title: Expression data from human gastric cancer cell AGS with or without NCAPD3 knockdown.

city: Fuzhou

first: Sheng

last: Yang

state: Fujian

address: Xinquan Load

institute: Fujian Medical University Union Hospital

summary:
In order to study the molecular mechanisms of malignant biological behavior in gastric cancer regulated by NCAPD3, GeneChip PrimeView human gene expression array was used to detect differentially expressed genes (DEGs) before and after NCAPD3 knockdown.
We used microarrays to detail the effect of NCAPD3 knockdown on gene expression in gastric cancer cell and identified differentially expressed genes during this process.

overall_design: AGS cells were transfected with shNCAPD3 lentiviruses and control vector to construct NCAPD3-knockdown and negative control cells. Next, qPCR was used to validate the efficiency of RNA interference. Then total RNA was extracted for an RNA quality test and following reverse transcription. The labeled RNAs were fragmented and hybridized. The Affymetrix GeneChip PrimeView human gene expression array was used for testing. GeneChip Scanner 3000 was used for data analysis.

first: Suyun

last: Zhang

first: Qiong

last: Luo

first: Lirong

first: Fan

first: Jian

last: Zhu

first: Xiangqi

last: Chen


title: Gene regulation using the flap endonuclease 1 guided by mis-hairpin DNA probes

status: Public on Apr 11 2024

city: NANJING

first: liang

last: wang

address: ZHONGYANGMEN

country: China

institute: CHINA PHARMACEUTICAL UNIVERSITY

type: Expression profiling by high throughput sequencing

summary: Here we characterized a genetic regulatory system named as the hpDNA-assisted structure-guided nuclease mediating interference (HpSGNi) system, which was composed of flap endonuclease 1 (FEN1) and mis-hairpin DNA probe (mis-hpDNA). To investigate gene regulation effective of the HpSGNi system, we co-transformed HEK293A (human embryonic kidney epithelial cells) with plasmids encoding FEN1 with NES and two groups of mis-hpDNAs targeting the EGFP gene and negative control, respectively. RNA-seq was used to examine the regulation effective. We proved the HpSGNi system can knock down specific gene in human cells. At the same time, it indicated that a degree of off-targets occur in HpSGNi-treated cells.

overall_design: Examination the gene regulation effective of the HpSGNi system.

first: Liang

last: Wang


title: Characterization of a new selective glucocorticoid receptor modulator with anorexigenic activity

status: Public on Apr 10 2024

city: Gwanak-gu

first: Chong-Su

last: Kim

state: --- Select One ---

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Dongduk Women's University

summary: Obesity, a worldwide epidemic, leads to various metabolic disorders threatening human health. In response to stress or fasting, glucocorticoid (GC) levels are elevated to promote food intake. This involves GC-induced expression of the orexigenic neuropeptides in agouti-related protein (AgRP) neurons of the hypothalamic arcuate nucleus (ARC) via the GC receptor (GR). Here, we report a selective GR modulator (SGRM) that suppresses GR-induced transcription of genes with non-classical glucocorticoid response elements (GREs) such as Agrp-GRE, but not with classical GREs, and via this way may serve as a novel anti-obesity agent. We have identified a novel SGRM, 2-O-trans-p-coumaroylalphitolic acid (Zj7), a triterpenoid extracted from the Ziziphus jujube plant, that selectively suppresses GR transcriptional activity in Agrp-GRE without affecting classical GREs. Zj7 reduces the expression of orexigenic genes in the ARC and exerts a significant anorexigenic effect with weight loss and increased energy expenditure in both high-fat diet-induced obese and genetically obese db/db mouse models. Transcriptome analysis showed that Zj7 represses the expression of a group of orexigenic genes including Agrp and Npy induced by the synthetic GR ligand dexamethasone (Dex) in the hypothalamus. Overall, our studies demonstrate that selectively targeting the orexigenic action of GR in AgRP neurons is a promising approach for the treatment of metabolic disorders with fewer side effects.

overall_design: 10 weeks old male mice were IP injected with vehicle, Dex (10 mg/kg), or Dex+Zj7 (50 mg/kg) for 24hrs. Hypothalamic ARC regions were dissected and total RNA was isolated.


title: RNA sequencing of isolated mouse CD8 T cells treated with IL2, IL7 or IL15

city: Philadelphia

first: Caitlin

last: Tilsed

state: Pennsylvania

address: 407F 4312 Chestnut St

country: USA

institute: The University of Pennsylvania

summary: The use of lipid nanoparticles (LNP) to encapsulate and deliver mRNA has become an important therapeutic advance. In addition to vaccines, LNP-mRNA can be used in many other applications. For example, targeting the LNP with anti-CD5 antibodies (CD5/tLNP) can allow for efficient delivery of mRNA payloads to T cells to express protein. As the percentage of protein expressing T cells induced by an intravenous injection of CD5/tLNP is relatively low (4-20%), our goal was to find ways to increase mRNA-induced translation efficiency. We showed that T cell activation using an anti-CD3 antibody improved protein expression after CD5/tLNP transfection in vitro but not in vivo. T cell health and activation can be increased with cytokines, therefore, using mCherry mRNA as a reporter, we found that culturing either mouse or human T cells with the cytokine IL7 significantly improved protein expression of delivered mRNA in both CD4+ and CD8+ T cells in vitro. By pre- treating mice with systemic IL7 followed by tLNP administration, we observed significantly increased mCherry protein expression by T cells in vivo. Transcriptomic analysis of mouse T cells treated with IL7 in vitro revealed enhanced genomic pathways associated with protein translation. Improved translational ability was demonstrated by showing increased levels of protein expression after electroporation with mCherry mRNA in T cells cultured in the presence of IL7, but not with IL2 or IL15. These data show that IL7 selectively increases protein translation in T cells, and this property can be used to improve expression of tLNP-delivered mRNA in vivo.

overall_design: CD8 T cells were isolated from the spleens of C57BL/6 mice and cultured with IL2, IL7 or IL15 for 48 hours. RNA was extracted and sequenced.

middle: M

first: Steven

last: Albelda

first: Hamideh

last: Parhiz


title: Transcriptomics and metabonomics study on the effect of combined exercise with curcumin supplementation on breast cancer in mice

city: HeFei

first: He

last: Kan

state: AnHui

address: No. 111 Jiulong Road, Furong community, Shushan District, Hefei City, Anhui province

institute: Anhui University

summary: Previous research reports have shown that curcumin and exercise have good anti-tumor effects. However, there is currently a lack of relevant research reports on the combined effect of physical exercise with curcumin supplementation on cancer and its mechanisms. This study constructed an anti breast tumor mouse model under the combined effects of curcumin treatment and swimming exercise. Transcriptomics and metabolomics techniques were used to screen differentially expressed genes and metabolites, evaluate the anti-cancer effect, and analyze the molecular regulatory mechanisms related to metabolism. Through the mouse phenotype observation, including the detection of tumor appearance, tumor imaging in vivo, and HE staining results of pathological sections, curcumin administration and exercise intervention combined treatment has more obvious inhibitory effect on breast cancer than a single treatment. The combined effect treatment group had a total of 445 differentially expressed genes, including 154 upregulated genes and 291 downregulated genes; Functional enrichment analysis showed that calcium signaling pathway, Wnt signaling pathway, PI3K Akt signaling pathway and IL-17 signaling pathway significantly participated in the anti breast cancer process of curcumin combined exercise. The results of inter group differential metabolite analysis showed that the combined effect of curcumin and exercise involves two unique pathways: amino sugar and nucleotide sugar metabolism, as well as amino acid biosynthesis. The metabolic pathways of amino sugars and nucleotide sugars include chitosan, D-glucosamine 6-phosphate, L-fucose, and N-acetyl beta-mannosamine; The biosynthetic pathway of amino acids includes DL isoleucine, DL tyrosine, and homocysteine. Finally, through the joint analysis of transcriptome and metabolomic data, it was found that the most significantly correlated genes among the positive ion mode differential metabolites under the combined exercise of curcumin were catechins, including 8 correlated genes Cpeb2, Grem1, Nid1, Samd5, Hsph1, Glis3, Mapk6, and Phldb2; The most significant negative ion mode differential metabolite is 1-myristyl-2-hydroxy-sn-glycerol-3-phosphate ethanolamine, which includes 27 correlated genes Mmp10, Dock4, Dpysl3, Tnfsfm13, Etf1, Dzip1, Scara5, Plcg2, Dusp18, Zmat3, Marf1, Tox4, Tmem119, Tep1, Cybc1, AW549877, Dynap, Hhip, Tpm3, Zc3hav1l, Sema5a, Txlng, Lrrc55, Pprrx1, Rtl8b, Adam19, and Frrs1.

first: Yong

last: Guo

first: Jinxing

last: Su

first: Shangquan

last: Jiang

first: Yan

last: Xu

first: Binbin

last: Dou

first: Ting

last: Li

first: Jiabin

first: Kan

last: He


title: Effect of disruption of IL-6 in cachectic C26 tumor on gene expression

city: Boston

first: Kwon

last: Young-Yon

state: Massachusetts

address: 655 Huntington Ave

department: Molecular metabolism

institute: Harvard University School of Public Health

summary: The IL-6 was reported as a key cachectic factor in mice inoculated with colon carcinoma 26 (C26) cells, a widely used cancer cachexia model. However, we identified We found that the growth of IL-6 KO tumors was dramatically delayed. More strikingly, while IL-6 KO tumors eventually reached the similar size as wild-type tumors, cachexia still took place, despite no elevation in circulating IL-6.  We further showed that IL-6 promotes tumor growth by facilitating immune evatioon but is dispensable for cachexia.

overall_design: To investigate the effect of IL-6 knock out (KO) in cachectic C26 (cxC26) tumor, we constructed C26 IL-6 KO cells using CRISPR/Cas9 and isolated a subclone (cxC26 IL6KOs1) . Then, we implanted wild-type (cxC26 scr) and IL-6 KOs1 cells into CD2F1 male mice. The tumor samples were isolated when the mice developed cachexia (more than 15% of body weight loss) and perfromed bulk RNA-seq.

first: Sheng

last: Hui

first: Young-Yon

last: Kwon


title: miR-146a-5p contributes to inflammation-mediated β cell mitochondrial dysfunction and apoptosis

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

summary: MicroRNAs (miRNAs) are small non-coding RNAs that function as modulators of gene expression. We previously showed that miR-146a-5p is upregulated in pancreatic islets treated with pro-inflammatory cytokines and in pancreatic sections from organ donors with type 1 diabetes (T1D). Other studies have associated overexpression of miR-146a-5p with β cell apoptosis and impaired insulin secretion; however, the molecular mechanisms mediating these effects remain elusive. To investigate the role of miR-146a-5p in β cell function, we developed stable MIN6 cell lines transduced with lentiviral vectors to either overexpress or inhibit the expression of miR-146a-5p. Monoclonal cell populations were treated with pro-inflammatory cytokines (IL1β, IFNg, and TNFα) to model T1D in vitro. We found that overexpression of miR-146a-5p increased the cell death of MIN6 cells under inflammatory stress, whereas inhibition of miR-146a-5p reversed these effects. Additionally, inhibition of miR-146a-5p increased mitochondrial DNA copy number, respiration rate, and ATP production, suggesting that miR-146a-5p inhibition improves mitochondrial function. In support of this finding, we also observed that miR-146a-5p is enriched in the mitochondria of MIN6 cells treated with cytokines. Consistently, bioinformatic analysis of RNA sequencing data using MIN6 stable cells showed enrichment of pathways related to insulin secretion, apoptosis, and mitochondrial function when the expression levels of miR-146a-5p were altered. Overall, the findings from our study show for the first time that miR-146a-5p upregulation during inflammatory stress may promote β cell dysfunction and death by suppressing mitochondrial function.

overall_design: We developed MIN6 stable cells using lentiviral vectors to overexpress / inhibit miR-146a-5p. MIN6 cells transduced with scrambled sequence was used as the control. mRNA sequencing was performed on MIN6 cells treated with and without proinflammatory cytokines and differentially expressed genes were identified by comparing different pairs.

first: Preethi

last: Krishnan

first: Farooq

last: Syed


title: Relationship between sex and disease resistance of Penaeus vannamei

city: qingdao

first: yuxi

last: Wang

address: Laoshan District Songling Road

institute: ocean university of china

summary: To investigate the relationship between the resistance of male and female Penaeus vannamei and their immunity， we collected hemocytes from shrimps stimulated by Vibrio parahaemolyticus.

overall_design: Analysis of hemocytes from male and female Penaeus vannamei stimulated by Vibrio parahaemolyticus using high-throughput techniques."

first: mengqiang


title: RNA-seq analysis in simulated microgravity unveils down-regulation of the beta-rhizobial siderophore phymabactin

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zürich

summary: Exploiting the symbiotic interaction between crops and nitrogen-fixing bacteria is a simple and ecological solution to promote plants growth in prospective extraterrestrial human outposts. In this study, we investigated the adaptation of the legume symbiont Paraburkholderia phymatum to simulated microgravity (s0-g) at the transcriptome level by performing an RNA-Seq analysis. The results revealed a drastic effect on gene expression, with roughly 23 % of P. phymatum genes being differentially regulated in s0-g. Among those, 951 genes were upregulated and 858 downregulated in the cells grown in s0-g compared to terrestrial gravity (1g). Genes involved in posttranslational modification, proteins turnover and chaperones production were upregulated in s0-g, while those involved in translation, ribosomal structure and biosynthesis, motility or inorganic ions transport were downregulated. Specifically, the whole phm gene cluster, previously predicted to be involved in the production of a hypothetical siderophore, phymabactin, was approximatively 20-fold downregulated in microgravity. Accordingly, a phm-gfp reporter strain showed less expression in s0-g and iron uptake was reduced in microgravity. By constructing a mutant strain (ΔphmJK) we confirmed that the phm gene cluster codes for the only siderophore secreted by P. phymatum. In fact, in contrast to P. phymatum wild-type, ΔphmJK did not produce any siderophores on chrome azurol S plates. These results not only provide a deeper understanding of the physiology of symbiotic organisms exposed to space-like conditions, but also increase our understanding of iron acquisition in rhizobia.

overall_design: Assessing the impact of simulated microgravity in P. phymatum and identification of a beta-rhizobial siderophore

first: Daphné

last: Golaz

first: Chad

middle: K

last: Papenfuhs

first: Paula

last: Bellés Sancho

first: Leo

last: Eberl

first: Marcel

last: Egli


title: Optimization of a Mouse Model of Pancreatic Cancer to More Closely  Simulate the Human Phenotypes of Metastasis and Cachexia

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

summary: Experment1: To study the difference between the parental KPC line and the KPCML1 metastatic cell line Experiment2: To study the differentially regulated genes in cachectic mice, we RNA sequenced the TA muscles of different mouse models of cachexia and their respective controls

overall_design: Experiment 1(Design) - KPC mouse pancreatic cancer parental cells were injected orthtopically into mouse pancreas. Cells were extracted from liver metastases to generatetthe KPCML1.  Experiment 2(Design) - Mice were injected with C26 (colon cancer) cells subcutaneously, LLC (lung cancer) cells intramuscularly, KPC or KPCML1 (pancreatic cancer cells) cells orthotopically, or tamoxifen to induce the pancreatic cancer genetic tumor model. Muscle were taken from tumor bearing mice as well as aged matched controls in each experiment

first: Deinis

last: Guttridge


title: Double-negative T cells ameliorate psoriasis by selectively inhibition on IL-17A producing γδ T cells

city: Beijing

first: Yunxiong

last: Wei

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District, Beijing, 100020

institute: Capital medical university

summary: Psoriasis is a chronic immune-mediated skin condition influenced by genetics and environmental factors. γδ T cells, as the main sources of IL-17A, play pivotal roles in the inflammatory processes of psoriasis. During psoriasis pathogenesis, inhibiting the secretion of IL-17A has emerged as a novel therapeutic approach for treating psoriasis. Double-negative T (DNT) cells is a novel type of immunosuppressive cells. Our preliminary research has unveiled that DNT cells play a significant immunoregulatory role in autoimmune and allergic diseases. In this study, we aimed to evaluate the protection of DNT cells and explore its underlying mechanism.

overall_design: We conducted adoptive transfer of CD4 T cell converted DNT cells (cDNT) into the IMQ-induced psoriasis mouse model through tail vein injection. Following cDNT treatment, there was a reduction in the inflammatory response in mouse skin, characterized by decreased skin folds, scales, and red patches. After cDNT treatment, the secretion of IL-17A by RORc+ γδlow T cells in the skin was suppressed, resulting in an amelioration of skin inflammation. Transcriptomic data suggested heightened expression of NKG2D ligands in γδlow T cell within the mouse model of psoriasis induced by IMQ. When blocked NKG2D ligand and NKG2D (expressed by cDNT) interaction, the cytotoxic efficacy of cDNT against RORc+IL17A+ γδlow T cells was attenuated. Using Ccr5-/- cDNT for treatment yielded evidence that cDNT migrate into the inflamed skin tissue, failed to pretocet IMQ induced skin lesion.

first: Guangyong

last: Sun

first: Xueling

last: Mei

first: Dong

last: Zhang


title: Regulation of Diseases Associated Microglia in the Optic Nerve by Lipoxin B4 and Ocular Hypertension [RNA-Seq]

city: Berkeley

first: Shubham

last: Maurya

address: Rm 596, Minor Hall

institute: University of California Berkeley

summary: The resident astrocytes-retinal ganglion cell lipoxin circuit is impaired during retinal stress that include exocytotoxic- and ocular hypertension-induced neuropathy. Two endogenous lipoxins (Lipoxin A4 and Lipoxin B4) produced by homeostatic astrocytes directly act on RGCs. LXB4 is the most potent lipoxin in the retina and directly increases RGC survival and function in ocular hypertension-induced neuropathy. Homeostatic roles and cellular targets of LXB4 in the retina and optic nerve are a critical gap in knowledge. Single-cell RNA sequencing was used to define cellular targets and signaling of LXB4 in the retina. For modeling neurodegeneration, sustained ocular hypertension was induced by silicone-oil injection in the anterior chamber of mouse eyes. For morphological characterization of microglia populations in the retina and optic nerve, we used MorphOMICs and pseudotime trajectory analysis. Bulk RNA sequencing of optic nerves was performed to characterize pathways and mechanism of action for LXB4. qPCR and immunohistochemistry were used for validation of transcriptomics data. Student’s t-test and one-way ANOVA were used to determine differences between experimental groups. Single Cell transcriptomic identified microglia as a primary target for LXB4 in the healthy retina. LXB4 downregulated genes that drive microglia environmental sensing and reactivity responses. Analysis of microglia function uncovered that ocular hypertension induces distinct, temporally defined and dynamic phenotypes in the retina and, unexpectedly, in the distal myelinated optic nerve.  Microglial expression of CD74, a marker of disease-associated microglia (DAM) in the brain, was only induced in a unique population of optic nerve microglia but not the retina. Genetic deletion of lipoxin formation correlated with presence of a CD74 optic nerve microglia population in normotensive eyes optic, while LXB4 treatment during ocular hypertension shifted optic nerve microglia toward a homeostatic morphology and non-reactive state and downregulated expression of CD74. Furthermore, we identified a correlation between CD74 and phospho-PI3K (p-PI3K) expression levels in the optic nerve, that was reduced by LXB4 treatment. Results  identify distal optic nerve microglial dynamic and reactive responses as a key feature of ocular hypertension induce neurodegeneration.  Our findings establish microglia regulation as a new LXB4 cell target in the retina and optic nerve. LXB4 maintenance of optic nerve microglia homeostatic phenotype and inhibition of a disease-associated phenotype are potential mechanisms for LXB4 neuroprotection.

overall_design: Three biological replicates were analyzed for each of optic nerves

first: Maggie

last: Lin

first: Shruthi

last: Karnam

first: Tanirika

last: Singh

first: Matangi

last: Kumar

first: Emily

last: Ward

first: John

middle: G

last: Flanagan

first: Karsten

last: Gronert


title: Regulation of Diseases Associated Microglia in the Optic Nerve by Lipoxin B4 and Ocular Hypertension [scRNA-Seq]

overall_design: Mouse retinal cells were dissociated to single cells and 10x genomics based single cell transcriptomics was done after depleting the rod cells


title: Antigen-level resolution of commensal-specific B cell responses enabled by phage-display screening and B cell tetramers

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Induction of adaptive immune responses to commensal microbes is critical for intestinal homeostasis, and perturbation of these responses is associated with multiple chronic inflammatory disorders. However, the mechanisms underlying the induction and regulation of mucosal B cells targeting commensal microbes remain poorly understood, in part due to a lack of tools to identify commensal-specific B cells ex vivo. To address this, we first sought to identify immunodominant protein epitopes recognized by Segmented Filamentous Bacteria (SFB) specific serum antibodies using a whole-genome phage display screen and identified immunogenic proteins engaging IgA, IgG1 and IgG2b responses. Using these antigens, we generated B cell tetramers to identify and track SFB-specific B cell responses in the gut associated lymphoid tissue during natural and de novo colonization. We identified a compartmentalized response in B cell activation between Peyer’s patches and mesenteric lymph nodes, with a gradient of IgA, IgG1 and IgG2b isotypes along the small intestine, and selective production of IgG2b with the mesenteric lymph node chain. VDJ sequencing analyses and generation of SFB-specific monoclonal antibodies identified that somatic hypermutation drives affinity maturation to SFB derived antigens under homeostatic conditions. By combining phage display screening and B cell tetramer technologies, we now enable antigen-level based studies of immunity to intestinal microbes, which will advance our understanding of the ontogeny and function of commensal-specific B cell responses in tissue immunity, inflammation and repair.

overall_design: Investigation of SFB-specific B cells isolated from mouse Peyer's patches. Cells are from ten individual mice (M1-M10), sorted, hashtagged, and pooled for paired gene expression and BCR sequencing.

first: Sheenam

last: Verma

first: Matthew

middle: J

last: Dufort

first: Tayla

last: Olsen

first: Jasmine

middle: C

last: Labuda

first: Samantha

last: Kimmel

first: Sam

last: Scharffenberger

first: Andrew

middle: T

last: McGuire

first: Oliver

last: Harrison


title: Effect of carboplatin-paclitaxel or -gemcitabine combinations on lung cancer cells spheroids

city: Nantes

first: Christophe

last: Blanquart

address: 8 Quai Moncousu

country: France

institute: INSERM UMR 1307/CNRS UMR 6075

summary:
Background: Lung cancers represent the main cause of cancer related-death in the world. Recently, immunotherapy alone or in combination with chemotherapies have deeply impacted the therapeutic care leading to an improved overall survival. However, relapse will finally occur, with no efficient second line treatments so far. The development of new therapies based on comprehension of mechanisms of resistance is necessary. However, the difficulties to obtain tumor samples before and after first line treatment hampers to clearly understand the consequence of these molecules on tumor cells and then, to identify adapted second line therapies.
Methods: To overcome this difficulty, we developed multicellular tumor spheroids (MCTS) using characterized Non-Small Cell Lung Cancer (NSCLC) cell lines, monocytes from healthy donors and fibroblasts (Human Foreskin Fibroblasts-2, HFF2). MCTS were treated with carboplatin-paclitaxel or -gemcitabine combinations according to clinic schedule of administration consisting on three repetitions of treatments (one combination and two single treatments (paclitaxel or gemcitabine)). The impact of treatments was studied using cell viability assay, histology, 3’RNA sequencing, real-time PCR, flow cytometry and confocal microscopy.
Results: We showed that treatments induced a decrease of cell viability and strong modifications in the transcriptomic profile notably at the level of pathways involved in DNA damages repair and the cell cycle. Interestingly, we also observed a modification of the expression of genes considered as hallmarks of response/resistance to immune check point inhibitors and immunogenicity and particularly an increase of CD274 gene expression, coding for PD-L1. This result was validated at the protein level and showed to be restricted to tumor cells on MCTS containing fibroblasts and macrophages. This increase was also observed on an additional cell line, expressing low basal level of CD274. These results are consistent with previous observations on patients showing higher PD-L1 tumoral expression after chemotherapy exposure.
Conclusions: This study shows that MCTS could be interesting models to study the impact of first line therapies using conditions close to the clinical practice and then, to identify more adapted second line or concomitant therapies for the treatment of lung cancers.

overall_design:
mRNA from control  (n=13), carboplatin-paclitaxel (n=5) or carboplatin-gemcitabine (n=5) treated MCTS were analyzed using 3'RNA sequencing
'X' correspond to 2 series of independent experiments
CT is for control group (untreated)
CaGe is for carboplatin-gemcitabine treated group
CaPa is for carboplatin-paclitaxel treated group

first: Pauline

last: Hulo

first: Elvire

last: Pons-Tostivint


title: Immune modulation with RANKL-blockade through denosumab treatment in cancer patients

city: San Francisco

first: Mark

last: Bridge

state: CA

address: 513 Parnassus Ave

institute: UCSF

summary: Denosumab is a fully human monoclonal antibody that binds receptor activator of nuclear factor-κB ligand (RANKL) and is routinely administered to cancer patients to reduce the incidence of new bone metastasis. RANK-RANKL regulates bone turnover by controlling osteoclast recruitment, development, and activity. However, this interaction also can regulate a broad range of immune cells including dendritic cells and medullary thymic epithelial cells (mTECs). Inhibition of the latter results in reduced thymic negative selection of T cells and could enhance the generation of tumor-specific T cells. We examined whether administering denosumab could modify modulate circulating immune cells in cancer patients. Blood was collected from 23 prostate cancer patients and 3 renal cell carcinoma patients, who provided written informed consent, with advanced disease who were receiving denosumab, prior to and during denosumab treatment. Using high-dimensional mass cytometry, we found that denosumab treatment by itself induced modest effects on circulating immune cell frequency and activation. We also found minimal changes in the circulating T cell repertoire and the frequency of new thymic emigrants with denosumab treatment. However, when we stratified patients by whether they were receiving chemotherapy and/or steroids, patients receiving these concomitant treatments showed significantly greater immune modulation, including an increase in the frequency of NK cells early and classical monocytes later. We also saw broad induction of CTLA-4 and TIM3 expression in circulating lymphocytes and some monocyte populations. These findings suggest that denosumab treatment by itself has modest immunomodulatory effects, but when combined with conventional cancer treatment, can lead to the induction of immunologic checkpoints.

overall_design: Serial blood samples were collected from patients starting standard of care denosumab at UCSF. Patients had blood drawn for PBMC isolation and cryopreservation from the following timepoints: TP1 is pre-denosuman treatment, TP2 is prior to dose 2, TP3 is prior to dose 3, and TP4 is prior to dose 6.

first: Hewitt

last: Chang

first: Jaqueline

last: Marquez

first: Brandon

last: Chen

first: Daniel

last: Kim

first: Michael

middle: L

last: Cheng

first: Eric

middle: V

last: Liu

first: Hai

last: Yang

first: Li

last: Zhang

first: Meenal

last: Sinha

first: Alexander

last: Cheung

first: Serena

middle: S

last: Kwek

middle: D

last: Chow

first: Rahul

middle: R

last: Aggarwal

first: Terence

middle: W

last: Friedlander

last: Small

last: Anderson

first: Lawrence

last: Fong


title: Regulation of Diseases Associated Microglia in the Optic Nerve by Lipoxin B4 and Ocular Hypertension

first: Shubham

last: Maurya

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

overall_design: Refer to individual Series


title: METABOLIC INSIGHTS INTO DIVERSION OF HYDROPHOBIC AND HYDROPHILLIC WASTE TOWARDS OMEGA FATTY ACID IN THRAUSTOCHYTRIDS

city: Luleå

first: ALOK

middle: KUMAR

last: PATEL

address: Department of Civil, Environmental and Natural Resources Engineering  Luleå University of Technology,  Luleå, Sweden SE-97187

country: Sweden

institute: LULEA UNIVERSITY OF TECHNOLOGY

summary: Here, we investigated marine thraustochytrid Schizochytrium limacinum SR21 for its ability to convert waste oil, mixture of commercial oils (mCOs) and volatile fatty acids i.e., acetic acid and butyric acid into ω-3 fatty acid; docosahexaenoic acid (DHA). Metabolic insights through whole cell transcriptomic aid in tracing the route of substrate assimilation.

overall_design: SR21 was cultivated in Glucose, waste cooking oil (WCO), mixture of commercial oils (mCOs), acetic acid and butyric acid with concentration 20 g/L each. Total RNA was extracted from cells harvested after entire carbon was consumed i.e., 72 hr for glucose, WCO and mCOs and 96 hr for acetate and butyrate.

first: Alok

last: Patel

first: Iqra

last: Mariam


title: Ovarian leptin signalling regulates NLRP3 inflammasome activation and macrophage infiltration in a cell specific manner

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: Background: Obesity is associated with increased ovarian inflammation and the establishment of local leptin resistance. We presently investigated the role of leptin signalling on Nod-Like Receptor Protein 3 (NLPR3) inflammasome and macrophage prevalence in the pathophysiology of ovarian failure of obese mice. Methods: We collected ovaries from: (i) diet induced obese (DIO) mice fed chow diet (CD) or high-fat diet (HFD) for 4 or 16 weeks (wk); (ii) mice lacking the long-isoform of leptin receptor (ObRb; db/db); (iii) mice lacking leptin (ob/ob); and (iv) pharmacologically hyperleptinemic (LEPT) mice for protein and mRNA expression analysis. Next, granulosa cells (GCs) from antral follicles isolated from db/db and ob/ob mice were subjected to transcriptome analysis. Results: We observed no changes in the mRNA and protein levels of NLRP3 inflammasome components in the ovaries of db/db mice, as well as in markers of M1 and M2 macrophage infiltration. This contrasted with the downregulation of NLRP3 inflammasome components and M1 markers in ob/ob -/- and 16 wk HFD mice. Transcriptional analysis revealed opposing profiles between genetic models, with genes associated with steroid metabolism and prostaglandin action in db/db mice and genes controlling extracellular matrix in ob/ob mice being downregulated, despite both processes being crucial for follicular development and ovulation. Conclusions: Leptin signalling regulated NLRP3 inflammasome activation and expression of M1 markers in ovaries of obese mice, in an ObRb-dependent and -independent manner. Absence of changes in the expression of leptin signalling and proinflammatory mediators in GCs from db/db and ob/ob mice was associated with impaired folliculogenesis.

overall_design:
Comparative gene expression  analysis of RNA-seq data for db/db  and ob/ob from granulosa cells: cells were collected from antral follicles after mechanical disruption, and libraries performed by pooling approximately 50 cells together.
Wild type (WT) and mutants (MUT) from either leptin receptor b deficient mouse (db) and  leptin deficient mouse (ob) formed the groups: db WT; db MUT; ob WT and ob MUT

first: Marek

last: Adamowski

first: Yashaswi

last: Sharma

first: Tomasz

last: Molcan

first: Karolina

last: Wo?odko

first: Gavin

last: Kelsey

first: António

last: Galvão


title: Gene expression in human monocyte-derived macrophages: effect of loss of MYC or USF1

city: Sheffield

first: Endre

last: Kiss-Toth

state: South Yorkshire

address: The Medical School, Beech Hill Road

department: Division of Clinical Medicine

institute: University of Sheffield

summary: Macrophage function declines with age, however the underlying mechanisms remain poorly understood. Here, we report that MYC and USF1 are key in driving age-related macrophage functional decline in humans, including reduction in phagocytosis and chemotaxis. We show downregulation with age of MYC and USF1 in human monocyte-derived macrophages (MDMs) and crucially, that knockdown of MYC or USF1 in young MDMs modelled the age-related functional changes. Transcriptomic analysis of these young knockdown MDMs revealed alteration in expression of genes crucial to these functions, as well as those linked to adhesion and extracellular matrix formation. Concordant dysregulation of these genes was also seen in older MDMs. Finally, we show that morphology and F-actin content were altered with loss of MYC or USF1, similarly to that seen in ageing. Together, these results define MYC and USF1 as key drivers of MDM age-related functional decline and identify downstream targets to improve macrophage function in ageing.

overall_design: To investigate the role of MYC and USF1 in monocyte-derived macrophage (MDM) functional decline with age, we knocked these genes down individually in young MDMs by siRNA transient transfection. This was done in MDMs isolated from blood of six healthy young donors that were differentiated for 7 days in M-CSF. Cell were then transfected for 72 hours and either left unstimulated (M0) or were stimulated for a further 24 hours with LPS and IFNγ (MLPS+IFNy). We then performed gene expression profiling using data obtained from RNA sequencing on knockdown vs control in the M0 and MLPS+IFNy phenotypes.

first: Charlotte

middle: E

last: Moss

first: Heather

last: Wilson


title: Genome wide RNA expression profiles of endometrial stromal cells stimulated by cAMP, cAMP+MPA, MPA and E2+MPA.

city: Ube

first: Yuichiro

last: Shirafuta

state: Yamaguchi

address: 1-1-1, minami-kogushi

country: Japan

institute: Yamaguchi university

summary: To know the differences of decidualization induced by different stimuli, we compared the mRNA expression profiles of decidualized ESCs stimulated by cAMP or cAMP+MPA for 4 days, or by MPA or E2+MPA for 14 days.

overall_design: ESCs were treated with cAMP or cAMP+MPA for 4 days or, MPA or E2+MPA for 14 days.Because the cultured period was different between the 4-days protocol and the 14-days protocol, we prepared two control ESCs that were cultured without stimulations for 4 days or 14 days, respectively. The mRNA-seq libraries were generated. After the quality of the library was validated using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), the samples were subjected to sequencing with a next-generation sequencer (Genome Analyzer GAIIx, Illumina, San Diego, CA). Gene expression values were calculated as “transcripts per million” (TPM).

first: N

last: Sugino

first: I

last: Tamura


title: Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation

city: PARIS

first: Anne-laure

last: Le gac

address: 26 rue d'ulm

institute: Institut Curie

summary: we compare the TCR repertoires of MAIT1 and MAIT17 cells from the mouse thymus using 5’ scRNAseq and scTCRseq of MR1:5-OP-RU tetramer positive thymocytes. A thorough analysis of TCR features between MAIT sub-populations did not show any difference between the repertoires of MAIT1 and MAIT17 subsets. Quantitative simulation of clonotype distributions of MAIT1 and MAIT17 cells allowed us to investigate the role of TCR characteristics in MAIT fate choice, and to pinpoint the stage at which lineage commitment occurs. Our results indicate that the TCR characteristics are not instructive in MAIT lineage choice and that MAIT1/17 commitment takes place during MAIT cell proliferation in the thymus. Finally, we performed analogous analysis of a published scRNA-seq and scTCR-seq dataset of iNKT from mouse thymus and demonstrated that our conclusions are also relevant for iNKT1 vs iNKT17 fate commitment.

overall_design: Cd3e-/-Mr1-/- mice were sublethally irradiated (420 rads) and reconstituted intravenously with 1 million bone marrow cells from B6-MAITCast RorcGFP mice. Seven weeks after reconstitution, thymus was harvested for further analysis of MR1:5-OP-RU restricted thymocytes. Single-cell suspension of thymus was obtained

first: Vadim

last: Karnaukhov

first: Anne-Laure

last: Le Gac

first: Linda

last: Bilonda Mutala

first: Aurélie

last: Darbois-Delahousse

first: Laetitia

last: Perrin

first: Francois

last: Legoux

first: Aleksandra

last: Walczak

first: Thierry

last: Mora

first: Olivier

last: Lantz


title: To understand the transcriptional changes in human HSPCs induced upon co-culture with OP9M2 Mesenchymal Stromal Cells and their conditioned medium.

city: Tel Aviv

first: Michael

last: Milyavsky

address: 35 Klatzkin st, TAU Faculty of Medicine, Room 435

department: Pathology

country: Israel

institute: Tel Aviv University

summary: Failure to precisely repair DNA damage in self-renewing Hematopoietic Stem and early Progenitor Cells (HSPCs) can disrupt normal hematopoiesis and promote leukemogenesis. HSPCs are widely considered a target of ionizing radiation (IR)-induced hematopoietic injury. In this project, we are studying conditions that can protect the HSPCs from IR.

overall_design: The experiment was done in three types of media and in two time-points (4h and 24h). Type of medium is: plain medium, medium with Mouse bone marrow fluid, and medium with Mouse bone marrow cells. each type was treated with IR for 4h or 24h and each has a control. Total samples: 3 medium types X (4 biological replicates X 2-time points X 2 (control and treated)) = 48 samples.

first: Siva

last: Muddineni

first: Chen

last: Even

first: Adi

middle: Z

last: Roitman

first: Eviatar

last: Weizman


title: Integration of Thermal Proteome Profiling with phosphoproteomic and transcriptomic data via mechanistic network models decodes the molecular response to PARP inhibition

city: Heidelberg

first: Stephan

last: Gade

address: Meyerhofstrasse  1

country: Germany

institute: GSK - Cellzome

summary: The deregulation of complex diseases often spans multiple molecular processes. A multimodal functional characterization of these processes can shed light on the disease mechanisms and the effect of drugs. Thermal Proteome Profiling (TPP) is a mass-spectrometry based technique assessing changes in thermal protein stability that can serve as proxies of  functional changes of the proteome. These unique insights of TPP can complement those obtained by other omics technologies. Here, we show how TPP can be integrated  with phosphoproteomics and transcriptomics in a network-based approach using COSMOS, a framework for causal integration of multi-omics, to provide an integrated view of  transcription factors, kinases and proteins with altered thermal stability. This allowed us to recover known mechanistic consequences of PARP inhibition in ovarian cancer cells on cell cycle and DNA damage response in detail and to uncover new insights into drug response mechanisms related to interferon and hippo signaling. We found that TPP complements the other omics data and allowed us to obtain a network model with higher coverage of the main underlying mechanisms. These results illustrate the added value of TPP, and more generally the power of network models to integrate the information provided by different omics technologies. We anticipate that this strategy can be used to broadly  integrate functional proteomics with other omics to study complex molecular processes.

overall_design: UWB1.289 cells were treated with the PARP inhibitor Olaparib (10uM) or a DMSO control (3 replicates each) for 24h and gene expression was profiled using RNASeq.

first: Mira

last: Burtscher

first: Massimo

last: Petretich

first: Anna

last: Rutkowska

first: Maria

last: Fälth-Savitski

first: Julio

last: Saez-Rodriguez


title: Astrocytes in the mouse suprachiasmatic nuclei respond directly to glucocorticoids feedback

city: Lübeck

first: Kristian

last: Händler

address: Ratzeburger Allee 160

department: Human Genetics

institute: UKSH

summary: The circadian timing system anticipates daily recurring changes in the environment to synchronize physiology. In mammals, the master pacemaker is the hypothalamic suprachiasmatic nuclei (SCN), which synchronizes “wake” functions by inducing the circadian release of Glucocorticoids (GCs) from the adrenal gland. GCs peak right before the active phase and set the time of peripheral clocks, however, it is still unclear whether the SCN respond to GCs feedback. While GCs influence directly the SCN during the perinatal period, the adult circuit is considered to be resistant to them, suggesting a reduction of GCs-sensitivity along development. To understand this mechanism, we followed the expression of GC receptor (GR) along mouse SCN development with single cell resolution and show that GR is up-regulated in astrocytes as the circuit matures. We provide in vivo and in vitro evidence that the adult SCN stays responsive to circulating GCs through the activation of GR in astrocytes. Astrocytes’ communication is necessary to induce the GC-dependent shift on the SCN clock. Our data provides insight into the development of the SCN and highlight a new role of astrocytes as time-keepers in the adult. This finding might shed light on how the circadian system adapts to jetlag or shift work.

overall_design: We have assessed the mRNA expression profile of the developing mouse SCN at single-cell resolution at three key developmental time points (gestational day (GD) 17.5, postnatal day (PND) 2, PND10) and at PND30 when the SCN circuit is fully mature. At GD17.5 a substantial increase in the synchrony of clock genes’ oscillations in SCN cells has been observed concurrent to the neurogenic-gliogenic switch. At PND02 neurons are differentiated and the first peak of astrocytes’ proliferation happens. At PND10 the maturation of the RHT and the innervation of the ventral SCN is complete and the eyes open, light entrainment would promote the final development of the circuit. At PND30, the SCN circuit architecture has reached the maturity of the adult nuclei.

last: Haendler

first: Varun

last: Sreenivasan

first: Violetta

last: Pilorz

first: Jon

last: Olano Bringas

first: Laura

last: Escobar Castañondo

first: Nora

last: Bengoa Vergniory

first: Henrik

last: Oster

first: Malte

last: Spielmann

first: Mariana

last: Astiz


title: Role of Mcam in breast cancer cell state using a model cell line (Py230) [single cell]

city: Salt Lake City

first: Benjamin

last: Spike

state: Utah

address: 1950 Circle of Hope Dr,

institute: Huntsman Cancer Institute, University of Utah

summary: Morphological changes suggested cell state switching and scRNASeq profiles were therefore generated to use in downstream comparative transcriptomics analysis and for identification of cell state regulators.

overall_design: Py230 cells with LV-shControl vs LV-shMcam cells were isolated from 2D cell culture and analyzed using scRNAseq via chromium 10x protocols

first: Ozlen

last: Balcioglu

first: Brooke

last: Gates

first: Berhane

last: Hagos


title: Role of Mcam in breast cancer cell state using a model cell line (Py230) [single cell Multiplex]

overall_design:
Py230 cells with LV-shControl vs LV-shMcam cells were isolated from 2D cell culture and analyzed using scRNAseq via chromium 10x protocols
Please note that processed data files generated from both GEX and Multiplex samples are linked to the corresponding GEX sample records.


title: Role of Mcam in breast cancer cell state using a model cell line (Py230) [bulk RNA-Seq]

summary: To investigate effect of Mcam KD on tumor gene expression profile  in orthotopic Py230 derived grafted tumors

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine mammary tumors derived from Py230 cells that are either scrambled control or shMcam knocked down.


title: Role of Mcam in breast cancer cell state using a model cell line (Py230)


title: Monocyte RNA after exposure to platelets

status: Public on Apr 12 2024

city: Rochester

first: Tyler

last: Stahl

state: NY

address: 601 Elmwood Ave

institute: University of Rochester Medical Center School of Medicine and Dentistry

summary: The effects of platelet expsoure on RNA expression in platelet naïve monocytes

overall_design: Monocytes were incubated overnight with platelets, washed and LPS stimulated

first: Craig

last: Morrell

first: Chen

last: Li


title: A requirement for interferon gamma signaling in injury induced cartilage regeneration

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

institute: Catholic University of Korea

summary: To elucidate the requirement of interferon gamma signaling in cartilage regeneration, we generated genetically interferon gamma receptor 1 or interferon gamma deficient mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of injured cartilages from young and adult mice at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for a evaluation of cartilage regeneration in young and adult mice

first: Hyunah

last: Kim

first: Juryoung


title: The helicase domain of Dicer ensures strict processing of evolutionarily optimized microRNAs

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

type: Non-coding RNA profiling by high throughput sequencing

summary: Ribonuclease Dicer generates small RNAs for RNA interference (RNAi) and microRNA (miRNA) pathways. Mammalian Dicer produces miRNAs but its tripartite N-terminal helicase domain inhibits processing of double-stranded RNA for RNAi. Mouse oocytes express Dicer, which enhances RNAi because it lacks the helicase’s proximal subdomain HEL1. Here we show that genetic removal of HEL1 in mice causes embryonic growth retardation, defects in the cardiopulmonary system, and perinatal lethality. HEL1 suppresses biogenesis of mirtrons, a non-canonical low-abundant class of miRNAs, and is required for high-fidelity cleavage and strand selection during biogenesis of canonical miRNAs. Essential is the HEL1 structure, not its helicase activity, because mutations of critical aminoacids do not affect viability or fertility and have minimal impact on miRNA biogenesis. Altogether, HEL1 is a critical structural component of Dicer in its role of a highly conserved structural “mold” that ensures high-fidelity processing and adaptive evolution of mammalian miRNA precursors.

overall_design:
Bulk small RNA-seq of 11 mouse E15.5 embryo samples:
- 3x WT
- 5x DicerX homozygotes
- 3x DicerX heterozygotes

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Eliska

last: Taborska


title: Cancer treatment with radiation-chemotherapy rapidly induces molecular pathways for both resistance and new therapeutic targets

city: Bethesda

first: Michelle

last: Bylicky

state: Maryland

address: 10 Center Drive

department: Radiation Oncology Branch

institute: National Cancer Institute

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
FaDu tumors were implanted into Athymic mice then treated with HSP90 inhibitor Onalespib (5 days per week, 55mg/kg for 2 weeks), radiation (3 x 2 Gy for 1 week) or combination (2 week Onalespib, 1 week radiation concurrent)
The purpose of this study was to understand short term (1 week and 2 week post treatment) gene changes in FaDu tumors that had been injected into hind limbs of athymic mice. A drug treatment, a radiation treatment, a combination treatment, or sham treatment was used. Mice with untreated tumors required early euthanasia as tumors became too large. Treated tumors were collected 5 and 12 days post treatment start while UNtreated tumors were collected Day 5 and Day 8. Control Day 1 samples (mice euthanized on the start date of treatment) were compared to other groups.

overall_design: Radiation, Onalespib or combination treatment induced gene changes to FaDu human xenograft samples grown on athymic mice were collected after 1 or 2 weeks of treatment. Tumor samples were collected and used for RNA microarray. 37 samples collected total, 3 samples minimum per treatment, Control Day 1, Control Week 1, Control Week 2, Drug Week 1 (55mg/kg 5 days per week), Drug Week 2, XRT (radiation, 3 x 2Gy, every other day) Week 1, XRT Week 2 (radiation week 1, no radiation week 2), Drug+XRT Week 1 (1 week radiation, 1 week drug on same schedule as Drug alone and XRT alone), Drug+XRT Week 2 (2 weeks of Drug, 1 week XRT)

middle: A

first: Uma

last: Shankravam

first: Molykutty

last: Aryankalayil

first: Sunit

last: Chopra

first: Sarwat

last: Naz

first: Anastasia

last: Sowers

first: Rajani

last: Choudri

first: Valeria

last: Calvert

first: Emanuel

middle: F

last: Petricoin

first: Kevin

last: Scott

first: Juan

last: Dalo

first: Iris

last: Eke

first: James

middle: B

last: Mitchell

first: C

middle: N

last: Coleman


title: Pyroptotic T-cell-derived active IL-16 has a driving function in endometriosis development

city: Hefei

first: Jinghe

last: Zhang

state: Anhui

address: Huangshan Road 443

institute: University of Science and Technology of China

summary: Endometriosis is a common, chronic inflammatory condition that frequently results in pain and infertility and is estimated to affect 6–10% of women of reproductive age. However, the mechanisms underlying the induction of inflammation in endometriosis remain unclear. Here, we identified that ectopic endometrial T-cell-derived active interleukin (IL)-16 acts as an inflammation-driving cytokine in endometriosis. Furthermore, we found that in ectopic endometrial T cells, the activation of IL-16 requires iron overload-induced caspase-3 activity and that the release of active IL-16 is reliant on GSDME-mediated pyroptosis. These observations suggest that active IL-16 may represent a promising target in the treatment of endometriosis.

overall_design: In this dataset contains 1 cases of transcriptome information from 3 normal endometrial tissue of patients with uterine leiomyoma (NE_1), 1 cases from ectopic endometrial tissue samples of  patients with endometriosis (EE).

first: Haiming

last: Wei


title: Che-1/miR-590-3p/TAZ axis sustains multiple myeloma disease

city: Rome

first: Giacomo

last: Corleone

address: via chianesi 43

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

summary: Multiple myeloma (MM) is a blood disease characterized by the malignant accumulation of monoclonal plasma cells in the bone marrow. Among the pathological consequences of the MM, defects in osteogenesis characterized by osteolytic lesions, osteopenia, and pathologic fractures are frequently described. Che-1/AATF (Che-1) is a co-transcriptional factor involved in MM transformation and proliferation. Here, we show that Che-1 expression in MM contributes to maintaining low level of WWTR1 (TAZ), a transcriptional coactivator downstream of the Hippo-signaling pathway. We report that the miR-590-3p, deriving from the mRNA splicing of the EIF4H host gene, can target TAZ, contributing to downregulating its expression in MM. Furthermore, we demonstrate by in vivo and in vitro experiments that Che-1 transcriptionally induces EIF4H gene. We provide data to support that miR-590-3p is secreted by MM cells in vitro and in vivo and that can inhibit TAZ levels and the physiological transcriptional expression of osteogenic-related genes, in mesenchymal stem cells. Our findings unveil an unexplored novel Che-1/miR-590-3p/TAZ axis in MM tumorigenesis by providing a rationale to explore the therapeutic potential of metastatic bone lesions.

overall_design: RNA-seq performed to probe the changes affecting the transcriptome upon HA-TAZ (overexpression). The experiment is performed by analysizing 3 KMS27 wild type replicates and 3 HA-TAZ KMS27 replicates

first: Tiziana

last: Bruno

last: Catena

first: Francesca

last: De Nicola

first: Maurizio

last: Fanciulli

first: Silvia

last: Di Agostino


title: High throughput transcriptomic profiling of MCF10A cells exposed to breast cancer disparities associated chemicals

city: Ann Arbor

first: Justin

last: Colacino

state: MI

address: 6651 SPH1, 1415 Washington Heights

department: Environmental Health Sciences

institute: University of Michigan

summary: Analyzing the US Center for Disease Control’s National Health and Nutrition Examination Survey chemical biomarker data, we identified a suite of toxicants, including metals, pesticides, and personal care product compounds, to which non-Hispanic Black women are disproportionately exposed. To characterize the impact of these toxicants on breast cancer pathways, we performed high throughput transcriptomic analysis of toxicant exposed breast cells.

overall_design: We treated non-tumorigenic mammary epithelial cells, MCF10A, with 21 chemicals prioritized for exposure disparities, at four doses (25nM, 250nM, 2.5µM, 25µM) for 48 hours. We conducted RNA-sequencing for these 408 samples, adapting the PlexWell plate-based RNA-sequencing method to analyze changes in gene expression resulting from these exposures.

first: Anagha

last: Tapaswi

first: Kimberley

last: Sala-Hamrick


title: Cisplatin resistance driver gene CLSPN product is a target for immunotherapy in urothelial carcinoma.

city: Sapporo

first: Yoshihiko

last: Hirohashi

address: South-1 West-17

institute: Sapporo Medical University

summary: Bladder cancer is a major and mortal disease in urological area. Cisplatin is a key drug for bladder cancer especially for muscle invasive cases. In most cases of bladder cancer, cisplatin is effective; however, resistance to cisplatin is critical for patient’s prognosis. Thus, treatment strategy for cisplatin resistant bladder cancer is essential to improve current prognosis. In this study, we established cisplatin resistant bladder cancer line (CR cells) using a urothelial carcinoma line UM-UC-3 cells. We screened potential targets for CR cells and found that claspin is overexpressed in CR cells. Claspin mRNA knockdown revealed that claspin has a role in cisplatin resistance in CR cells. In our previous study, we found HLA-A*02:01-restricted CLSPN peptide by an HLA ligandome analysis. We thus generated CLSPN peptide specific CTL clone and found that CLSPN peptide-specific CTL clone recognized CR cells at higher levels compared with that of UM-UC-3 wild type cells. These findings indicate that claspin is a driver for cisplatin resistance and claspin peptide-specific immunotherapy is effective for cisplatin resistant cases.

overall_design: Cisplatin (CDDP) resistant (CR) subline was induced from an urothelial carcinoma cell line UM-UC-3 wild type (WT) cells. mRNA was isolated from UM-UC-3 CR cells and WT cells, then analyzed by CAGE.

first: Shuhei

last: Yamada


title: Small RNA-seq of chronic pancreatitis patient plasma samples

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

institute: Baylor Research Institute

summary: The purpose of our study was to identify miRNAs that can predict islet transplantation outcomes. We hypothesize that miRNAs may be used to predict islet function post-transplantation in TPIAT patients

overall_design: There are 24 samples.  6 are healthy controls; 18 are chronic pancreatitis. There are no replicates. The pacreatitis samples are classified based on aetiology of chronic pancreatitis into the following-Idiopathic, Alcoholic, Hereditary, Oddi dysfunciton, pancreatic divisum. The objectives are to identify miRNAs that can be correlated to islet transplantation outcomes. Since the normal healthy donor samples were not part of the transplantation, the normal samples will be used as control for miRNAs. Only those miRNAs that are not measured in normal healthy conditions will be taken further for investigations

first: Vasu

last: Srividya

first: Naziruddin

last: Bashoo


title: Tnik depletion induces inflammation and apoptosis in injured renal proximal tubule epithelial cells

city: Saint Louis

first: Shayna

middle: T. J.

last: Bradford

state: MO

address: MCDONNELL MEDICAL SCIENCES BUILDING, 4565 Mckinley Ave ST 852

department: Department of Medicine, Division of Nephrology

institute: Washington University in Saint Louis

summary: We performed bulk RNA-seq on primary and immortalized human renal proximal tubule epithelial cells (RPTECs) subjected to siRNA mediated TNIK silencing.

overall_design: primary or hTERT-immortalized RPTECs were treated with non-targeting siRNA or pooled siRNA targeting human TNIK for 48- or 72-hours.

first: Haojia

last: Wu

first: Yuhei

last: Kirita

first: Changfeng

last: Chen

middle: P

last: Malvin

first: Yasuhiro

last: Yoshimura

first: Yoshiharu

last: Muto

first: Benjamin

last: Humphreys


title: Susceptibility of pediatric acute lymphoblastic leukaemia to STAT3 inhibition depends on p53 induction

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Advances in the clinical management of pediatric B cell Acute Lymphoblastic Leukemia (B-ALL) have dramatically improved outcomes for this disease. However, relapsed and high-risk disease still contribute to significant numbers of treatment failures. Development of new, broad range therapies is urgently needed for these cases. We previously reported the susceptibility of ETV6-RUNX1+ pediatric B-ALL to inhibition of signal transducer and activator of transcription 3 (STAT3) activity. In the present study, we demonstrate that pharmacological or genetic inhibition of STAT3 results in p53 induction and that CRISPR-mediated TP53 knockout substantially reverses susceptibility to STAT3 inhibition. Furthermore, we demonstrate that sensitivity to STAT3 inhibition in patient-derived xenograft (PDX) B-ALL samples is not restricted to any particular disease subtype, but rather depends on TP53 status, the only resistant samples being TP53 mutant. Induction of p53 following STAT3 inhibition is MDM2-independent and exhibits synergistic in vitro and in vivo anti leukemia activity when combined with MDM2 inhibition. Taken together with the relatively low frequency of TP53 mutations in this disease, these data support the future development of combined STAT3/MDM2 inhibition in the therapy of refractory and relapsed pediatric B-ALL.

overall_design: ChIP sequencing of TP53 in REH cells, treated for 6h with either S3I-201 or DMSO

first: Luca

last: Gasparoli

first: Clemence

last: Virely

first: Alexia

last: Tsakaneli

first: Noelia

last: Che

first: Darren

last: Edwards

first: Jack

last: Bartram

first: Mike

last: Hubank

first: Deepali

last: Pal

first: Olaf

last: Heidenreich

middle: H

first: Jasper

last: de Boer

first: Owen

last: Williams


title: Profibrotic subsets of SPP1+ macrophages and POSTN+ fibroblasts contribute to fibrotic scarring in acne keloidalis

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

summary: Acne keloidalis (AK) is a primary scarring alopecia characterized by longstanding inflammation in the scalp leading to keloid-like scar formation and hair loss. Histologically, AK is characterized by mixed leukocytic infiltrates in the acute stage followed by a granulomatous reaction and extensive fibrosis in later stages. To further explore its pathogenesis, bulk RNA-sequencing and single-cell RNA sequencing were applied to scalp biopsy specimens of lesional and adjacent non-lesional skin in patients with clinically active disease. Unbiased clustering revealed 18 distinct cell populations, including two notable populations, POSTN+ fibroblasts with enriched extracellular matrix signatures, and SPP1+ myeloid cells M2 macrophages. Cell communication analyses indicate that fibroblasts and myeloid cells communicate by collagen and SPP1 signaling networks in lesional skin. Tissue immunofluorescence staining demonstrated SPP1+ myeloid cells and POSTN+ fibroblasts at the upper segment of outer root sheath of the hair follicle in the subacute stage, confirming micro-anatomic specificity with relevant disease activity. Therapy with intralesional corticosteroids reduced SPP1 and POSTN expression, and lessened AK progression. In summary, the communication between POSTN+ fibroblasts and SPP1+ myeloid cells by collagen and SPP1 axis may contribute to the pathogenesis of AK.

overall_design:
We conducted droplet-based scRNA-seq (10X Genomics, California, USA) on paired 6 mm punch biopsies of AK lesional skin (n = 1) and adjacent healthy non-lesional skin (n = 1) from an individual patient
Please note that raw data are not available due to patient privacy concerns.

first: Chao-Kai

last: Hsu


title: Detection of internal m7G modification in the human transcriptome in a quantitative manner and at single-nucleotide resolution

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary: RNA modifications play an important role in regulating RNA stability and gene expression, however the development of reliable detection techniques has been a major burden in the field. Here, we describe two different methodologies for global identification of N-7-methylguanosine (m7G) in human tRNAs. An antibody and northdot blot based quantitative approach that allows global detection of m7G levels. And borohydride reduction sequencing (Bo-Seq), a chemically based approach that maps m7G modification at single nucleotide resolution. The specificity of Bo-Seq lies on RNA size-selection, optimized RNA scission using NaBH4, aniline and m7GTPs, and elimination of complex chemical steps or bioinformatic analysis included in similar methods, and reduces the protocol to four days. Bo-Seq and our antibody based approach are specifically developed for easily and globally detect tRNA m7G-methylation in human cells. We also validated METTL1 as the methyltransferase that methylates tRNAs in human cells.

overall_design: Small RNA from prostate cancer cells DU145  were extrated. RNA were either non chemically treated or treated wih NaBH4 and aniline (BH4). Two replicates were used per condition. A total of 4  samples were sequenced.

first: Sandra

last: Blanco

first: Silvia

last: D'Ambrosi

first: Raquel

last: García-Vílchez

first: Sabine

last: Dietmann

middle: M


title: Gene Editing of Gibberellin-Oxidase20 improves plant architecture and drought tolerance in maize

city: Changchun

first: Ziqi

last: Chen

state: Jilin

address: No. 1363, Eco Street

department: Institute of Agricultural Biotechnology

institute: Jilin Academy of Agricultural Sciences

summary: As a major plant abiotic stress, drought stress suppresses crop yield performance severely. However, the trade-off between crop drought tolerance and yield performance becomes a great challenge in drought-resistant crop breeding. Several phytohormones have been reported to participate in plant drought response, including gibberellin (GA), which also plays an important role in plant growth and development. Using CRISPR technology, we constructed the null mutant of ZmGA20ox3, a key enzyme in GA biosynthesis. The null mutant plants show lower plant height and ear height with no yield loss under the normal condition than wild-type plants. Transcriptome analysis revealed that genes affected by ZmGA20ox3 were enriched in signal transduction and stress response processes. In addition to the decrease of GA, a significant increase of ABA and JA level were also detected in mutant plants. Compared with wild-type plants, the growth and ASI of mutant plants were less affected, and the yield loss was also reduced under drought conditions. These results suggest a potential role of ZmGA20ox3 in maize drought response. Our result shows that regulating GA biosynthesis is applicable for maize drought-resistant breeding.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ZmGA20ox3 KO mutant plants and WildType (WT) plants.

first: Yang

last: Liu

first: Xiangguo

first: Yidan

last: Li


title: An in vitro neurogenetics platform   for precision disease modeling in the mouse

city: BAR HARBOR

first: Dan

last: CORTES

state: Maine

address: 600, Mn Str, 600 main st

institute: The Jackson Lab

summary: The mouse is often the model of choice for genetic analysis of neurological disorders, but the introduction of disease mutations into a particular inbred strain sometimes fails to yield phenotypes relevant to human disease.  Interrogating genetically diverse panels of mice can identify better models of human sensitivity and resistance to candidate disease variants. We developed an in vitro methodology for modeling multiple stages of central nervous system development using a panel of genetically diverse mouse embryonic stem cell lines.  Chemical knockdown of the neurodevelopmental gene Dyrk1a demonstrated profound strain differences in the cellular response to the ablation of DYRK1A activity throughout development in vitro.  Responsive strains showed in vitro developmental defects consistent with observations in vivo on Dyrk1a knockout mice, and transcriptomic analysis of sensitive and resistant cell strain backgrounds successfully identified key molecular pathways in neural development known to be associated with Dyrk1a haploinsufficiency in vivo.  Thus we demonstrate that high throughput comparative phenotype analysis of differentiated cells from human and genetically diverse mouse pluripotent stem cells bearing disease mutations can provide a facile route to identification of optimal mouse strains for precision disease modeling in vivo.

overall_design: mESC from C57BL/6J (B6) and WSB/EiJ (WSB) were differentiated into neurons and compared at the neural progenitor stage, neuronal maturation stage and axonal injury stage by bulk-RNAseq

first: Daniel

last: Cortes

first: Martin

last: Pera


title: Genome-wide DNA methylation analysis for cartilage tissues

city: Tokyo

first: Makii

last: Fukami

address: 2-10-1 Okura, Setagaya

department: Department of Molecular Endocrinology

institute: National Research

type: Methylation profiling by high throughput sequencing

summary: We performed reduced representation bisulfite sequencing (RRBS) for cartilage tissues to compare sex differences of DNA methylation status of X chromosomes including the pseudoautosomal region.

overall_design: DNA methylation profiles of cartilage tissues obtained from two men and two women.

first: Atsushi

last: Hattori

first: Kazuhiko

last: Nakabayashi

first: Keisuke

last: Ishiwata

first: Maki


title: Hepatocyte-derived liver progenitor-like cells attenuate liver cirrhosis via induction of apoptosis in hepatic stellate cells

city: Shanghai

first: hexin

last: Yan

address: Pujian Road

institute: Shanghai Reji Hospital

summary: Cell therapy shows great promise as an alternative therapy for the cirrhotic liver. We have previously developed an approach for efficient expansion of both murine and human hepatocyte-derived liver progenitor-like cells (HepLPCs) in vitro without genetic modification. The current study aimed to apply HepLPCs to treatment of liver cirrhosis. The effects of allogeneic HepLPCs transplantation were studied in rat models of liver cirrhosis induced by carbon tetrachloride (CCl4) . Liver tissues were collected and analyzed by RNA sequencing array to analyze changes in histology or gene expression patterns. Transplantation of HepLPCs reduced active fibrogenesis and net fibrosis in model of liver cirrhosis. Apoptosis of hepatic stellate cells (HSCs) was observed in vivo after HepLPCs treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for whole liver samples of control rats (normal) or rats injected with PBS or rat HepLPCs, n=3. Control livers were obtained from animals that received neither CCl4 nor cell transplants.

first: Hexin

first: Xu

last: Zhou


title: Transcriptome analysis for knee cartilage tissues of adults and cultured finger chondrocytes of children

summary: To evaluate sex differences of expression levels of X chromosomal genes, we performed transcriptome analysis for knee cartilage tissues and cultured finger chondrocytes.

overall_design: Microarray-based transcritome analysis was performed for cartilage samples of four adults (two men and two women) and chondrocyte samples of 12 children (six boy and six girls).

first: Kazue

last: Takeda

first: Kenji

last: Matsumoto

first: Kuniko

last: Tatsumi

first: Akihiro

last: Umezawa


title: Exome analyses for RNA and genome DNA of fibroblast single-cell clones

summary: We performed RNA exome sequencing for skin fibroblast single-cell clones along with exome sequencing of genome DNA to detect monoallelically expressed genes.

overall_design: Allele-specific gene expression profiles of four skin fibroblast single-cell clones.


title: Sex-biased and random monoallelic expression of SHOX: implications for sex difference in height

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

overall_design: Refer to individual Series


title: Functionally distinct subset of monocytes in mouse and human blood

city: Boston

first: David

middle: T

last: Scadden

state: MA

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: MGH


title: Studies on the photosynthetic characteristics and mechanism of the upland cotton virescent recessive genic male sterile line Yt30

status: Public on Apr 09 2024

city: nanjing

last: Yang

state: 选择一项...

address: 江苏省南京市卫岗一号南京农业大学

institute: Nanjing Agricultural university

summary: Clarified the relationship between the photosynthetic performance and photosynthetic pigment metabolism of Yt30.

overall_design: We performed transcriptome sequencing using the Virescent mutant (Yt30) and its green wild-type first true leaf.


title: Single-cel RNA-seq of Mouse Olfactory Epithelium for Understanding Age-associated Neuronal Injury Response

city: Berkeley

first: John

last: Ngai

address: Department of Molecular & Cell Biology

institute: University of California, Berkeley

summary: This study aims to identify the molecular basis for age-related decline in olfactory function and regeneration. To extend our characterization of olfactory stem cell regeneration during aging, we performed single-cell RNA sequencing on whole olfactory epithelium (OE) of 2-month-old and 18-month-old mice in uninjured state and at 24 hours after injury.

overall_design: Whole olfactory epithelium cells are FACS-purified via live cell repoter in young and old adult mice under uninjured (UI) and 24 Hours Post Injury (HPI) condition. A minimum of two biological replicates were collected for each time-point/experimental condition.

first: Boying

last: Gong

first: Rebecca

last: Chance

first: Hsin-Jung

last: Chou


title: ABERRANT PANICLE ORGANIZATION2 controls multiple steps in panicle formation through common direct-target genes

first: Yiling

last: Miao

address: Xian Street NO.5333

institute: Jilin University

summary: At the transition from vegetative to reproductive growth in rice, a developmental program change occurs, resulting in panicle (rice inflorescence) formation. The initial event of the transition is the change of the shoot apical meristem (SAM) to an inflorescence meristem (IM), accompanied by a rapid increase in the meristem size. Suppression of leaf growth also occurs, resulting in the formation of bracts. The IM generates branch meristems (BMs), indeterminate meristems that reiteratively generate next-order meristems. All meristems eventually acquire a determinate spikelet meristem identity and terminate after producing a floret. ABERRANT PANICLE ORGANIZATION2 (APO2) is the rice ortholog of Arabidopsis (Arabidopsis thaliana) LEAFY (LFY), a plant-specific transcription factor. APO2 is a positive regulator of panicle branch formation. Here, we show that APO2 is also required to increase the meristem size of the IM and suppress bract outgrowth. We identified genes directly and indirectly regulated by APO2 and identified APO2-binding sites by ChIP-seq analysis. These analyses showed that APO2 directly controls known regulators of panicle development, including SQUAMOSA PROMOTER BINDING PROTEIN LIKE14 and NECK LEAF1. Furthermore, we revealed that a set of genes act as downstream regulators of APO2 in controlling meristem cell proliferation at the reproductive transition, bract suppression, and panicle branch formation. Our findings indicate that APO2 acts as a master regulator of rice panicle development by regulating multiple steps in the reproductive transition through directly controlling a set of genes.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for plant transcription factor ABERRANT PANICLE ORGANIZATION2 (APO2) in rice young infloreacence meristems.


title: Global change of microRNA expression induced by vitamin C treatment on immature boar Sertoli cells

city: jingzhou

first: wu

middle: zi

last: wei

state: Hubei

department: Animal Science

institute: yangtze university

summary: Sertoli cells (SCs), the only somatic constituent of the testicular seminiferous epithelium, are vital to spermatogenesis. We previously found that vitamin C (ascorbic acid, AA) can reprogram the transcriptome, and promote the proliferation and reproductive function of pig immature SCs (iSCs). However, the global change of microRNAs (miRNA) expression and its effect on pig iSCs as induced by vitamin C treatment is still unknown. Here, we performed small RNA sequencing on pig iSCs after 250μM AA2P (L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate) treatment for 36h. Total number of detected miRNAs ranged from 326-335 known, and 400-570 novel miRNAs. Of the top ten highly expressed miRNAs, we found that 8 were common (miR-21-5p, let-7i-5p, miR-30a-5p, let-7f-5p, let-7g, miR-100, miR-10a-5p and miR-30d), which were predicted to target mRNAs involved in cell development and differentiation. We identified 78 differentially expressed (DE) miRNAs (|log2 foldchange|≥1; Padj.<0.05), including 7 known and 71 novel miRNAs. We further selected 13 highly and stably expressed DE miRNAs (4 up-regulated: miR-184, novel-miR-610, novel-miR-316 and novel-miR-1274; 9 down-regulated: miR-222, miR-221-5p, miR-221-3p, miR-210, miR-146b, miR-146a-5p, novel-miR-182, novel-miR-1088 and novel-miR-1016), and performed integrated analysis on the miRNA-mRNA regulatory network. DE mRNAs negatively targeted by these 13 DE miRNAs were enriched in multiple GO and KEGG signaling pathways (e.g. pyruvate and steroid metabolic processes, developmental process in reproduction, response to oxidative stress, Glycolysis/Gluconeogenesis and HIF-1). We validated 8 DE miRNAs and their 12 DE mRNA targets, with expression patterns consistent with (mi)RNA-seq results. Taken together, our findings demonstrate that vitamin C could induce the global change of miRNAs, which possibly regulate cell proliferation, energy metabolism and male reproduction as induced by vitamin C treatment on pig iSCs.

overall_design: The abundantly expressed miRNAs and key DE miRNAs in pig immature Sertoli cells after AA2P-treated

first: Cai-Xia

first: Zhi-Qiang

last: DU


title: Sexual dimorphism in skin immunity is mediated by androgen-ILC2-dendritic cell axis

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH


title: Exogenous and endogenous serine modulate polarization of tumor-associated macrophages to influence development of nasopharyngeal carcinoma

city: Nanchang

first: Yishan

last: Xiong

state: Jiangxi Province

address: 永外正街17号

institute: 南昌大学第一附属医院

summary: To investigate the global gene expression pattern in response to removal of exogenous serine/glycine from the medium, RNA-seq was performed using C666-1 cells cultured in CM or -SG medium for 24 h. The volcano plot exhibited 60 up-regulated and 123 down-regulated genes in C666-1 cells subjected to exogenous serine/glycine deprivation.

overall_design: After C666-1 cells were cultured in complete or serine/glycine deficient medium for 24 h, total RNA was extracted using TRizol reagent and sequenced on the MGISEQ-2000RS platform.

first: Daofeng

last: Dai

first: Jing

last: Ye

first: Ningwu

last: Chen


title: Functionally distinct subset of monocytes in mouse and human blood [RNA-Seq]

summary: Here, we used an inducible and reversible system to pause myeloid differentiation at a self-renewing state. These cells were clonally isolated and allowed to differentiate to test whether function was clone-specific and clonally restricted.  We found that monocytic subsets exist with inherent, restricted capabilities which differ in their capacity to perform traditional monocytic functions.

overall_design: We performed high-throughput RNA-sequencing on both progenitors and monocyte ER-Hoxb8 clones, clonally paired as progenitors and mature cells.


title: Functionally distinct subset of monocytes in mouse and human blood [ATAC-Seq]

overall_design: We performed high-throughput ATAC-sequencing on both progenitors and monocyte ER-Hoxb8 clones, clonally paired as progenitors and mature cells.


title: HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells

city: Wuhan

first: Dong

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: High-mobility group B1 (HMGB1) is both a DNA binding nuclear factor modulating transcription and a crucial cytokine that mediates the response to both infectious and noninfectious inflammation.Recently data show that HMGB1is a RNA-binding protein also affecting splicing.Howerer we still lack understanding of the functional roles of HMGB1 in protein translation.To address theses we  applied Improved RNA immunoprecipitation by UV cross-linking and deep sequencing (iRIP-seq) experiment revealed that HMGB1 selectively bound to mRNAs and structured RNAs. We also integrated RNA-seq data from knockdown and overexpress HMGB1 to show that HMGB1 affected some genes expression. Taken these data together, our findings highlight that HMGB1 binds to multiple RNA species including mRNA and snoRNA

overall_design:
Transcrptional analysis of HMGB1 overexpression and control in Hela cells.
iRIP-seq was performed to assess the RNA-binding properties of HMGB1 in HeLa cell. Two biological replicates (knockdown and overexpress HMGB1) were performed in HeLa cells.

first: Sen

first: Zhihui

last: Jin

first: Zhigang

last: Nie

first: Shuang

last: Deng

first: Hao

last: Peng

first: Ruiqiang

last: Guo

first: Wen

first: Yaxun

last: Wei

first: Yaqiang

last: Xue

first: Yi

last: Zhang

first: Meimei

last: Liao


title: Endogenous Nodal switches Wnt interpretation from posteriorization to germ layer differentiation in geometrically constrained human pluripotent cells

city: Houston

first: Aryeh

last: Warmflash

state: TX

address: 6100 Main St

institute: Rice University

summary: We conducted bulk RNA sequencing on cells sorted by fluorescence from micropatterned colonies treated with FGF8 and different concentrations of WNT3a, using a SOX2::mCitrine cell line to distinguish between SOX2 positive and negative cells. The sequencing revealed that SOX2 negative cells exhibited a definitive endoderm identity, while SOX2 positive cells showed epiblast identity.

overall_design: SOX2::mCitrine cells were seeded into 4 separate micropattern glass coverslips CYTOO: (1) Control consisting of colonies in N2B27 medium only, (2) Colonies treated with FGF8 (200 ng/ml) with WNT3a (100 ng/ml), (3) Colonies treated with FGF8 (200 ng/ml) with WNT3a (300 ng/ml), and (4) Colonies treated with FGF8 (200 ng/ml) with WNT3a (1000 ng/ml); all for 3 days. Colonies were dissociated into single-cell suspensions using Accutase at 37ºC for 5 minutes. Cells were collected, centrifuged at 1000 rpm for 4 minutes, and re-suspended in PBS-EDTA (10 mM). Cells were then filtered through a 5ml Polystyrene Round-Bottom tube with cell-strainer mesh 40um cap (FALCON). A Sony SH800S Cell Sorter with a 488 nm laser was used to separate the SOX2 positive cells from the negative ones. RNA was collected with the Invitrogen RNAqueous-Micro Total RNA Isolation Kit. Sequencing was performed by Novogene Co. using the Illumina paired-end 150 platform (Novaseq 6000). Another biological repeat of all conditions except (3) was performed using the same protocol.

first: Miguel

last: Ortiz-Salazar

first: Elena

last: Camacho-Aguilar


title: Co-existence of CBB cycle and rTCA carbon fixation pathway in thermophilic Actinomycetota Carbonactinospora thermoautotrophica StC and correlation with the CO2-concentrating microcompartment

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

country: Brazil

institute: UFRJ

summary: Seven carbon autotrophic fixation pathways were described so far. However, it is not common to find the co-existence of more than one cycle in a single cell. Here, we describe a thermophilic bacterium Carbonactinospora thermoautotrophica StC with a unique and versatile carbon metabolism. StC was isolated from a consortium found in a burning organic pile that exhibits an optimal growth temperature between 55° and 65° C. The genome analyses suggested that the strain StC potentially performs two-carbon fixation pathways, Calvin-Benson-Bassham (CBB) cycle and the Reductive citrate cycle (rTCA) and preserve a microcompartment related with CO2 concentration. To better understand the carbon fixation in StC strain, the expression of the genes of bacterial cells grown autotrophically and heterotrophically were analyzed. For our surprise the data showed the co-existing of the both carbon fixation pathways - CBB and rTCA cycles - in a cultivable thermophilic chemoautotrophic bacterium Carbonactinospora thermoautotrophica strain StC, based on integrated omics of genomics, transcriptomics, and proteomics. These two cycles working together may help microorganisms to improve the CO2 fixation.  The knowledge about the co-occurrence of carbon cycle in a single cell leads open a question ‘why microorganisms use multiple pathways to fix carbon and what the advantage for this strategy?’. Advancing on this is a key to better understand the biological carbon fixation mechanism in thermophiles and prospecting the repurposing of enzymes in synthetic biology for biotechnological applications.

overall_design: The cells of Carbonactinospora thermoautotrophica strain StC were grown for four days at 60 °C under three different conditions: i) autotrophically in a N-FIX solid culture medium with a gas atmosphere (CO/CO2/N2/O2); ii) heterotrophically in R2A culture medium (glucose and peptone as carbon and nitrogen source respectively) solidified with Noble Ágar (Sigma-Aldrich) and iii)  N-FIX solid culture medium with a gas atmosphere (CO/CO2/) + NH4Cl2. The experiment was conducted in quadruplicate, and RNA  was extracted using NucleoSpin TriPrep kit (Macherey-Nagel) with some modifications, as follows: 480 µL of 0.5M EDTA and 120 µL of lysozyme (100 mg/mL) were used to lyse the bacterium cells by incubating at 37 °C for 30 minutes, followed by FastPrep grind and homogenization (MP Biomedicals). Total RNA was then purified with the Ambion’s Dnase Treatment Kit (Thermo Fisher Scientific) and quantified by spectrophotometry, using NanoDrop 2000 (Thermo Fisher Scientific) and Qubit® dsDNA HS Assay Kit (Thermo Fisher Scientific).

first: Sulamita

last: Santos Correa

first: Alexandre

last: Soares Rosado

first: Júnia

last: Schultz


title: Sexual dimorphism in skin immunity is mediated by androgen-ILC2-dendritic cell axis [scRNA-seq]

first: Verena

last: Link

summary: Males and females exhibit profound differences in immune responses and disease susceptibility. However, the factors responsible for sex differences in tissue immunity remain poorly understood. Here, we uncover a dominant role for type 2 innate lymphoid cells (ILC2) in shaping sexual immune dimorphism within the skin. Mechanistically, negative regulation of ILC2 by androgens leads to a reduction in dendritic cell (DC) accumulation and activation in males, and reduced tissue immunity. Collectively, this work uncovers an androgen-ILC2-DC axis in controlling sexual immune dimorphism. Moreover, this work proposes that tissue immune set-points are defined by the dual action of sex hormones and the microbiota, with sex hormones controlling the strength of local immunity and microbiota calibrating its tone.

overall_design: 5' single cell RNA-seq from T cells and dendritic cells from male and female mice following control or S. epidermidis treatment. Different treatments were labeled using BioLegend TotalSeq antibodies. DC and T cell libraries were loaded on two 10X Genomics lanes (lane1 and lane2).

first: Yasmine

last: Belkaid

first: Liang

last: Chi


title: Sexual dimorphism in skin immunity is mediated by androgen-ILC2-dendritic cell axis [Bulk RNA-seq]

overall_design: Bulk RNA-seq from skin keratinocytes of male and female mice in either control or S. epidermidides treated conditions.


title: T&T-seq Reveals Impaired Translation Regulation Abilities of POI-associated EIF4ENIF1 Mutations

city: Beijing

first: Yuxi

last: Ding

address: D110, Medical Building, 30 Shuangqing Road

institute: Tsinghua University

summary: Premature Ovarian Insufficiency (POI) refers to the decline and stagnation of ovarian function in women before the age of 40.POI-associated EIF4ENIF1 mutations and the distribution of functional domains in the EIF4ENIF1 protein have been separately described. However, not all the clinically observed EIF4ENIF1 mutations in POI cases fall in clearly defined functional domains of the EIF4ENIF1 protein. Herein, we introduce T&T seq as a new evaluation tool to sensitively measure the translation regulation capacities of EIF4ENIF1 proteins with clinically discovered mutations. The sequencing results showed that POI-associated EIF4ENIF1 mutations impaired its translation repression function to different degrees.

overall_design: We employed T&T-seq, a translation-transcription dual-omic sequencing method in which actively translating mRNAs were captured by affinity beads, to examine the transcriptional and translational states in 293FT cell lines upon the overexpression of wild-type and mutated EIF4ENIF1 proteins. For the first experiment, Flag-tagged EIF4ENIF1 WT, Q842P, (1-684) truncation proteins were overexpressed in 293FT cells and the transcriptional-translational gene expression states were compared to that of 293FT cells transfected with empty vector plasmids. For the second experiment, EIF4ENIF1 WT, R208H and GFP proteins were simultaneously overexpressed in 293FT cells and the transcriptomes and translatomes were compared.

first: Lin

last: Li

first: Kehkooi

last: Kee


title: TSG-6 mediated extracellular matrix modifications regulate hypoxic-ischemic brain injury

city: Portland

first: Taasin

last: Srivastava

address: 3181 SW Sam Jackson Park Road

department: Pediatrics

institute: Oregon Health & Science University

summary: Proteoglycans containing link-domains modify the extracellular matrix (ECM) to regulate cellular homeostasis and can also sensitize tissues/organs to injury and stress. Hypoxic-Ischemic (H-I) injury disrupts cellular homeostasis by activating inflammation and attenuating regeneration and repair pathways. In the brain, the main component of the ECM is the glycosaminoglycan (GAG), Hyaluronic Acid (HA), but whether HA modifications of the ECM regulate cellular homeostasis and response to H-I injury is not known. In this report, employing both male and female mice, we demonstrate that link-domain containing proteoglycan, TNF-stimulated gene-6 (TSG-6), is active in the brain from birth onwards and differentially modifies ECM HA during discrete neurodevelopmental windows. ECM HA modification by TSG-6 enables it to serve as a developmental switch to regulate activity of the Hippo pathway effector protein, Yes Associated Protein 1 (YAP1) in the maturing brain and in response to H-I injury. Mice that lack TSG-6 expression display dysregulated expression of YAP1 targets, excitatory amino acid transporter 1 (EAAT1; GLAST) and 2 (EAAT2; GLT-1). Dysregulation of YAP1 activation in TSG-6-/- mice coincides with age- and sex-dependent sensitization of the brain to H-I injury such that 1-week-old neonates display an anti-inflammatory response in contrast to an enhanced pro-inflammatory injury reaction in 3-month-old adult males but not females. Our findings thus support that a key regulator of age- and sex-dependent H-I injury response in the mouse brain is modulation of the Hippo-YAP1 pathway by TSG-6 dependent ECM modifications.

overall_design: Forebrain slice cultures were prepared from postnatal day 4 TSG-6+/+ aand TSG-6-/- mouse pups. Level matched slices were exposed to 5% Horse serum containing HBSS media. After 4 hours of treatment, the slices were processed for total RNA extraction using Qiagen RNAeasy kits. The resulting RNA was analyzed by BioAnalyzer and all preps were designated with a RIN >9. We prepared cDNA libraries using Smart Seq V4 chemistry (Takara) and sequenced the libraries on an HiSeq 2500 (Illumina). We then performed gene expression profiling analysis using the RNA-seq datasets of the 6 samples (3 WT replicates and 3 KO replicates).

first: Stephen

last: Back


title: Chemotherapy induces cell plasticity; controlling plasticity increases therapeutic response.

city: Valencia

first: Francisco

middle: José

last: Iborra

state: Valencia

address: C/ JAIME ROIG, 11

institute: Instituto de Biomedicina de Valencia (CSIC)

summary:
One of the most serious issues in modern oncology is the ineffectiveness of treatments in destroying tumours, which leads to tumour recurrence and, ultimately, patient death
To investigated this we analyze plasticity of chemotherapy-resistant cells

overall_design: Gene expression profiling analysis of RNA-seq data for HeLa control cells versus Hela cells treated 24 hours with TRAIL (30 ng/ml), Camptothecin (10 µM) or Doxorrubicin  (2 µM).

middle: J

first: Cristina

last: Marti

first: Virtu

last: Calabuig-Navarro

first: Petros

last: Papadopoulos

first: Salvador

last: Mesegue

first: Pedro

last: García

first: Ana

last: Calatrava

first: Antonio

last: Martínez-Lorente

first: Fernando

last: Almazán

first: Juana

last: Calabuig


title: Ecological Adaptability and Response Mechanism to Salt Stress of Wild Apocynum venetum

city: Hohhot

first: xi

last: zhen

address: Genghis Khan Street

institute: College of Grassland Resources and Environment, Inner Mongolia Agricultural University

summary: We selected wild A. venetum of four distributed regions (jinta county, minqin county, hangjinqi and baicheng) as the test materials in the study. Based on the study of community composition, population genetic diversity and soil environmental properties of wild A. venetum, physiological characteristics, transcriptomics and proteomics analysis of A. venetum under salt stress, and key regulatory proteins and genes of A. venetum salt tolerance were measured and identified to reveal the ecological adaptability of wild A. venetum and underlying mechanisms in response to salt stress. The study is beneficial to promote the protection and rational development and utilization of germplasm resources of wild A. venetum, and is of great significance to the development of national pharmacology and the construction of ecological civilization in China.

overall_design: In this study, 18 well-growing wild P. apocinae seedlings were selected and divided into two groups of salt stress treatment group and control group, each treatment was repeated 3 times. 300 mmol/L was selected as the stress concentration for transcriptome test. The test group of P. apocynum plants were carefully washed in pure water, and then transferred to the configured stress nutrient solution (containing 300 mmol/L NaCl). The control plants were washed and transferred to a new nacl-free nutrient solution. At 0 h, 2 h, 6 h, 12 h, 24 h and 48 h stress, Apocynum japonicum leaves were taken and quickly put into the frozen tube for liquid nitrogen deep freezing, and then the samples were stored in the refrigerator at -80℃ for reserve.

first: Xi

last: Zhen

first: Tao

last: Wan


title: ChIP-seq analysis reveals key target genes of TCF on HUVECs

first: yanru

last: duan

state: Beijing

address: Beijing, Chaoyang

institute: Capital Medical University

summary: Our research is helpful to understand the physiological and pathological level changes of endothelial cells caused by diabetes.

overall_design: In this study, the control group and the model group were subjected to ChIP sequencing.

first: Duan

last: Yanru


title: Resistance to PRMT5-targeted therapy in mantle cell lymphoma

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

summary: Mantle cell lymphoma (MCL) is an incurable B-cell non-Hodgkin lymphoma, and patients who relapse on targeted therapies have poor prognosis. Protein arginine methyltransferase 5 (PRMT5), an enzyme essential for B-cell transformation, drives multiple oncogenic pathways and is overexpressed in MCL. Despite the antitumor activity of PRMT5 inhibition (PRT-382/PRT-808), drug resistance was observed in a patient-derived xenograft (PDX) MCL model. Decreased survival of mice engrafted with these PRMT5 inhibitor-resistant cells vs treatment-naive cells was observed (P = .005). MCL cell lines showed variable sensitivity to PRMT5 inhibition. Using PRT-382, cell lines were classified as sensitive (n = 4; 50% inhibitory concentration [IC50], 20-140 nM) or primary resistant (n = 4; 340-1650 nM). Prolonged culture of sensitive MCL lines with drug escalation produced PRMT5 inhibitor-resistant cell lines (n = 4; 200-500 nM). This resistant phenotype persisted after prolonged culture in the absence of drug and was observed with PRT-808. In the resistant PDX and cell line models, symmetric dimethylarginine reduction was achieved at the original PRMT5 inhibitor IC50, suggesting activation of alternative resistance pathways. Bulk RNA sequencing of resistant cell lines and PDX relative to sensitive or short-term-treated cells, respectively, highlighted shared upregulation of multiple pathways including mechanistic target of rapamycin kinase [mTOR] signaling (P < 10-5 and z score > 0.3 or < 0.3). Single-cell RNA sequencing analysis demonstrated a strong shift in global gene expression, with upregulation of mTOR signaling in resistant PDX MCL samples. Targeted blockade of mTORC1 with temsirolimus overcame the PRMT5 inhibitor-resistant phenotype, displayed therapeutic synergy in resistant MCL cell lines, and improved survival of a resistant PDX.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single splenocytes were isolated using the 10X Genomics 5' Immune profiling kit.

first: Mackenzie

last: Long

first: Shirsha

last: Koirala

first: Shelby

last: Sloan

first: Fiona

last: Brown-Burke

first: Christoph

last: Weigel

first: Lynda

last: Villagomez

first: Kara

last: Corps

first: Archisa

last: Sharma

first: Ian

last: Hout

first: Margaret

last: Harper

first: JoBeth

last: Helmig-Mason

first: Sheetal

last: Tallada

first: Zhengming

last: Chen

first: Peggy

last: Scherle

first: Kris

last: Vaddi

first: Selina

last: Chen-Kiang

first: Maurizio

last: Di Liberto

first: Cem

last: Meydan

first: Jonathan

last: Foox

first: Daniel

last: Butler

first: Christopher

last: Mason

first: Lapo

last: Alinari

middle: W

first: Robert

last: Baiocchi