets of intervention to tackle the increasing fertility decline due to climate change-associated seasonal heat stress. We aimed to study the response of granulosa cells to seasonal thermal stress. Dry beef cows (n=11) were kept together during the study and subjected to synchronization and stimulation for follicular dynamics. Ovum pick-up (OPU) was conducted on all animals in the winter and summer. Once OPU-fluid settled, cumulus-oocyte-complexes (COCs) and granulosa cells were isolated from the OPU fluid and stored in a -80 freezer after snap freezing. In addition, blood samples and rectal temperature data were collected on each OPU. Environmental data were collected daily for three weeks before each OPU using the Florida Automated Weather Network. Data were analyzed using SAS. Data are presented as mean ± standard error of the mean. RNA was extracted from five pools of granulosa cells followed by library preparation and sequencing (NovaSeq; Illumina). As expected, environmental conditions were contrasting: average air temperature (11.5°C vs. 27.5°C), average max air temperature (16.9°C vs. 33.7°C), relative humidity (83.5% vs. 82.3%), and temperature-humidity index (53.39 vs. 79.16) for winter and summer, respectively. The average rectal temperature was higher (P = 0.03) in summer (39.2 ± 0.2°C) than in winter (38.8 ± 0.2°C). Of the total differentially expressed genes, granulosa cells during summer showed up and downregulation of 1083 and 1126 transcripts, respectively compared to the winter season (Fold Change ≤ -2 or ≥ 2 and FDR p-value ≤ 0.05). Many of the downregulated transcripts were found to be involved in the inhibition of immunological pathways such as activation of lymphatic system cells and activation of lymphocytes. In conclusion, exposure of cows to thermal stress can induce significant alteration in the transcriptome of granulosa cells which may have a negative impact on follicular physiology.

overall_design: Multiparous angus dry beef cows (n = 11) were kept together during the study and subjected to synchronisation and stimulation of follicular growth using a 5-day CIDR and follicle-stimulating hormone (FSH) protocol. Ovum pick-up (OPU) was conducted on all animals in the winter (January) and summer (August). Granulosa cells (GCs) were isolated from the follicular fluid aspirated during the OPU procedure, snap frozen, and stored at −80 °C until further use for RNA sequencing

first: Kamryn

last: Joyce

first: Nico

middle: G

last: Menjivar

first: Samuel

last: Gebremedhn

first: Daniella

last: Heredia

first: Georgia

last: Dubeux

first: María

middle: C

last: López Duarte

first: Joao

last: Bittar

first: Angela

last: Gonella-Diaza

first: Dawit

last: Tesfaye


title: Potential cardiac-derived exosomal miRNAs involved in cardiac healing and remodeling after myocardial ischemia-reperfusion injury

city: chengdu

first: yu

last: liu

address: shier

institute: chengdu university of traditional Chinese medicine

summary: Migratory cells exist in the heart, such as immune cells, fibroblasts, endothelial cells, etc. During my-ocardium injury, such as ischemia-reperfusion (MIRI), cells migrate to the site of injury to perform repair functions. However, excessive aggregation of these cells may exacerbate damage to the structure and function of the heart, such as acute myocarditis and myocardial fibrosis. Myocardial injury releases exosomes, which are a type of vesicle with signal transduction function and the miRNA carried by exosomes can control cell migration function. Therefore, regulating this migratory cell population through cardiac-derived exosomal miRNA is crucial for protecting and maintaining cardiac function. Through whole transcriptome RNA sequencing, exosomal miRNA sequencing and single-cell dataset analysis, we (1) determined the potential molecular regulatory role of the lncRNA‒miRNA‒mRNA axis and an important lncRNA (MSTRG.91411.6) in MIRI, (2) screened four important exosomal miRNAs that could be released by cardiac tissue, and (3) screened seven genes related to cell locomo-tion that are regulated by four miRNAs, among which Tradd and Ephb6 may be specific for promoting migration of different cells of myocardial tissue in myocardial infarct. We generated a core miRNA‒mRNA network based on the functions of the target genes, which may be not only a target for cardiac repair but also a potential diagnostic marker for interactions between the heart and other tissues or or-gans. In conclusion, we elucidated the potential mechanism of MIRI in cardiac remodeling from the perspective of cell migration, and inhibition of cellular overmigration based on this network may pro-vide new therapeutic targets for MIRI and to prevent MIRI from developing into other diseases.

overall_design: Rats were treated with left coronary artery ligation for 30 min and then perfused for one week, and heart tissue was taken for transcriptome sequencing

first: Jiao

last: Chen


title: Transcriptome response of oocytes to seasonal heat stress in beef cows

summary: Introduction: Reduced reproductive performance due to seasonal heat stress is a major problem in the beef and dairy industries. Examining the effects of heat stress on the molecular mechanism of bovine oocytes can help to better understand their alterations on a transcriptional level and to plan and mitigate those effects. We aimed to study the response of oocytes to seasonal thermal stress.  Materials and Methods: Multiparous angus dry beef cows (n = 11) were kept together during the study and subjected to synchronisation and stimulation of follicular growth using a 5-day CIDR and follicle-stimulating hormone (FSH) protocol. Ovum pick-up (OPU) was conducted on all animals in the winter (January) and summer (August). Cumulus-oocyte-complexes (COCs) were isolated from the follicular fluid aspirated during the OPU procedure. Denuded oocytes were further isolated from the COCs, snap frozen, and stored at −80 °C until further use for library sequencing, RNA sequencing, bioinformatics and gene enrichment analysis. Additionally, rectal temperatures were recorded on the day of each OPU. Environmental data were collected daily three weeks before the day of each OPU using the Florida Automated Weather Network. Statistical analysis for average rectal temperature included overall mean (average rectal temperature), treatment effects (season), and the residual. Treatment effect was considered significant at P ≤ 0.05. Data are presented as mean ± standard error of the mean. RNA was extracted from five biological replicates/pools of oocytes (each containing n = 2) followed by library preparation and sequencing (NovaSeq; Illumina).  Results: As expected, environmental conditions were contrasting [average air temperature (11.5 °C vs 27.5 °C), average max air temperature (16.9 °C vs 33.7 °C), relative humidity (83.5% vs 82.3%), and temperature-humidity index (53.39 vs 79.16) for winter and summer, respectively]. Average rectal temperature was greater (P = 0.03) in summer (39.2 ± 0.2 °C) than in the winter (38.8 ± 0.2 °C). Data analysis revealed an up-regulation of 446 transcripts and a down-regulation of 940 transcripts in oocytes collected during summer compared to winter (Fold Change ≥ 2; FDR P-value ≤ 0.05). Upregulated transcripts are involved in protein digestion and absorption, ATP-binding cassette transporter, oocyte meiosis, and progesterone-mediated oocyte maturation pathways. Conversely, down-regulated transcripts are involved in pathways related to extracellular matrix-receptor interaction, focal adhesion, and PI3K-Akt signaling.  Conclusions: In conclusion, exposure of cows to thermal stress can significantly alter the transcriptome of oocytes, which may negatively impact subsequent developmental competence.

overall_design: Multiparous angus dry beef cows (n = 11) were kept together during the study and subjected to synchronisation and stimulation of follicular growth using a 5-day CIDR and follicle-stimulating hormone (FSH) protocol. Ovum pick-up (OPU) was conducted on all animals in the winter (January) and summer (August). Cumulus-oocyte-complexes (COCs) were isolated from the follicular fluid aspirated during the OPU procedure. Denuded oocytes were further isolated from the COCs, snap frozen, and stored at −80 °C until further use for RNA sequencing


title: Split-pool combinatorial barcoding sequencing of murine immune cells

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19-A1038

department: Department of Biomedicine

country: Estonia

institute: Institute of Biomedicine and Translational Medicine

summary: Single-cell RNA sequencing experiments commonly use 10x Genomics kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. The Parse technology allows the analysis of more cells from multiple samples in a single run without using additional reagents or specialized microfluidics equipment. To assess the efficacy of both platforms, we carried out a benchmark study using biological and technical replicates of young murine thymus as a complex immune tissue. To optimally utilize the capacity of Parse high-throughput kits, we also performed sequencing of murine splenocytes from a chronic stress model and control animals.

overall_design: Thymic and splenic samples from young and adult mice (20 in total) were extracted and pooled together to run on a single Parse WT kit. The resulting Parse library was split into nine sublibraries (PWT_1-PWT_9). Thymocytes from separate biological replicates were processed with the Parse Mini kit and split into two sublibraries. The 10x Genomics data contains thymocytes from two biological and two technical replicates multiplexed using cell hashing technology.

first: Chinna

middle: S

last: Philip

first: Igor

last: Filippov


title: The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins (Spec-Seq)

city: Hong Kong

first: Daisylyn Senna

middle: Young

last: Tan

state: HONG KONG

address: B1202, 9 Lung Wah Strert, Kennedy Town

country: Hong Kong

institute: The University of Hong Kong

summary: Pluripotent stem cells are a hallmark of animal multicellularity. Sox and POU family transcription factors are pivotal for stemness and were believed to be animal innovations as they were reported absent from the genomes of their unicellular relatives. Here we describe new unicellular holozoan orthologues to Sox and POU families, indicating that they emerged before the appearance of animals. We show that choanoflagellate and filasterean Sox genes have DNA binding specificity similar to Sox2. Choanoflagellate Sox can partner with the POU member Oct4 on DNA elements found in pluripotency enhancers. Consistently, choanoflagellate – but not filasterean – Sox genes can replace Sox2 to reprogram mouse somatic cells into induced pluripotent stem cells (iPSC). In contrast, choanoflagellate POU harbors a unique DNA-binding profile that differs from Oct4 and cannot generate iPSCs. Pluripotency reprogramming with reconstructed ancestral Sox genes shows that their molecular ability to induce stemness was already present in the last common ancestor of animals and their unicellular relatives. Our findings imply that the evolution of stem cells exploited a pre-existing set of transcription factors, where the critical innovation involved an initial change in DNA specificity of POU and the exaptation of the ancestral capacity to interact with Sox transcription factors.

overall_design: To investigate the binding specificity of Sox and POU proteins found in unicellular organisms such as Salpingoeca helianthica (Salhel) and Pigoraptor chileana (Pchi), the DNA binding domains (DBD) of Sox proteins from Salhel and Pchi, as well as the POU protein from Salhel, were purified. These proteins along with DBDs of mouse Sox2 and Oct4 proteins were then subjected to Specificity by sequencing (Spec-seq) experiments using  libraries of degenerate sequences of Sox motif (CATTGTT) and Octamer motif (ATGCTAAT), respectively.

first: Daisylyn

first: Gao

last: Ya

first: Ralf

last: Jauch


title: Physiological, Biochemical, and Transcriptomic Analyses Reveal the Response to Oxidative Stress Under Drought Stress in Castor (Ricinus communis L.)

city: Baicheng City

first: Yong

last: Zhao

address: No. 57, Zhongxingxi Road, Baicheng City, Jilin Province, China

institute: Baicheng Normal University

summary: Castor is an important industrial raw material. Drought leads to delayed development and reduced yield of castor plants. However, the molecular mechanism of the response of castor plants to drought stress has not been determined. In this study, physiological, biochemical, and RNA-seq analyses were conducted on castor roots under PEG-6000 stress for 3, 7, and 4 d (11 d) of rehydration. The activities of GR, APX, SOD, and CAT in the roots of the castor plants under PEG-6000 stress increased at 3 d and decreased at 7 d, while the activity of POD continued to increase. A total of 2926, 1507, and 111 DEGs were identified in castor roots stressed with PEG-6000 for 3 d and 7 d and rehydrated for 4 d (11 d), respectively. GO analysis revealed that antioxidant activity was significantly enriched under PEG stress. In addition, KEGG enrichment analysis revealed that the DEGs were significantly involved in glutathione metabolism, fatty acid metabolism, and plant hormone signal transduction. KEGG combined with WGCNA was used to screen two drought stress-related genes, PP2C39 and GA2ox4. We propose an oxidative stress model for castor plants under drought stress based on GO terms, KEGG pathway, and WGNA analyses. This study identified high-quality genes for the genetic and molecular breeding of drought-resistant castor beans.

overall_design: RNA-seq analysis of castor roots under 15% PEG-6000 Stress for 3, 7, and 4 d (11 d) of rehydration.


title: Establishment and comparison of human term placenta-derived trophoblast cells

city: Galveston

first: Manuel Jr

middle: Sabalo

last: Vidal

state: Texas

address: 301 University Drive

department: Department of Obstetrics and Gynecology

institute: UTMB

summary: We established an immortalized term placenta-derived trophoblast cell line and demonstrated functional and transcriptomic differences against chorion trophoblasts and BeWo cells.

overall_design: Cells were isolated from term placenta utilizing enzymatic digestion, modified Percoll gradient-density isolation, and immunomagnetic purification. The resulting HLA-ABC (-) placental trophoblast cells (PTC) were immortalized using SV40T transfection to generate immortalized human PTC cytotrophoblasts (hPTCCTB). Additionally, these cells were transformed into syncytiotrophoblasts (hPTCSTB) using forskolin. The hPTCCTB cells were compared with their pPTC origin, choriocarcinoma cells (BeWo), and a commercially available PTC cell line using total RNA sequencing followed by principal component analysis (PCA) to determine differences in transcriptome profiles. The hPTCCTB cells were further compared with their pPTC origin for cell-specific markers (immunocytochemistry) and function (NF-kB and p38MAPK activations) after treatment with LPS and cigarette smoke extract (oxidative stress inducer).

first: Manuel


title: Seasonal variations of extracellular vesicle-coupled microRNAs in equine follicular fluid

first: Ahmed

last: Gad

summary: Ovarian follicular fluid (FF) comprises a dynamic milieu whose composition alters under seasonal variation, influencing follicle development and oocyte developmental competence. Various cell subtypes (e.g. granulosa, theca, and cumulus) produce cell-secreted nanoparticles, coined extracellular vesicles (EVs), which contain bioactive regulatory molecules such as microRNAs (miRNAs) known to mediate intrafollicular communication through various forms of signaling and information transfer. Markedly, the hallmark feature of EVs transferring cellular knowledge propagates their appealing nature as direct indicators of cellular status, albeit homeostasis, dysfunction, or disease. Photoperiod alterations influencing the regulatory content of FF-EVs as downstream modifiers remain largely unknown, particularly in seasonal breeding animals. Here, we aimed to unpack the impacts of seasonal variation on the miRNA expression profiles of FF-EVs in the mare. Equine pre-ovulatory follicles were monitored and aspirated using ultrasound-guided transvaginal techniques to obtain follicular fluids during non-breeding (spring anovulatory, SAN) and breeding seasons (spring ovulatory, SOV; summer, SUM; and fall ovulatory, FOV). 97 miRNAs were found to be differentially expressed between groups. Pairwise comparisons revealed specific clusters, including six miRNAs involved in the spring transition (miR-149-200b-206-221-328-615) and many others dysregulated during that of the summer (miR-143-192451- 302b-100, and let 7c), the peak time point for breeding. Bioinformatic analyses led to unveiling significant enrichments in various biological functions, such as transcription factor activity, transcription and transcription regulation, nucleic acid binding, sequence-specific DNA binding, p53 signaling, and post-translational modifications. Ultimately, the miRNA content of seasonally divergent FF-EVs poses as potentially relevant indicators of intrafollicular mechanisms directing seasonal transitions and their functional regulatory roles in the pre-ovulatory stage, governing subsequent ovulation.

overall_design: Seventeen Quarter horse mares weighing 400 to 600 kg, spanning the ages 8 to 14 years old were used for in vivo collections of FF samples during the SAN, SOV, SUM, and FOV seasons. During the SAN season, ovarian follicles ≥6 mm in diameter were ablated under ultrasound guidance. During the SOV, SUM, and FOV seasons, dominant follicles (≥ 28 mm in diameter) were monitored daily via ultrasonography until ovulation, and thereafter,  follicle ablations were performed on days 10–12 post-ovulation to induce new follicular waves. Daily ultrasonographic tracking of healthy/growing follicles was performed until follicles reached the pre-ovulatory diameter size (30-35 mm). After a minimum of three consecutive days of tracking, selected pre-ovulatory follicles (n = 6-12) were assigned to experimental groups, consisting of SAN (March, the transition season, when dominant anovulatory follicles develop after the deep anestrus season, before the spring ovulatory season), SOV (April and May, the beginning of the ovulatory season, with regular cyclic activity), SUM (June to July; Ovulatory season) and FOV (September, the final period of the ovulatory season), before the mares approached the receding phase (fall anovulatory) and inactive phase (winter anestrous). Only animals showing continuous ultrasonographic follicle growth for at least three consecutive days, the presence of uterine edema (estrus-like), and the absence of a corpus luteum at the time of FF collection were used.

first: Jean

middle: M

last: Feugang

first: Nico

last: Menjivar

first: Ghassan

last: Ishak

first: Samuel

last: Gebremedhn

first: Melba

middle: O

last: Gastal

first: Notsile

middle: H

last: Dlamini

first: Radek

last: Prochazka

first: Eduardo

middle: L


title: P-stalk ribosomes act as master regulators of cytokine-mediated processes

city: Amsterdam

first: William

last: Faller

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

summary: HLA Class I antigen processing and presentation (APP) is a highly regulated process that enables CD8+ T cell immunosurveillance. APP begins with the ribosomal synthesis of a source antigen, yet the role of ribosomes, particularly specialized ribosomes, in antigen presentation is poorly understood. Here, we show that the presence of the “P-stalk” on the ribosome enhances antigen presentation. The addition of the P-stalk to the ribosome is stimulated by cytokines that upregulate APP components, and knockdown of one of the P-stalk proteins (P1) reduces T cell recognition of tumor cells. Mechanistically, we show that P1-containing ribosomes exhibit enhanced translation of HLA Class I molecules and accessory APP components. Finally, analysis of patient data reveals that the mRNA expression of the P-stalk proteins positively correlates with CD8+ T cell infiltration, a trend not seen for other ribosomal proteins. In all, we demonstrate that the presence of the P-stalk defines a specialized ribosome population that enhances antigen presentation, something that may be exploited by cancer cells to escape immunosurveillance.

overall_design: Ribosome profiling with HA-tagged RPLP1 (P1) and RPL22 (eL22) ribosomal proteins in cytokine treated Mel624 melanoma cell lines.

first: Anna

last: Dopler

first: Ferhat

last: Alkan

middle: J


title: Effect of depletion of MED23 on  H3K27AC histone modifications during mouse OPC differentiation [ChIP-seq]

city: Shanghai

first: Shuai

last: Zhang

address: 220 Handan Rd., Shanghai

institute: fudan university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To determine the role played by Med23 in the genome wide H3K27AC histone modifications.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27AC  in iOLs.

first: Chonghui

last: Li

first: Yuanming

last: Zheng


title: ALKBH5 modulates endoderm fate diversion from hESCs through the ALKBH5-GATA6-WNT/β-catenin regulatory axis [CUT&Tag]

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

summary: N6-methyladenonsine (m6A) modification locates ubiquitously in mammalian mRNA, and profoundly impacts various physiological processes and pathogenesis. However, the precise involvement of m6A in early endoderm development has yet to be fully elucidated. Here, we reported that depletion of the m6A demethylase ALKBH5 in human embryonic stem cells (hESCs) severely impaired definitive endoderm (DE) differentiation. Within this process, ALKBH5-/- hESCs failed to undergo the primitive streak (PS) intermediate transition, which is considered as a prelude to endoderm specification. Mechanistically, we demonstrated that ALKBH5 deficiency induced m6A hypermethylation around the 3’ untranslated region (3’UTR) of GATA6 transcripts and destabilized GATA6 mRNA in a YTHDF2-dependent manner. Moreover, dysregulation of GATA6 expression ablated its occupancy with critical regulators of Wnt/β-catenin signaling pathway, thereby disrupting the signaling logic underlying DE formation. Overall, our findings unveil a mechanism whereby the ALKBH5-GATA6-WNT/β-catenin axis modulates human in vitro DE induction, and present novel insights on m6A modification in early embryonic development.

overall_design: We analyzed the endogenous GATA6 protein occupancy during primitive streak specification from hESCs

first: Junqi

last: Kuang

first: Duanqing

last: Pei


title: ALKBH5 modulates endoderm fate diversion from hESCs through the ALKBH5-GATA6-WNT/β-catenin regulatory axis [meRIP-seq]

type: Methylation profiling by high throughput sequencing

overall_design: We analyzed epitranscriptome-wide m6A methylation level  during PS specification from hESCs and ALKBH5 KO hESCs.


title: ALKBH5 modulates endoderm fate diversion from hESCs through the ALKBH5-GATA6-WNT/β-catenin regulatory axis [RNA-seq]

overall_design: We analyzed the transcriptome expression profiles (RNA-seq) in human stem cells H9 upon knockout of ALKBH5 during endoderm differentiation


title: ALKBH5 modulates endoderm fate diversion from hESCs through the ALKBH5-GATA6-WNT/β-catenin regulatory axis.

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Aberrant Cdk5 phosphorylates Mcm2 and promotes pituitary tumorigenesis

city: Guangzhou

first: Yafang

last: Hu

state: Guangdong

address: No.1838, Guangzhou Avenue North

department: Dept. of Neurology

institute: Nanfang Hospital, Southern Medical University

summary: We used scRNA-seq to study the heterogeneity and origin of Pcna cells from the pituitary tumors of p25 transgenic mouse model.

overall_design: The mouse (C57BL/6) pituitaries of transgenic overexpression of p25 (p25OE) and the wild-type (WT) littermates at week 14 and 40 were performed with scRNA-seq. The WT samples were controls.

first: Yingwei

last: Huang

first: Qiqi

last: Wang

first: Kai

last: He

first: Hong

last: Wu

first: Wei

first: Yawei

last: Jiang

first: Lijuan

last: Liu

first: Yue

last: Pan

first: Yihua

first: Zirui

last: Chen

first: Yaowei

first: Guanchuan

last: Lin

first: Yulong

first: Yongyan

last: Ren

first: Kaibiao

last: Xu

first: Yanlin

last: Yu

first: Yuping

last: Peng

first: Xinghua

first: Suyue


title: Transcriptome and epigenome analysis of DIAMOND mice

city: Pamplona

first: Ana

middle: Rosa

last: López-Pérez

address: Calle Irunlarrea, 3

country: Spain

institute: Navarrabiomed - Fundacion Migues Servet


title: Genome-wide DNA-binding analysis for Stat92E and escargot(esg) in Drosophila testis by DamID

city: Beijing

first: Ruiyan

last: Kong

address: 105 Xi San Huan Bei Lu, Haidian District, Beijing

institute: Capital Normal University

summary: Purpose: Genome-wide DNA-binding analysis for Stat92E and escargot(esg) in Drosophila testis cyst cells by DNA adenine methyltransferase identification(DamID).Methods: DNA adenine methyltransferase identification (DamID) on Stat92E and escargot(esg) driven by c587Gal4ts

overall_design: Dam(Control),  Stat92E-Dam or esg-Dam transgenes were expressed in testis cyst cells by c587Gal4ts.The testis with 1 day at 29℃ was used for DamID-seq, followed by deep sequencing analysis.

first: Zhouhua

last: Li


title: miRNA array data of EZH2-knockdown small cell lung cancer cells

city: Kawagoe-shi

first: Nobuyuki

last: Koyama

state: Saitama

address: 1981 Kamoda

institute: Saitama Medical Center, Saitama Medical University

summary:
Enhancer of zeste homolog 2 (EZH2) is highly expressed in small-cell lung cancer (SCLC). Epigenetic modifications through EZH2 induce epithelial-mesenchymal transition (EMT). MicroRNAs (miRNAs) are small non-coding RNAs that modulate EMT to determine tumor phenotypes.
miRNA expression profiles were compared between EZH2 siRNA-transfected SCLC cells and negative control-transfected SCLC cells, using miRNA array analysis. We identified miR-4448 as a target miRNA of EZH2 showing significant expressional differences in EZH2-knockdown cells.

overall_design: Two sets using SBC3 and SBC5 cells were analyed. Each set cosisted of one target and one control sample.


title: Loss of DNA glycosylases promotes health span/neuroprotection in a C. elegans model of human tauopathy

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: We utilized a Caenorhabditis elegans (C. elegans) model of human tauopathy to investigate the role of DNA glycosylases (Ung-1 and Nth-1 knockout worms) in disease development and progression. We then performed gene expression profiling analysis using data obtained from RNA-seq of 12 different genotypes grown under normal conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for normal (N2), glysosylases mutant (Ung-1 and Nth-1), tau-aggregate worm (BR5270), anti-tau-aggregate (BR5271) and their cross with respective tau worms. We used ~5000 worms per sample, one sample per genotype.

first: Vilhelm

middle: A

last: Bohr

first: Vinod

last: Tiwari

first: Elisabeth

last: Buvarp

first: Chandrakala

last: Puligilla

first: Deborah

last: Croteau

first: Konstantinos

last: Palikaras


title: Monocyte membrane-coated nanoparticles (MoNP)-Verteporfin (VP) treatment alleviated the TNFalpha-induced inflammatory response in Endothelial cells

city: Tempe

first: Ting-Yun

last: Wang

state: Arizona

address: 550 E. Orange Street,  ISTB1 Building, Room 281

department: School for Engineering of Matter, Transport and Energy

institute: arizona state university

summary: Atherosclerosis, characterized by the buildup of plaque in arteries, is a major cause of cardiovascular mortality worldwide, as there is no efficient strategy for targeted therapy. However, we have developed a new drug delivery platform called MoNP, which is loaded with VP, a potent inhibitor of YAP/TAZ signaling. To investigate the MoNP-VP treatment effect, EC were pretreated with MoNP or MoNP-VP then induced the inflammation by TNFalpha. After TNFalpha treatment, the cells were collected and extracted the RNA for RNA sequencing (RNA-Seq). The results showed that MoNP-VP significantly decreased the expression of YAP/TAZ-targeted genes and inflammatory markers while upregulating atheroprotective genes. Overall, these findings suggest that MoNP-VP has the potential to serve as an effective drug delivery platform for atherosclerosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TNF-alpha treated EC in response to MoNP vs MoNP-VP

first: Hui-Chun

last: Huang

first: Kuei-Chun


title: Effect of depletion of MED23 on genome-wide occupancy of Sp1 and P300 during mouse OPC differentiation [cut&tag]

first: Shuai

last: Zhang

summary: To determine the role played by Med23 in the cooperation between Sp1 and P300.

overall_design: CUT& Tag for SP1,P300  in primary mouse OPCs treated by T3 for 1day.

first: Chonghui

first: Yuanming

last: Zheng


title: Single-cell sequencing of pancreatic tissues of mice with acute pancreatitis under the background of normal diet and high-fat diet was compared

status: Public on Oct 22 2024

city: jinan

first: wang

last: qiang

address: West Wenhua Road.

institute: Qilu Hospital.

summary: Background: Acute pancreatitis (AP) is a common severe digestive disorder, with severity linked to high-fat diets (HFD). HFD may exacerbate AP by promoting inflammation and altering gut microbiota. Astragalus polysaccharides (APS) possess anti-inflammatory properties, but it is unclear if APS supplementation can mitigate HFD's detrimental effects on AP by modulating gut microbiota. This study investigates the mechanisms by which APS improves HFD-induced AP exacerbation. In this study, C57BL/6 mice were fed HFD or a standard diet, with or without APS, for 12 weeks. AP was induced via intraperitoneal caerulein injection. Analyses included ELISA, Western blotting, histology, immunohistochemistry, immunofluorescence, single-cell RNA sequencing (scRNA-seq), 16S rRNA sequencing of gut microbiota, and short-chain fatty acid (SCFA) analysis to evaluate inflammation and cellular changes. Results: HFD significantly increased AP severity, indicated by elevated serum enzyme and pro-inflammatory cytokine levels, along with extensive pancreatic damage. Single-cell RNA sequencing (scRNA-seq) showed a notable rise in ICAM1+ neutrophils and activation of the NF-κB/necroptosis pathway in HAP mice. APS alleviated these effects by decreasing ICAM1+ neutrophil infiltration, downregulating the NF-κB pathway, and reducing necroptosis. Moreover, APS restored gut microbiota balance, significantly boosting Lactobacillus reuteri (L. reuteri) abundance and propionate (PA) levels. Treatments with L. reuteri and PA independently mitigated HFD-induced AP severity, indicating that APS's protective effects are microbiota-dependent. Conclusion: APS improves HFD-induced gut dysbiosis and intestinal barrier dysfunction by enriching L. reuteri and PA, effectively reducing AP exacerbation. Our findings highlight the gut-pancreas axis as a promising target for addressing AP severity.

overall_design: C57BL/6 mice were fed a high-fat diet or a standard diet with or without APS for 12 weeks. Acute pancreatitis was induced by intraperitoneal injection of caerulein (50 ug/kg), once per hour for a total of 12 times. Then, pancreatic tissues from each group were taken out and subjected to 10x single-cell sequencing. The groups included normal control group (NC), acute pancreatitis group induced by normal diet (AP), high-fat diet group (HFD), and acute pancreatitis group induced by high-fat diet (HAP). Astragalus polysaccharides were added or not added to AP mice on a high-fat diet to observe the therapeutic effect of astragalus polysaccharides.

first: Dongbo

last: Xue

first: Qiang


title: A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis [ATAC-Seq]

city: Stanford

first: Emily

middle: Lorin

last: Ashkin

address: 279 Campus Drive

institute: Stanford University School of Medicine

summary: The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and show that STAG2 is uniquely tumor suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo, and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relates STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin mediated mechanisms of lung tumor suppression.

overall_design: To assess whether Paxip1 deficiency  impacts the underlying chromatin state, we performed ATAC-seq on neoplastic cells isolated from KTC sgInert and KTC sgPaxip1 mice.


title: Effect of depletion of MED23 on gene expression during primary mouse OPC differentiation [RNA-seq]

summary:
To determine the role played by Med23 in OPC differentiation, OPCs were isolated from the Med23cKO (i.e., Med23-/-OPCs) or control mice (i.e., Med23+/+OPCs) and induced to differentiate in vitro.
We then performed gene expression profiling analysis using data obtained from RNA-seq of Med23+/+iOLs and Med23-/-iOLs .

overall_design: Comparative gene expression profiling analysis of RNA-seq data forMed23+/+iOLs and Med23-/-iOLs .


title: Intraperitoneal activation of myeloid cells clears ascites and reveals IL27-dependent regression of metastatic ovarian cancer.

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Patients with metastatic ovarian cancer (OvCa) have a 5-year survival rate of less than 30% due  to persisting dissemination of chemoresistant cells in the peritoneal fluid and the immunosuppressive microenvironment in the peritoneal cavity. Here, we report that intraperitoneal administration of β-glucan and IFNγ (BI) induced robust tumor regression in clinically relevant models of metastatic OvCa. BI induced tumor regression by controlling fluid  tumor burden and activating localized antitumor immunity. β-glucan alone cleared ascites and eliminated fluid tumor cells by inducing intraperitoneal clotting in the fluid and Dectin-1-Syk-dependent NETosis in the omentum. In omentum tumors, BI expanded a novel subset of immunostimulatory IL27+ macrophages and neutralizing IL27 impaired BI efficacy in vivo. Moreover, BI directly induced IL27 secretion in macrophages where single agent treatment did not. Finally, BI extended mouse survival in a chemoresistant model and significantly improved chemotherapy response in a chemo-sensitive model. In summary, we propose a new therapeutic strategy for the treatment of metastatic OvCa.

overall_design: scRNASeq of CD45+CD19- immune cells from ometum tumor samples

first: Brennah

last: Murphy

first: Taito

last: Miyamoto


title: The influence of melanoma extracellular vesicles on benign melanocytes, dermal fibroblasts and microvascular endothelial cells (part1)

city: Oklahoma City

first: Jeffrey

middle: Don

last: McBride

state: OK

address: 1000 NE 13th St

department: Dermatology

institute: University of Oklahoma

summary: This study investigates the role of PRAME (Preferentially Expressed Antigen in Melanoma), a cancer-testis antigen, in melanoma progression, particularly its function in melanoma-derived extracellular vesicles (EVs) and its impact on benign primary melanocytes (PM), primary fibroblasts(PF)  and microvascular endothelial cells (EN).

overall_design: To investigate the effects of extracellular vesicles from melanoma cells on neighboring benign cells, we treated PM, PF, and EN cell lines with melanoma-derived conditioned medium from A375 cells. We then extracted total RNA and performed RNA sequencing.

first: Xiaochen

last: Liu

first: Ralf

last: Janknecht

first: Sepideh

middle: N

last: Asadbeigi

first: Lisa

last: Perry

first: Adul-Rafeh

last: Naqash

first: Wei-Qun

last: Ding

middle: D


title: Single nuclei RNAseq of the periosteal response to bone fracture and musculoskeletal traumatic injury in mice

city: Créteil

first: Céline

last: Colnot

address: 8 rue du Général Sarrail

country: France

institute: INSERM U955

summary: Bone regeneration is a highly efficient process allowing scarless healing after injury. Yet, musculoskeletal traumatic injury, when fracture is combined with adjacent muscle injury, alters bone healing leading to fibrous nonunion. The periosteum, the outer layer of bones, is a critical source of skeletal stem/progenitor cells (SSPCs), as well as immune, endothelial and neural cells during bone repair. We generated single nuclei datasets from the injured perioteum and hematoma at day 1-post fracture and from the hematoma/callus at day 5 post-musculoskeletal traumatic injury. These datasets were analyzed in combination with datasets from GSE234451.

first: Simon

last: Perrin


title: Suppression of melanoma by mice lacking MHC-II: mechanisms and implications for cancer immunotherapy

city: Dallas

first: Hexin

last: Shi

address: 5323 Harry Hines Blvd

institute: UT southwestern medical center

summary: Immune checkpoint inhibitors interfere with T cell exhaustion but often fail to cure or control cancer long-term in patients. Using a genetic screen in C57BL/6J mice, we discovered a mutation in host H2-Aa that caused strong immune-mediated resistance to mouse melanomas. H2-Aa encodes an MHC class II α chain, and its absence in C57BL/6J mice eliminates all MHC-II expression. H2-Aa deficiency, specifically in dendritic cells (DC), led to a quantitative increase in type 2 conventional DC (cDC2) and a decrease in cDC1. H2-Aa–deficient cDC2, but not cDC1, were essential for melanoma suppression and effectively cross-primed and recruited CD8 T cells into tumors. Lack of T regulatory cells, also observed in H2-Aa deficiency, contributed to melanoma suppression. Acute disruption of H2-Aa was therapeutic in melanoma-bearing mice, particularly when combined with checkpoint inhibition, which had no therapeutic effect by itself. Our findings suggest that inhibiting MHC-II may be an effective immunotherapeutic approach to enhance immune responses to cancer.

overall_design: WT or H2-Aa deficient (cit) splenic DC were enriched from splenocyte suspensions using EasySep Mouse CD11c Positive Selection Kit. Then, CD45.2+ CD11c+ cells were FACS sorted for scRNA-seq.

first: Ashwani

last: Kumar


title: Bacterial Elimination via Cell Membrane Penetration by Violet Phosphorene Peripheral Sub-Nanoneedles Combined with Oxidative Stress

city: Hohhot

first: qiudi

last: shen

address: 235 University Street West

institute: Inner Mongolia University

summary: The effectiveness of antibacterial agents is strongly influenced by its antibacterial mechanism, which, in turn, is dependent on the agent’s topological structure. In addition to oxidative stress (especially caused by reactive oxygen species), known to be a key mechanism for 2D phosphorene structures, physical penetration of bacterial cell membranes is predicted for violet phosphorene nanosheets. In this study, we demonstrate that violet phosphorus (VP) and its exfoliated product, violet phosphorene nanosheets (VPNS), have superior antibacterial capability against pathogens.A series of antibacterial tests and theoretical calculations show that VPNS can inactivate >99.9% of two common pathogens (Escherichia coli and Staphylococcus aureus) and >99% of two “superbugs” (i.e., antibiotic-resistant bacteria, Escherichia coli pUC19 and methicillin-resistant Staphylococcus aureus) via oxidative stress combined with cell membrane penetration by VPNS Moreover, VPNS have higher antibacterial activity than black phosphorene nanosheets in vitro and in vivo. We believe VPNS as special rigidly structured nanoagents have great potential for eradicating pathogens.

overall_design: Violet Phosphorene

first: Qiudi

last: Shen

first: Lihui

last: Zhang

first: Jinying

first: Alideertu

last: Dong


title: HD2B and HD2C interact with Argonaute 4 to promote tolerance and heterochromatin stabilization during heat stress [ChIP-Seq]

city: Wuhan

first: Xiangsong

last: Chen

state: Hubei

address: Bayi Road

institute: Wuhan university

summary: In this study, we show that HD2B/C work with AGO4 to promote heat tolerance

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and hd2b/c plants under normal and heat-treated conditions,whole-genome bisulfite sequencing in WT and hd2b/c under both normal and heat conditions,high-throughput small RNA sequencing in WT and hd2b/c

first: Yingnan

last: Sun

first: Fangfang

last: Yang


title: Opposing regulation of the STING pathway in hepatic stellate cells by NBR1 and p62 determines the progression of hepatocellular carcinoma [Quantseq]

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: Hepatocellular carcinoma (HCC) emerges from chronic inflammation to which activation of hepatic stellate cells (HSCs) contributes by shaping a pro-tumorigenic microenvironment. Key to this process is p62, whose inactivation leads to enhanced hepatocarcinogenesis. Here, we show that while p62 positively regulates STING ubiquitination by TRIM32 by displacing NBR1, which results in the activation of the interferon (IFN) cascade, NBR1 prevents TRIM32 interaction with and the activation of STING, leading to impaired IFN synthesis. NBR1 also antagonizes STING function by promoting its trafficking from the Golgi to the endosome-lysosomal degradative cascade independent of autophagy. Importantly, NBR1 deletion completely reverts the tumor-promoting function of p62-deficient HSCs. The upregulation of the STING-IFN pathway by NBR1 deficiency enhances the anti-tumor response mediated by CD8+ T cells. These results identify NBR1 as a synthetic vulnerability of p62-deficiency in HSCs. NBR1 loss, by promoting the STING/IFN pathway, boosts anti-tumor CD8+ T cell responses to restrain HCC.

overall_design: Nbr1 knock-out and wild type hepatic stellate cells were profiled in three biological replicates under normal conditions.

first: Sadaaki

last: Nishimura

first: Juan

middle: F

last: Linares

first: Antoine

last: L'Hermitte

first: Angeles

last: Duran

first: Marc

last: Ruiz-Martinez

first: Tania

last: Cid-Diaz

first: Yotaro

last: Kudo

first: Maria

middle: T

last: Diaz-Meco

first: Anxo

last: Martinez-Ordoñez

first: Antonio

last: Marzio

first: Mathias

last: Heikenwalder

first: Lewis

middle: R

last: Roberts


title: ACE2 Enhances Sensitivity to PD-L1 Blockade by Inhibiting Macrophage-Induced Immunosuppression and Angiogenesis [RNA-seq, anti-PD-L1 therapy]

city: Shanghai

first: Peiyi

last: Xie

address: Fenglin Road No.180

institute: Zhongshan Hospital, Fudan University

summary: Anti-PD-L1-based combination immunotherapy has become the first-line treatment for unresectable hepatocellular carcinoma (HCC). However, the objective response rate is lower than 40%, highlighting the need to identify mechanisms of tolerance to immune checkpoint inhibitors and accurate biomarkers of response. Here, we employed next-generation sequencing to analyze HCC samples from 10 patients receiving anti-PD-L1 therapy. Activation of the renin-angiotensin system was elevated in nonresponders compared with responders, and ACE2 expression was significantly downregulated in nonresponders. ACE2 deficiency promoted HCC development and anti-PD-L1 resistance, whereas ACE2 overexpression inhibited HCC progression in immune competent mice. Mass cytometry by time of flight (CyTOF) revealed that ACE2 deficient murine orthotopic tumor tissues featured elevated M2-like tumor-associated macrophages (TAMs), displayed a CCR5+PD-L1+ immunosuppressive phenotype, and exhibited high VEGFα expression. ACE2 downregulated tumor intrinsic CCL5 expression by suppressing NF-κB signaling through the ACE2/angiotensin-(1–7)/Mas receptor axis. The lower CCL5 levels led to reduced activation of the JAK-STAT3 pathway and suppressed PD-L1 and VEGFα expression in macrophages, blocking macrophage infiltration and M2-like polarization. Pharmacological targeting of CCR5 using maraviroc enhanced the tumor suppressive effect of anti-PD-L1 therapy. Together, these findings suggest that activation of the ACE2 axis overcomes the immunosuppressive microenvironment of HCC and may serve as an immunotherapeutic target and predictive biomarker of response to PD-L1 blockade.

overall_design: RNA- sequencing was used to analyze HCC samples from 10 patients (4 non-responders and 6 responders) receiving anti-PD-L1 therapy


title: Caffeine modulates immunoproteasome activity and content in colorectal adenocarcinoma cells

city: Moscow

first: Alexander

middle: Petrovich

last: Rezvykh

address: Obninsk, Zvyozdnaya st. 15 - 130

country: Russia

institute: EIMB

summary: Proteasomes hydrolyze most intracellular proteins. Immunoproteasome is a specific form of proteasome implicated in inflammation, cancer and autoimmune diseases. Modulation of immunoproteasome activity and content is a promising direction for the management of socially important pathologies. Using previously obtained reporter colorectal cancer cell lines, we tested how various commonly used compounds including ibuprofen, acetylsalicylic acid, vitamin C, caffeine and others, affect immunoproteasome expression. Methods: Immunoproteasome subunit expression was assessed by flow cytometry, qPCR and Western blot. Proteasome activity was tested using fluorogenic substrates and the activity probe. Transcriptome analysis was performed to identify patterns of gene expression changes. Results: Among the tested compounds caffeine was the only drug that revealed modest reduction in quantity of immunoproteasomes. The effect of caffeine on immunoproteasomes varied between cell lines and was stronger as a result of prolonged treatment. The reduction of immunoproteasome content in cells treated with caffeine coincided with decreased expression of immunoproteasome subunits and downregulation of Nrf3 transcription factor and a PAC4 proteasome assembly chaperone. Moreover, decreased expression of immunoproteasome subunits in cells treated with caffeine coincided with the reduction of oxidative stress levels. Caffeine did not affect the degradation of immunoproteasomes by autophagy. Conclusions: Modulation of immunoproteasome expression by caffeine might help to optimize existing and develop novel strategies for the treatment of colorectal cancer and several autoimmune diseases.

overall_design: Single-end poly-A RNA-seq of caffeine-treated cells

middle: P


title: Transcriptome and epigenome analysis of DIAMOND mice (RNA-Seq)

first: Ana

last: López-Pérez

summary: The purpose of this experiment is to characterize changes in the transcriptome and epigenome in diet-associated liver cancer. For that we used the DIAMOND mice as a model organism and performed RNA-seq and H3K27Ac and H3K27Me3 ChIP-seq in livers from control mice (fed with a regular diet) and livers and tumours from western diet fed mice.

overall_design: Liver samples from 5 RD fed DIAMOND mice and 7 liver and 5 tumour samples from WD fed DIAMOND mice

first: Saba

last: Parween

first: Silvia

last: Remeseiro

first: Andreas

last: Hörnblad


title: Skeletal Muscle Transcriptome of Young and Old Humans and Response to Training

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

summary: Skeletal muscle biopsies were obtained from humans before (rest), immediately after (3hr_post) and 48 hours (48hr_post) after a training bout.

overall_design: A total of 80 subjects particiapted in the study and a total of 185 samples were collected.

first: Ian

last: Lanza

first: Kelly

last: Michie


title: A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis [RNA-Seq]

first: Emily

last: Ashkin

overall_design:
To characterize the molecular effects of STAG2-deficiency, we initiated tumors in KT and KT;Stag2flox mice and used FACS to isolate neoplastic cells (DAPIneg, lineageneg, Tomatopos cells) for molecular analyses
To capture any changes in the molecular output of STAG2 deficiency during tumor development, we collected samples after 8 and 16 weeks of tumor growth. We initiated tumors using different viral titers such that mice would have similar overall tumor burden at time of analysis
We performed RNA-seq on samples from each timepoint and of each genotype.

first: E


title: Gene expression analysis of prostate cancer cells resistant to CDK7 inhibitors

city: London

first: Simak

last: Ali

state: London

address: 1/F ICTEM, Hammersmith Hospital

department: Cancer

country: United Kingdom

institute: Imperial College London

summary: CDK7 has emerged as a cancer target because of its pivotal roles in cell cycle progression and transcription. Several small molecule CDK7 inhibitors (CDK7i) are now in clinical evaluation. Identifying patients most likely to respond to treatment and early detection of tumour evolution towards resistance, are necessary for optimal implementation of cancer therapies. Continuous culturing of prostate cancer cells with Samuraciclib, an ATP-competitive/non-covalent CDK7i, led to outgrowth of resistant cells. RNA-seq expression analysis was undertaken to identify changes in gene expression, revealing acquistion of a mutation, c.289G>A in the CDK7 gene, causing the p.Asp97Asn change.

overall_design: To model acquired resistance in cancer, we cultured 22Rv1 prostate cancer cells in culture medium containing 500nM of Samuraciclib for 4 months. To investigate transcriptomic changes in Samuraciclib-resistant cells, RNA-seq was performed using 6 bioreplicates of RNA prepared from 22Rv1 Samuraciclib-resistant cells (SAMRES) and parental 22Rv1 cells (SAMSEN).

first: Laki

last: Buluwela

first: Chun-Fui

last: Lai


title: Tyrp1 is the mendelian determinant of the Axolotl (Ambystoma mexicanum) copper mutant

city: Lexington

first: Jeramiah

middle: James

last: Smith

state: KY

address: 101 Morgan Building

department: Biology

institute: University of Kentucky

summary: Several dozen Mendelian mutants have been discovered in axolotl (Ambystoma mexicanum) populations, including several that affect pigmentation. Four pigment mutants have been described in the scientific literature and genes for three of these have been identified. Here we report on copper, a Mendelian mutant with an albino-like phenotype known only from the pet trade. To identify the gene for copper, we performed a cross segregating copper and wildtype color phenotypes and used Bulked Segregant RNA-Seq to identify a region on chromosome 6 that was enriched for single-nucleotide polymorphisms (SNPs) between the color phenotypes. This region included Tyrosinase-like Protein 1 (Tyrp1), a melanin synthesis protein that when mutated, is associated with lighter than black melanin coloration in animal models and oculocutaneous albinism in humans. Inspection of RNA-Seq reads identified a single nucleotide deletion that is predicted to change the coding frame, introducing a premature stop codon in exon 6 and yield a truncated Tyrp1 protein in copper individuals. Using CRISPR-Cas9 editing, we show that wildtype Tyrp1 crispants exhibit copper pigmentation, thus confirming Tyrp1 as the copper locus. Our results suggest that commercial and hobbyist axolotl populations may harbor useful mutants for biological research.

overall_design: RNAseq was performed on two pools of individuals displaying the copper phyentype and two pools of their siblings displaying wildtype coloration. Alll individulas were from the same cross between a homozygous copper mutant male and a heterozygous female.

first: Raissa

last: Cecil

first: Lloyd

last: Strohl

first: Maddie

middle: K

last: Thomas

first: James

last: Schwartz

first: Nataliya

last: Timoshevskaya

first: S

last: Randal Voss


title: A latent Axin2+/Scx+ progenitor pool is the central organizer of tendon healing

city: Boston

first: Mor

last: Grinstein

state: MA

address: 2114 Cambrisge street

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

summary: A tendon’s ordered extracellular matrix (ECM) is integral for transmitting force and highly prone to injury. Whether and how tendon cells, or tenocytes, embedded within this dense ECM mobilize and contribute to healing is unknown. Here, we identify a specialized Axin2+ tenocyte population in mouse and human tendons that remains latent in homeostasis yet serves as a major source of tendon progenitors during healing. We show that Axin2+ tenocytes readily expand in vitro and express stem cell markers. In vivo, Axin2+ cells are major functional contributors to repair: Axin2+ tenocytes de-differentiate, expand, and re-adopt a tenocyte fate post-injury. Specific loss of Wnt secretion in Axin2+ cells alters their stem cell identity and disrupts their activation upon injury, severely compromising healing. Our work highlights Axin2+ tenocytes as quiescent stem cells embedded in dense matrix, which are uniquely regulated in an autocrine manner and are central organizers of robust tendon healing.

overall_design: Investigation of transcriptional differences in Axin2+ vs. Axin2- tendon cell populations

first: Jenna

last: Galloway


title: DNA methylation mediated Rbpjksuppression protects against fracture nonunion caused by systemic inflammation

city: St Louis

first: Jie

last: Shen

state: MO

address: 425 S. Euclid Ave

institute: Washington University in St Louis

summary: Challenging skeletal repairs are frequently seen in patients experiencing systemic inflammation. Current therapies aimed at mitigating inflammation or enhancing stem cell function with osteogenic factors yield inconsistent clinical outcomes. To tackle the complexity and heterogeneity of fracture repair process, we performed single-cell RNA sequencing and revealed that progenitor cell was one of the major lineages responsive to elevated inflammation and this response adversely affected progenitor differentiation by upregulation ofRbpjkin fracture nonunion.We then validated the interplay between inflammation (via Ikk2ca) and Rbpjkspecifically in progenitors by using genetic animal models. Focusing on epigenetic regulation, we identifiedRbpjkas a direct target of Dnmt3b. Mechanistically, intrinsic inflammation decreased Dnmt3b expression in progenitor cells, consequently leading toRbpjkupregulation via hypomethylation within its promoter region. We also showed thatDnmt3bloss-of-function mice phenotypically recapitulated the fracture repair defects observed inIkk2camice, whereasDnmt3btransgenic mice alleviated fracture repair defects induced byIkk2ca. Moreover,Rbpjkablation restored fracture repair in bothIkk2camice andDnmt3bloss-of-function mice. Altogether, this work elucidates a common mechanism involving NF-kB/Dnmt3b/Rbpjkaxis within the context of inflamed bone regeneration. Building upon this novel mechanistic insight, we applied local treatment with epigenetically modified progenitor cells in RA mice and showed a functional restoration of bone regeneration under inflammatory condition through an increase in progenitor differentiation potential. These findings underscore the promise of epigenetic-based therapeutic interventions for addressing delayed fracture union and nonunion particularly associated with systemic inflammation.

overall_design: Four fracture calluses were dissociated by scraping newly formed tissue along the periosteal surface from injured bone as a pool for each experiment. Callus samples were further dissociated in 1 mg/ml Collagenase P at room temperature for one hour. Then, cell suspension was filtered through a diameter of 30-mm strainer to generate a single-cell suspension. Four batches of single cell libraries for sequencing: callus cells from 4-dpf control fractures (control_4d, n=4), 7-dpf control fractures (control_7d, n=4), 4-dpf RA fractures (RA_4d, n=4), 7-dpf RA fractures (RA_7d, n=4). 10,000 cells for each sample were loaded in aim of preparing single-cell mRNA libraries for each group, barcoded, purified using Chromium Single Cell 3’ kit (v3.1 Chemistry, 10x Genomics Inc), and sequenced using 2 x 150 bp pair-end configuration on an Illumina NovaSeq platform.


title: Microprotein-Encoding RNA Regulation in Cells Treated with Pro-inflammatory and Pro-Fibrotic Stimuli

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Targeting Plk1 re-establishes the response to immune checkpoint therapy in pancreatic cancer

city: West Lafayette

first: Sagar

middle: M

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

summary: Purpose: Standard RNA-Seq analysis using Plk1 knock-in mouse model.

overall_design: The Plk1 knock-in mouse (Plk1LSL) was designed by the Xiaoqi Liu lab at Purdue University, and constructed by Taconic, Germany. Plk1LSL mice were subsequently obtained from these recombinant ES cells. Mist1Cre/+/KrasG12D/+ mice were generated by the Konieczny lab at Purdue University, whereas Rosa26CreERt2 mice were purchased from the Jackson Laboratory. To generate Mist1CreER/+/Plk1LSL mice, we crossed the Plk1LSL line to Mist1CreER/+ line. To generate Mist1CreER/+/KrasG12D/+/Plk1LSL mice, we crossed the Mist1CreER/+/KrasG12D/+ line to the Plk1LSL line. To generate Rosa26CreERt2/Plk1LSL mice, we crossed the Plk1LSL line to Rosa26CreERt2 line.  All procedures involving mice were guided by Purdue University Animal Care and Use Committee (Protocol no: 1111000133E001) and University of Kentucky Animal Care and Use Committee (Protocol no: 2020-3685).

first: Zhuangzhuang

last: Zhang

first: Lijun

last: Cheng

last: Li

first: Qi

last: Qiao

first: Anju

last: Karki

first: Derek

middle: B

last: Allison

first: Nuha

last: Shaker

first: Kunyu

first: Nadia

last: Lanman

first: Xiongjian

last: Rao

first: Stephen

last: Konieczny

first: Lang

first: Qing

last: Shao

first: Xiaoqi

last: Liu


title: Transcriptome and epigenome analysis of DIAMOND mice (ChIP-Seq)

city: Pamplona

first: Ana

last: López-Pérez

address: Calle Irunlarrea, 3

institute: Navarrabiomed - Fundacion Migues Servet

first: Saba

last: Parween

first: Silvia

last: Remeseiro

first: Andreas

last: Hörnblad


title: Setdb1 regulates proper differentiation of adult intestinal stem cells via restraining permissive chromatin structure and transcriptional variability

status: Public on Oct 21 2024

city: Heraklion

first: Dimitrios

last: Botskaris

address: Nikolaou Plastira 100

country: Greece

institute: IMBB FORTH

summary: The histone methylase Setdb1 plays a pivotal role in embryonic stem cell maintenance and developmental lineage specification. However, its function in adult stem cells remains elusive. Here we show that conditional inactivation of Setdb1 in Lgr5+ intestinal stem cells alters the transcriptional programs of the progeny cell types and results in increased cell-to-cell transcriptional variability. Loss of Setdb1 blocked differentiation towards the absorptive enterocyte lineage, while the generation of secretory cell types was only marginally affected due to the activation of alternative developmental trajectories. Setdb1 inactivation did not alter H3K9 methylation at large heterochromatin domains but led to reduced localized modifications at islands of gene-rich areas around transposase-accessible chromatin regions, which have doubled in number, became broader and more heterogeneous in size. The results demonstrate that Setdb1 regulates intestinal stem cell properties and epithelial lineage specification by limiting chromatin accessibility at open genomic areas and controlling cell-to-cell transcriptional variability.

overall_design: To study the role of Setdb1 in Lgr5 stem cell population we used FACS-sorted cells from mice (GFP_WT and GFP_Setdb1-KO) mice 5 days after Tamoxifen treatment. To study the role of Setdb1 in Lgr5 stem cell progeny, we used FACS-sorted cells from mice (GFP_WTnTnG and GFP_Setdb1-KOnTnG) mice 5 days after Tamoxifen treatment. Single cell RNA-seq and single cell ATAC-seq assays were performed in the samples, as indicated. In addition, FACS-sorted GFP_WT and GFP_Setdb1-KO cells we performed total RNA sequencing and mapped H3K9Me3 locations in the genome by CUT&Tag assays.

first: Dimitris

first: Ioannis

last: Deligiannis

first: Ioanna

last: Peraki

first: Haroula

last: Kontaki

first: Marianna

last: Stagaki

first: Matthieu

last: Lavigne

first: Celia

last: Martinez-Jimenez

first: Iannis

last: Talianidis


title: Bruton’s tyrosine kinase inhibitor leads to bidirectional transcript regulation of Nurr1: A new key to Parkinson’s disease

city: Seoul

first: Jeung Hee

last: An

address: 47 Kkachisan-ro 24-gil, Gangseo-gu

institute: Gangseo University

summary: Parkinson’s disease (PD) is a progressive neurological movement diseases with few therapeutic targets identified to date. The primary treatment for PD is levodopa, but it is only effective in the initial stage and induces side effects of the disease. To address this problem, we unveil the hitherto uncharacterized crucial role of Bruton’s tyrosine kinase protein (BTK) as a bidirectional transcriptional bio-regulator of tyrosine hydroxylase (TH) expression via the modulation of nuclear receptor-related transcription factor 1 (Nurr1). The proteomics competition binding assay revealed that BTK binds to Nurr1 and transactivates TH promoter activity via Nurr1. The BTK inhibitor demonstrated remarkable effects in the mitochondrial permeability transition pore-induced oxidative stress model by significantly attenuating the levels of proinflammatory mediators via WNT/β-catenin and MAPK kinase signaling. These findings highlight the potential efficacy of BTK inhibitors as innovative therapeutics for PD.

overall_design: To investigate the function Bruton’s tyrosine kinase inhibitor in the Parkinson's disease, the mice were randomly divided into five groups, with eight mice in each group: (1) normal control group, (2) MPTP-induced group, (3) MPTP + levodopa (2 mg/kg/day) group, (4) MPTP + BTK low-dose (1 µg/kg/day) group, and (5) MPTP + BTK high-dose (2 µg/kg/day) group.

first: Soo Youn

last: Lee

first: Yu-Rim


title: Intestinal Muscle Gene Expression Profiling of PI-IBS Subjects

first: Surendra

last: Dasari

summary: Intestinal muscle samples were obtained from PI-IBS and healthy subjects and were subjected to gene expression profiling using high-throughput sequencing.

overall_design: A total of 31 PI-IBS samples were compared with a total of 25 healthy volunteer samples.

first: Madhu

last: Grover

first: Adam

last: Edwinson


title: scRNAseq analysis of DENV-2 infected B cells

city: Syracuse

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

summary: Dengue virus (DENV) is the causative agent of dengue, a mosquito-borne disease that represents a significant and growing public health burden around the world. A unique pathophysiological feature of dengue is immune-mediated enhancement, wherein preexisting immunity elicited by a primary infection can enhance the severity of a subsequent infection by a heterologous DENV serotype. A leading mechanistic explanation for this phenomenon is antibody dependent enhancement (ADE), where sub-neutralizing concentrations of DENV-specific IgG antibodies facilitate entry of DENV into FcR expressing cells such as monocytes, macrophages, and dendritic cells. Accordingly, this model posits that phagocytic mononuclear cells are the primary reservoir of DENV. However, analysis of samples from individuals experiencing acute DENV infection reveals that B cells are the largest reservoir of infected circulating cells, representing a disconnect in our understanding of immune-mediated DENV tropism. In this study, we demonstrate that the expression of a DENV-specific B cell receptor (BCR) renders cells highly susceptible to DENV infection, with the infection-enhancing activity of the membrane-restricted BCR correlating with the ADE potential of the IgG version of the antibody. In addition, we observed that the frequency of DENV-infectable B cells increases in previously flavivirus-naïve volunteers after a primary DENV infection. These findings suggest that BCR-dependent infection of B cells is a novel mechanism immune-mediated enhancement of DENV-infection.

overall_design: The DENV-specific B cell line 7B9 was infected with DENV-2 for 24 hrs, washed, then incubated for and additional 24 hours prior to harvest and analysis by scRNAseq. A parallel uninfected/control culture was cultured and analyzed in a parallel fashion.

first: Céline

middle: S

last: Hardy

first: Chad

last: Gebo


title: Transcriptomic signature of in vitro heat stress challenged porcine granulosa cells

city: Guwahati

first: Jaya

last: Bharati

state: ASSAM

address: ICAR-NRC on Pig, Rani

department: Animal Physiology

country: India

institute: ICAR-National Research Centre on Pig, Guwahati, Assam

summary: Exploration of heat stress induced genes in granulosa cells is critical to characterization of candidate genes for thermal stress research in pigs. This study aimed to gain insight into the differentially expressed genes (DEGs) and signalling pathways regulating porcine granulosa cell adaptation to in vitro heat stress challenge at 42OC for 6 hours. Transcriptome profiling of heat stressed (treated) and non-heat stressed (control) granulosa cells was conducted using Illumina NextSeq2000 sequencing platform. The significant DEGs were selected using NOISeq R package with cut-offs, probability value ≥ 0.95 and absolute log2(fold change) ≥1. Bioinformatics analysis of DEGs were conducted to explore functional annotations enrichment, protein-protein interaction network and hub genes regulating the cellular homeostasis and survivability during heat stress challenge.

overall_design: Primary cell culture system of porcine granulosa cells isolated from small ovarian follicles was established, which was subjected to in vitro heat stress challenge at 42OC for 6 hours. RNA sequencing and analysis was conducted for heat stressed (treated) and non-heat stressed (control) groups to investigate the global expression dynamics of heat stress induced genes in porcine granulosa cells.

first: Satish

last: Kumar

first: N

middle: H

last: Mohan

first: Vivek

last: Gupta


title: Senescent lung fibroblasts in idiopathic pulmonary fibrosis facilitate non-small cell lung cancer progression by secreting exosomal MMP1

city: shanghai

first: Yuqiong

last: Lei

state: 上海市

address: 600 Yishan Road

institute: Shanghai jiaotong university

summary: Lung cancer is a fatal complication of idiopathic pulmonary fibrosis (IPF) with a poor prognosis. Current treatments are insufficient in improving the prognosis of lung cancer patients with comorbid idiopathic pulmonary fibrosis (IPF-LC). Senescent fibroblasts play a pivotal role within the tumor microenvironment, influencing tumor progression by secreted exosomes. With evidence that fibroblast senescence is an important mechanism of IPF, we sought to investigate the impact of senescent IPF lung fibroblast-derived exosomes on non-small cell lung cancer (NSCLC). Our results show that IPF fibroblasts (diseased human lung fibroblasts, DHLF) express significant senescence markers, promoting NSCLC proliferation, invasion, and epithelial-mesenchymal transition. Specifically, we observed senescent DHLFs secret more exosomes (DHLF-exosomes), which could enhance proliferation and colony-forming ability of cancer cells. Proteomic analysis of DHLF-exosomes identified upregulation of SASP factors, notably MMP1, which activates the surface receptor PAR1. Knocking down MMP1 or using PAR1 inhibitors reduced the tumor-promoting effects of DHLF-exosomes in vivo and in vitro. Mechanistically, MMP1 acted via activating the PI3K-AKT-mTOR pathway. In conclusion, our results suggest that exosomal MMP1 derived from senescent IPF fibroblasts promotes NSCLC proliferation and colony formation by targeting PAR1 and activating the PI3K-AKT-mTOR pathway. These findings provide a novel therapeutic approach for patients with IPF-LC.

overall_design: To elucidate the pro-tumorigenic mechanisms of exosomes derived from IPF lung fibroblasts(DHLF-exo), we performed RNA-seq analysis on SK-MES-1 cells incubated with and without DHLF-exos. The experimental procedure was as follows: SK-MES-1 cells were initially seeded in 6-well plates. On the following day, the medium was replaced with complete medium containing 20 μg/ml DHLF-exos (N=3), while a parallel control group was maintained without exosome supplementation(N=3). After 72 hours of incubation, total RNA was extracted from SK-MES-1 cells, both with and without exosome treatment, using Trizol reagent (Invitrogen). Subsequently, RNA sequencing was performed using the NovaSeq 6000 platform.

first: Tao

last: Ren

first: Qiong

middle: Y


title: Tet3 regulates terminal cell differentiation at the metabolic level

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

summary: To study the role of tet3 and 5-hydroxymethylation in mouse intestine homeostasis our objectives are: To determine the cell types that show a 5hmC reduction level in the absence of Tet3. Identify the role of Tet3 on transcriptional regulation in the small intestinal epithelium. Define the physiological functions impaired in Tet3 -/- small intestine epithelium.

overall_design: Single cell RNA-seq analysis of control and Tet3 knockout mice. The Control data is split in 6 fastq files.  The Tet3 knockout data is split into 6 fastq files.

first: Isabel

last: Mulet

first: Daniela

last: Gerovska

first: Guangming

last: Wu

middle: J

first: Natalia

last: Tapia


title: METTL3 alters capping enzyme expression and its activity on ribosomal proteins in NSCLC cell model

city: Richmond

first: Daniel

last: Del Valle-Morales

state: VA

address: 417 N 11th St

department: Division of Pulmonary Diseases and Critical Care Medicine

institute: Virginia Commonwealth University

summary: The 5’ cap, catalyzed by capping enzyme, RNGTT, is a vital mRNA modification for the functionality of mRNAs and dysregulated in cancer cells. The m6A writer METTL3 is a regulator of mRNA stability and protein translation, and its expression is altered in various cancers, including lung cancer cells. We identified a METTL3 motif in the mRNA of RNGTT and investigated whether METTL3 could regulate the expression of RNGTT. Knock down of METTL3 resulted in destabilizing RNGTT mRNA, reduced protein expression and activity. Sequencing of capped mRNAs and m7G immunoprecipitation identified an underrepresentation of ribosomal protein mRNA.

overall_design:
To investigate the regulatory relationship between METTL3 and RNGTT, we generated a stable cell line of A549 expressing either an sh- control or shMETTL3
We then performed a cDNA enrichment of capped mRNAs in biological triplicate of A549sh- and A549 shMETTL3.
The then performed gene expression profile analysis using data obtained from DNAseq with the resulting cDNA.

last: del Valle-Morales

first: Mario

last: Acunzo


title: scRNA-seq of colon tumors from myeloid miR-34a knockout mice

city: Munich

first: Matjaz

last: Rokavec

address: Thalkirchner Str. 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University Munich

summary: miR-34aF/F and miR-34aF/F ;LysM_CRE mice were treated with AOM/DSS to induce coloitis associated cancer (CAC). Tumors were isolated and subjected to scRNA-seq

overall_design: Single cells were loaded on the 10x Chromium system and labeled with the 3’ CellPlex kit set A (10x Genomics) according to the manufacturer’s recommendations. The loaded cell numbers for each genotype were 30,000. Barcoded sequencing libraries were prepared with the Chromium Single Cell 3’ v.3.1 Gene Expression Kit (10x Genomics). Paired-end sequencing (2x100bp) was performed on Illumina NovaSeq 6000 (Illumina) targeting 90,000 reads/cell according to the standard workflow.

first: Janine

last: Koenig

first: Heiko

last: Hermeking


title: Mouse modeling of pediatric glioma, MYCN reveals intratumoral heterogeneity including neuronal and oligodendroglial lineage signatures [EPIC Beadchip]

city: Hamburg

first: Melanie

last: Schoof

address: Martinistr. 52

institute: Research Institute Childrens Cancer Center Hamburg

type: Methylation profiling by genome tiling array

summary: Pediatric glioma of the subclass MYCN are highly aggressive tumors frequently carrying MYCN amplifications, TP53 mutations, or both alterations. In order to understand the biology of these tumors better and to improve treatment options, we generated a genetically engineered model by breeding hGFAP-cre::TP53Fl/Fl::lsl-MYCN mice. All such mice developed aggressive forebrain tumors early in lifetime that mimic their human counterparts regarding histology, DNA methylation, and gene expression.

overall_design: The DNA of five HGG-MYCN tumors was extracted from FFPE samples after histological assessment and analyzed by the EPIC methylation array (Illumina).

first: Ulrich

last: Schüller

first: Kornelius

last: Kerl

first: Julia

middle: E

last: Neumann


title: Ageing-associated long non-coding RNA extends lifespan and reduces translation in non-dividing cells [aal1OE_RNAseq]

first: Shajahan

last: Anver

address: Gower Street London

department: Genetics, Evolution and Environment

institute: University College London

summary: Genomes pervasively produce long non-coding RNAs (lncRNAs) of largely unknown functions. Some of these lncRNAs have been implicated in roles related to ageing and associated diseases. Here we characterize aal1 (ageing-associated lncRNA 1) which is induced in non-dividing, ageing cells of fission yeast. Deletion of aal1 shortens the chronological lifespan of non-dividing cells, while ectopic overexpression of aal1 from a plasmid prolongs their lifespan, indicating that this lncRNA acts in trans. We find that aal1 genetically interacts with coding genes functioning in processes related to protein translation, and aal1 overexpression leads to repression of ribosomal protein genes and inhibition of cell growth. The aal1 RNA localizes to the cytoplasm and associates with ribosomes. Notably, aal1 deletion or overexpression is sufficient to increase or decrease the cellular ribosome content, respectively. We identify the mRNA rpl1901, encoding a ribosomal protein, as a binding target of aal1. The expression of rpl1901 is moderately repressed by aal1, and such moderate repression is critical and sufficient to extend the chronological lifespan. Remarkably, expression of the yeast aal1 lncRNA in the fly gut triggers a significant extension of the lifespan in flies. Based on these findings, we propose that the aal1 RNA can reduce the ribosome content by decreasing the levels of the Rpl1901 ribosomal protein, thus attenuating protein translation and promoting longevity. Although the aal1 lncRNA itself is not conserved, its effects in the fly raise the possibility that other organisms feature related mechanisms involving conserved ribosome-associated processes to control ageing.

overall_design: Transcriptional landscape of aal1 ectopically overexpressing cells relative to cells expressing an empty vector control during chronological ageing (day6)


title: Systemic coordination of whole-body tissue remodeling during local regeneration in sea anemones

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

institute: EMBL Heidelberg

summary: The complexity of regeneration extends beyond local wound responses, eliciting systemic processes engaging the entire organism. However, their functional relevance, and the spatial and temporal orchestration of the underlying molecular processes distant from the injury site remain unknown. Here, we demonstrate that local regeneration in the cnidarian Nematostella vectensis involves a systemic homeostatic response, leading to coordinated whole-body remodeling. Leveraging spatial transcriptomics, endogenous protein tagging, and live imaging, we comprehensively dissect this systemic response at the organismal scale. We identify proteolysis as critical process driven by both local and systemic upregulation of metalloproteases. We show that metalloproteinase expression levels and activity scale with the extent of tissue loss, leading to proportional long-range movement of tissue and its associated extracellular matrix. Our findings demonstrate the adaptive nature of the systematic response in regeneration. We propose that this integrated regenerative mechanism enables the organism to maintain shape homeostasis while coping with injuries.

overall_design: We performed tomo-seq (Junker et al. 2014) on intact and regenerating Nematostella vectensis polyps after an aboral tip amputation over a time course of 4 days. 3-6 unfed polyps were investigated per time point by extracting 96 tissue slices across the whole body axis, respectively.

first: Aissam

last: Ikmi


title: Opposing regulation of the STING pathway in hepatic stellate cells by NBR1 and p62 determines the progression of hepatocellular carcinoma [RNAseq]

city: New York

first: Jorge

last: Moscat

address: 1188 York Avenue

institute: WEILL CORNELL MEDICINE

summary: Hepatocellular carcinoma (HCC) emerges from chronic inflammation to which activation of hepatic stellate cells (HSCs) contributes by shaping a pro-tumorigenic microenvironment. Key to this process is p62, whose inactivation leads to enhanced hepatocarcinogenesis. Here, we show that while p62 positively regulates STING ubiquitination by TRIM32 by displacing NBR1, which results in the activation of the interferon (IFN) cascade, NBR1 prevents TRIM32 interaction with and the activation of STING, leading to impaired IFN synthesis. NBR1 also antagonizes STING function by promoting its trafficking from the Golgi to the endosome-lysosomal degradative cascade independent of autophagy. Importantly, NBR1 deletion completely reverts the tumor-promoting function of p62-deficient HSCs. The upregulation of the STING-IFN pathway by NBR1 deficiency enhances the anti-tumor response mediated by CD8+ T cells. These results identify NBR1 as a synthetic vulnerability of p62-deficiency in HSCs. NBR1 loss, by promoting the STING/IFN pathway, boosts anti-tumor CD8+ T cell responses to restrain HCC.

overall_design: Nbr1 knock-out and wild type hepatic stellate cells were profiled in three biological replicates under normal conditions.

first: Sadaaki

last: Nishimura

first: Juan

middle: F

last: Linares

first: Antoine

last: L'Hermitte

first: Angeles

last: Duran

first: Marc

last: Ruiz-Martinez

first: Tania

last: Cid-Diaz

first: Yotaro

last: Kudo

first: Maria

last: Diaz-Meco

first: Anxo

last: Martinez-Ordoñez

first: Antonio

last: Marzio

first: Mathias

last: Heikenwalder

first: Lewis

last: Roberts


title: Effect of nano-enzyme on gene expression during oxidative stress of human mesenchymal stem cells

city: Chengdu

first: Mingru

last: Bai

address: Renmin Road No.14

institute: Sichuan University

summary: Stem cells are severely weakened by elevated reactive oxygen species (ROS) in the inflammatory bone defect microenvironment. It is therefore of critical importance to modulate the level of extracellular ROS for the reversal of stem cell unfavorable environment. Here, we present a stable monatomic ruthenium biocatalyst anchoring on the surface of cobalt nickle layered double hydroxides (Ru-LDH) for catalytic reactive oxygen species (ROS) scavenging. We here report the changes of transcription factors human mesenchymal stem cells (hMSCs) with/without treatment with Ru-LDH under the oxidative stress condition.

overall_design: To investigate the function of Ru-LDH in stem cell protection in high level of ROS microenvironment. We then performed gene expression profiling analysis using data obtained from RNA-seg of hMSCs in 4 conditions (Ctrl, H2O2, LDH+H2O2, Ru-LDH+H2O2).


title: ZNF207-YWHAZ Enhances Breast Cancer Proliferation and Chemotherapy Resistance by Activating the HIF-1alpha-PPARgamma-PKM2 Signaling Axis

city: Shenyang

first: Huanyu

last: Wu

state: Liaoning

address: No. 77 Puhe Road

department: Pathology Teaching and Research Office of Basic Medical College

institute: China Medical University

summary: Hypoxia is closely linked to chemotherapy resistance and accelerates breast cancer progression. However, the underlying mechanism of resistance to hypoxic chemotherapy remains uncertain. ZNF207 was identified as a differentially expressed gene involved in hypoxia and chemotherapy resistance by RNA-sequencing array. ZNF207 expression was elevated in lung, breast, liver, colon, and ovarian cancers, and its positive expression was correlated significantly with advanced TNM stage, lymph node metastasis, and poor prognosis. ZNF207 overexpression promoted the proliferation, invasion capabilities, and stemness of breast cancer cells by activating the HIF-1alpha-PPAR-gamma-glycolysis signaling pathway. Notably, ZNF207 was directly bound to the coiled-coil domain of YWHAZ, thereby accelerating HIF-1alpha deacetylation in an HDAC4-dependent manner. Furthermore, ZNF207 might stabilize YWHAZ by inhibiting its degradation via TRIM67 through a ubiquitin-dependent mechanism. ZNF207 overexpression enhanced resistance to doxorubicin and vinorelbine. Conversely, ZNF207-DeltaGLE overexpression disrupted HIF-1alpha-PPAR-gamma-glycolysis signaling and abolished chemotherapy resistance. Additionally, ZNF207 expression was higher in patients with breast cancer who exhibited poor treatment outcomes (Miller/Payne grades 1-2) than in those with more favorable outcomes (Miller/Payne grades 3-5). Sappanchalcone, a specific ZNF207 inhibitor, impedes breast cancer progression while exerting a synergistic effect with chemotherapy. Our findings revealed that ZNF207 expression was elevated in breast cancer under hypoxic conditions, promoting proliferation and invasion by activating HIF-1alpha through accelerated deacetylation in a positive feedback loop. The interaction between ZNF207 and YWHAZ enhances HIF-1alpha stability, ultimately accelerating therapeutic resistance in breast cancer.

overall_design: Aerobic treatment of MCF-7 cells rep1, rep2, rep3;Treatment of MCF-7 cells with 2% O2 for 24 hours rep1, rep2, rep3


title: Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics.

city: Poznań

first: Arkadiusz

last: Kajdasz

state: wielkopolskie

address: ul. Z. Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series