title: Effect of FTO-KD or FTO-OE on gene expression in GH3 cell line

city: Guangzhou

first: Zhixiang

last: Zuo

address: No. 651 Dongfeng Dong road

department: Cancer Center

institute: Sun Yat-sen University

summary: Growth hormone-secreting pituitary adenomas account for approximately 10% of endocrine pituitary tumors and are pathologically classified into densely granulated adenomas (DGGH) and sparsely granulated adenomas (SGGH). m6A has been reported to play an important role in tumorigenesis and development, but its potential role in the pathogenesis of these two subtypes has not yet been thoroughly investigated. Consequently, we performed MeRIP-seq analysis of pituitary adenomas and the GH3 cell line. We observed that the expression of FTO was significantly increased in SGGH, leading to a reduction in m6A modification and a disruption of desmosome organization.

overall_design: To explore the effect of FTO on gene expression and m6A modification, we established FTO-KD and FTO-OE GH3 cell lines.

first: Xiaobing

last: Jiang


title: L.J. could rescure the adverse effects induced by busulfan on the kidney

status: Public on Sep 25 2024

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

type: Expression profiling by high throughput sequencing

summary: We report the side-effects of busulfan on the kidney, and foud that the L.J. could rescure the side-effect of busulfan in many factors,such as lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged kidney induced by busulfan

first: Y

last: Hao


title: Adipose-derived mesenchymal stem cells overexpressing thrombomodulin reduce thrombogenic risk and enhance therapeutic efficacy

status: Public on Sep 24 2024

city: Hiroshima

first: Yoshiki

last: Tanaka

address: 1-2-3 Kasumi, Minami-ku

department: Department of Nephrology

country: Japan

institute: Hiroshima University Hospital

summary: Adipose-derived mesenchymal stem cells (ASCs) are expected to be a new therapy to prevent progression of renal fibrosis; however, they were reported to have procoagulant activity, raising concerns about thrombogenic risk. Thrombomodulin (TM) acts as an anticoagulant factor by binding to thrombin, leading to the hypothesis that ASCs overexpressing TM (TM-ASCs) could be safely used for cell therapy by reducing the risk of thromboembolism. Overexpression of TM using adeno-associated virus (AAV) reduced rat deaths related to renal infarction and pulmonary embolism induced by ASCs. Interestingly, TM-ASCs alleviated renal inflammation and fibrosis potently in ischemia-reperfusion injury (IRI) rats. The therapeutic mechanism of TM-ASCs involved increased prostaglandin E2 (PGE2) secretion, a shift in the macrophage phenotype to immunosuppressive M2 in vitro, and potent M2 macrophage polarization in the damaged areas in vivo. We produced ASCs with enhanced TM expression by pretreatment with a selective inhibitory kappa-B kinase-β (IKKβ) inhibitor. These ASCs also improved thrombotic mortality and markedly attenuated renal fibrosis induced by IRI, similar to TM-ASCs generated by AAV. ASCs with enhanced TM expression by IKKβ also increased PGE2 secretion, leading to a more pronounced polarization of M2 macrophages. Taken together, ASCs with enhanced TM expression eliminated the risk of thrombosis and reinforced therapeutic efficacy. These ASCs might become a standard cellular therapy for renal fibrosis via the intravascular injection of mesenchymal stem cells in the future.

overall_design: To investigate changes in the gene expression of adipose-derived mesenchymal stem cells upon an inhibitory kappa-B kinase-β (IKKβ) inhibitor (BMS-345541) stimulation.

first: Ayumu

last: Nakashima

first: Naoki

last: Ishiuchi


title: Comparative transcriptomic analyses reveal genetic factors underlying susceptibility of largemouth bass to transport stress

city: Wuhan

last: Long

address: No. 7 Donghu South Rd.

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: Live fish transport often results in mass mortality, but the underlying mechanisms are not well known. Largemouth bass (LMB, Micropterus salmoides) juveniles were subjected to 4-hour transportation followed by 5 days of recovery. Mortality (33.61 ± 10.58 %) of the transported fish mainly occurred between 2 and 3 days of recovery. Except for the dead fish, the survivors demonstrating abnormal symptoms were considered more sensitive to the transport stress than the normal ones. Liver of the abnormal fish had significantly (p < 0.05) lower glutathione (GSH) content and superoxide dismutase (SOD) activity, and irregular cellular morphology. The liver and spleen collected before transportation (T0), at the end of transportation (Te), after 1 day of recovery (R1d), and after 3, 4 and 5 days of recovery (R3d, R4d and R5d, from both the normal and abnormal fish) were subjected to RNA-sequencing. Time series gene expression data of the T0, Te, R1d, R3d-R5d (from the normal fish) samples were analyzed to explore transcriptional responses elicited by the transport stress. Transportation-activated transcriptional regulations could be classified as immediate response (Te), and early (R1d) and late recovery (R3d to R5d) phase in both tissues. High tissue specificity was found for functional enrichments of the up-regulated genes. The up-regulated genes of the liver are highly enriched in cholesterol, sterol and steroid biosynthesis, while those of the spleen are primarily associated with hemopoiesis and immune response. However, large numbers of functional enrichments were shared by the down-regulated genes of the liver and spleen, especially during the recovery phase. Representatives of the depressed processes included neurogenesis, angiogenesis and cell migration, etc. Moreover, large numbers of differentially expressed genes (DEGs) were identified between the normal and abnormal fish. Functional enrichment analyses for the DEGs revealed that failing to terminate the stress responses in the spleen and over depression of the physiological roles of the liver are critical for stress susceptibility of the abnormal fish. Furthermore, an array of core genes associated with stress susceptibility were identified. Our data provide novel insights into the genetic factors underlying susceptibility of LMB to the transport stress.

overall_design: Sampling was performed before transportation (immediately after being netted from the pond, T0), at the end of transportation (Te), and after 1, 3, 4 and 5 d of recovery (R1d, R3d, R4d and R5d). At R3d, R4d and R5d, both normal (NO) and abnormal (AB) fish were sampled. The fish were dissected after being euthanized by immersion in 250 mg/L MS-222. After dissection, the liver (L) and spleen (S) tissues were collected individually. In total, 18 treatment groups and 68 samples were included in the study.

first: Guili

last: Song

first: Yi

last: Chen

first: Jun

last: Xiao

first: Leyang

last: Peng

first: Hui

last: Qiao

first: Shuning

last: Liu

first: Cheng

last: Luo


title: A single-nucleus census of immune and non-immune cell types for the major immune organ systems of chicken

city: Columbia

first: Rachel

middle: Ann

last: Carroll

state: MO

address: 1201 Rollins St.

department: Bond Life Science Center

country: USA

institute: University of Missouri

summary: In the avian host, comprehensively cataloging immune cell types, their transcriptome profiles, and varying molecular responses to pathogen challenges are necessary steps toward a better understanding of the interplay between genetics and disease resilience. We present a first nuclei atlas of immune cell types derived from the three main immune organs of layer chickens, including spleen, bursa, and thymus. In bursa we also present, an accounting of cell type activation with the bacterial toxin lipopolysaccharide (LPS). Our analysis includes 36,370 total nuclei and 16, 12, and 12 transcriptionally distinct clusters for spleen, bursa, and thymus, respectively. We discover nuclei molecular profiles that uniquely distinguish states of the transcriptome within cell type that could serve as new means to characterize avian immune subtypes. We further subcluster refined immune cell type classifications, specifically highlighting the transcriptomic diversity of B and T cell subtypes. In the bursa, inferred intercellular communication and signaling pathway enrichment analyses across immune and non-immune cell types demonstrate the unappreciated complexity of the B cell repertoire in a model mimicking systemic bacterial infection. This census of all cell types in both primary and one major secondary avian immune organ system, although preliminary, provides a first review of how nuclei transcribe numerous genes, known and unknown, a critical prerequisite for the study avian immunogenetics by cell type.

overall_design: We used the Singulator2 instrument per manufacturer’s protocols (S2 Genomics; Livermore, CA) with storage buffers containing 0.4U/ul RNase inhibitor (source), prior to microfluidic encapsulation on the 10X Chromium instrument (10x Genomics®, Pleasanton, CA) to nanoliter-scale Gel bead-in-EMulsions (GEMs). Single-nuclei libraries were generated using the GemCode Single-Cell Instrument and Single Cell 3′ Library and Gel Bead Kit v3 and Chip Kit (10x Genomics®, Pleasanton, CA) according to the manufacturer’s protocol. Before sequencing, every library was analyzed on a Bioanalyzer high sensitivity chip to ensure the expected cDNA fragment size distribution was achieved. The appropriate number of individually barcoded GEM libraries were pooled and sequenced on a NovaSeq 6000 instrument (Illumina) with 2×150bp length using these sequencing parameters: 26 bp read 1 – 8 bp index 1 (i7) – 98 bp read 2 with 200 cycles.

first: Elaina

middle: R

last: Sculley

first: Wesley

middle: C

last: Warren

first: Edward

middle: S

last: Rice

first: Jacqueline

last: Smith

first: Jim

last: Kaufman

first: John

last: Driver

first: Yvonne

last: Dreschler

first: Hans

last: Cheng

first: Cari

last: Hearn

first: Melissa

last: Monson

first: Paula

first: Susan

last: Lamont

first: Skyler

middle: T

last: Kramer

middle: A


title: ATAC-seq for C42B treated with SR8278 or OE NR1D1; Lucap35CR treated with SR8278

city: Sacramento

first: yatian

last: yang

state: CA

institute: UC Davis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide measurements of chromatin accessibility in prostate cancer cells to study the tumorigenic programs.

first: Yatian

last: Yang

first: Xiong

last: Zhang

first: Demin

last: Cai

first: Hong-wu

last: Chen


title: mRNA level comparison of control and IPF

city: minneappolis

first: LiBang

state: MN

address: 420 delaware st

department: medicine

institute: University of minnesota

summary: In order to distinguish difference between control and IPF, primary cell lines were used to extract mRNA and the RNAseq was conducted. Some genes related to fibrosis were higher in IPF samples.

overall_design: 5 each of control and IPF cell lines were cultured and used in RNAseq. Qiagen mRNA extraction kit was used.

first: Libang

first: Adam

last: Gilbertsen

first: Craig

last: Henke


title: Exploring the Landscape of Microproteins in T Cells: Insights Gained from Nascent Protein Profiling and Global Proteomics Approaches

city: Hong Kong

first: Qian

last: Zhao

state: Hong Kong

address: Room Y1125, Block Y, The Hong Kong Polytechnic University Lee Shau Kee Building, Yuk Choi Rd, Hung Hom

department: ABCT

institute: The Hong Kong Polytechnic University

summary: Microproteins, as hidden players in the proteomic club, are encoded by small open reading frames (sORFs) and have garnered increasing attention in recent years. T cells play a critical role in the immune system's response to cancer, however, the exploration of novel microproteins in T cells remains an unexplored area. In this study, we employed an integrated approach combined nascent protein profiling and quantitative global proteomics to identify novel microproteins in human T cells.

overall_design: In brief, we isolated CD3+ T cells from human peripheral blood mononuclear cells (PBMCs). T cell activation was performed either with phorbol PMA 25 ng/mL and Iono 1 μg/mL or with anti-CD3/CD28-coated microbeads (ThermoFisher Scientific, #11161D) at a bead to cell ratio of 1: 1, at 37 °C with 5% CO2 for 24 hours. Then RNA-Seq data were acquired for inactivated T cells, activated T cells with PMA/Iono treatment, and activated T cells with anti-CD3/CD28 stimulate.

first: Yang

first: Kecheng

last: Li


title: Effect of TDP-43 and FUS silencing on gene expression of inmortalised human myoblast 8220 cell line

city: San Sebastian

first: Lorea

last: Blazquez

address: Dr Begiristain

country: Spain

institute: Biogipuzkoa Health Research Institute

summary: To investigate the effects on human muscle precursor cells of a loss of function of Mendelian genes related to familial ALS, such as TARDBP (TDP-43) or FUS, we established human inmortalised myoblast cell lines in which each target gene has been transiently knocked down (KD) by shRNA.

overall_design: Differencial gene expression analysis of RNA-seq data for inmortalised human myoblast 8220 cell line and its KD derivatives (shTDP-43, shFUS).  The used plasmids were: SHC001: shRNA Empty Vector Control Plasmid DNA, TRCN000016038: human, TARDBP MISSION shRNA, TRCN0000288639: human, FUS MISSION shRNA, (all from Sigma-Aldrich)).

first: Mónica

last: Zufiría

first: Oihane

last: Pikatza-Menoio

first: Xabier

last: Bengoetxea

first: Maddi

last: Garciandia

first: Olatz

last: Arnold-García

last: Blázquez

first: Adolfo

last: López de Munain

first: Sonia

last: Alonso-Martín

first: Francisco

last: Gil-Bea


title: Transfer of mitochondrial DNA into the nuclear genome during induced DNA breaks [c.MYC_DdCBE_ND4_TREX]

city: Beijing

first: Jinchun

last: Wu

address: No. 5, Yiheyuan street

institute: Peking University

summary: Mitochondria serve as the cellular powerhouse, and their distinct DNA makes them a prospective target for gene editing to treat genetic disorders. However, the impact of genome editing on mitochondrial DNA (mtDNA) stability remains a mystery. Our study reveals previously unknown risks of genome editing that both nuclear and mitochondrial editing cause discernible transfer of mitochondrial DNA segments into the nuclear genome in various cell types including human cell lines, primary T cells, and mouse embryos. Furthermore, drug-induced mitochondrial stresses and mtDNA breaks exacerbate this transfer of mtDNA into the nuclear genome. Notably, we observe that mitochondrial editors, including mitoTALEN and recently developed base editor DdCBE, can also enhance crosstalk between mtDNA and the nuclear genome. Moreover, we provide a practical solution by co-expressing TREX1 or TREX2 exonucleases during DdCBE editing. These findings imply genome instability of mitochondria during induced DNA breaks and explain the origins of mitochondrial-nuclear DNA segments.

overall_design: We employed primer-extension-mediated sequencing (PEM-seq) to study the level of mitochondrial DNA integration into the nuclear genome caused by genome editing.

last: Liu

first: Liqiong

last: Ou

first: Tingting

last: Gan

first: Zhengrong

last: Zhangding

first: Shaopeng

last: Yuan

first: Xinyi

first: Mengzhu

first: Jiasheng

first: Jianhang

last: Yin

first: Changchang

last: Xin

first: Ye

last: Tian

first: Jiazhi

last: Hu


title: Transfer of mitochondrial DNA into the nuclear genome during induced DNA breaks [DdCBE_ND4_TREX]

first: Yang

last: Li


title: Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [scRNA-Seq]

city: South San Francisco

first: J

middle: Graham

last: Ruby

state: California

address: 1170 Veterans Blvd

institute: Calico Life Sciences

summary: Finite replicative potential is a defining feature of non-transformed somatic cells, first established by Leonard Hayflick in vitro using WI-38 human lung fibroblasts. Once proliferative capacity is exhausted due to telomere shortening, cells enter into a state called replicative senescence, which can be avoided through ectopic expression of telomerase reverse transcriptase (hTERT). As WI-38 cells approach replicative arrest, molecular pathways linked to mechanotransduction are induced, including YAP signaling, but the potential interplay between replicative lifespan and the mechanical environment of the cell remains unexplored. Here, we investigate the influence of mechanosensation on the trajectory towards replicative arrest taken by WI-38 cells by growing cells on substrates of varying stiffnesses. Matrix softening slowed proliferation, altered cellular phenotypes, and shortened proliferative lifespan while hTERT expression abrogated or reduced these responses. Our analyses of bulk and single-cell RNA-sequencing and ATAC-sequencing revealed the emergence of a unique G1 transcriptional state on soft substrates, characterized by an AP-1 transcription factor program, which failed to manifest with hTERT expression. Together, these findings reveal how the mechanical environment alters WI-38 cell proliferative lifespan and dictates unique paths towards growth arrest.

overall_design: Human fetal lung cells in culture were analyzed by scRNA-seq. See README file for samples information.

first: Alyssa

middle: M

last: Kaiser

middle: G


title: Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [RNA-Seq 2]

overall_design: Human fetal lung cells in culture were analyzed by RNA-seq


title: Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [RNA-Seq 1]


title: Neoadjuvant anti-PD1 immunotherapy for surgically accessible recurrent glioblastoma: clinical and molecular outcomes of a stage 2 single-arm expansion cohort

city: Los Angeles

first: Lu

last: Sun

address: 10833 Le Conte Avenue

institute: University of California, LA

summary: Glioblastoma is immunologically “cold” and resistant to single-agent immune-checkpoint inhibitors (ICI). Our previous study of neoadjuvant pembrolizumab in surgically-accessible recurrent glioblastoma identified a molecular signature of response to ICI and suggested that neoadjuvant pembrolizumab may improve survival. To increase the power of this observation, we performed bulk-RNA seq on resected tumor tissue in an additional 25 patients with surgically-accessible recurrent glioblastoma.  Neoadjuvant pembrolizumab was associated with suppression of cell cycle/cancer proliferation genes and upregulation of T-cell/interferon-related gene expression. This signature was unique to patients treated with neoadjuvant pembrolizumab and was an independent risk factor for survival. Our results demonstrate a clear pharmacodynamic effect of anti-PD1 therapy in glioblastoma and identify pathways that may mediate resistance. However, we did not confirm a survival benefit to neoadjuvant pembrolizumab in recurrent glioblastoma.  Our new data suggests some patients may exhibit innate resistance to pre-surgical ICI and require other concomitant therapies to sensitize effectively.

overall_design: Total RNA was extracted from the resected tumor specimens of patients enrolled in the neoadjuvant expansion cohort who received pembrolizumab. The extracted RNA was then sent for RNA sequencing.

last: McFaline-Figueroa

first: Yu

last: Qiao

first: Gilbert

last: Youssef

first: Gang

first: Jiyoon

last: Kim

first: Eudocia

last: Lee

first: Lakshmi

last: Nayak

first: Ugonma

last: Chukwueke

first: Rameen

last: Beroukhim

first: Tracy

last: Batchelor

first: E

last: Chiocca

first: Lisa

last: Doherty

first: Jennifer

last: Stefanik

first: Kathryn

last: Partridge

first: Amanda

last: Spearman

first: Alexa

last: Myers

first: Catharina

last: Westergaard

last: Russ

first: Maria

last: Lavallee

first: Anna

last: Smokovich

first: Corey

last: LaForest-Roys

first: Rachel

last: Fox Garcia

first: Christine

last: McCluskey

first: Wenya

middle: L

last: Bi

first: Omar

last: Arnaout

first: PierPaolo

last: Peruzzi

first: G

last: Cosgrove

first: Keith

last: Ligon

first: Isabel

last: Arrillaga-Romany

last: Clarke

first: David

last: Reardon

first: Timothy

middle: F

last: Cloughesy

first: Robert

last: Prins

first: Patrick

middle: Y

last: Wen


title: Circulating immune cells from early- and late-onset preeclampsia displays distinct profiles with differential impact on endothelial activation

city: Rochester

first: Sylvie

last: Girard

state: Minnesota

address: 200 First Street

institute: Mayo Clinic

summary: Preeclampsia (PE) affects 5-8% of pregnancies and has detrimental effects on maternal-fetal health. PE is characterized by de novo hypertension after 20 weeks of gestation and end-organ damage. Systemic inflammatory imbalance has been associated with PE, but its contribution to the pathology is poorly understood. Our objective was to investigate maternal systemic immune changes in early-onset PE (EOPE) and late-onset PE (LOPE) vs uncomplicated pregnancies (CTRL), and their contribution to endothelial activation, hallmark of hypertension. Blood samples were analyzed by flow cytometry, multiplex assay, intracellular cytokine staining (ICS), and single-cell RNA sequencing. We performed co-cultures between circulating immune cells and human umbilical veins endothelial cells (HUVECs) to assess endothelial activation. We found that EOPE had decreased Treg (4.64±0.33, p<0.05) and monocytes (33.92±3.08, p<0.01), whereas LOPE had decreased Treg (4.60±0.30, p<0.05) and Th2 cells (7.50±0.62, p<0.01) vs CTRL. Compared to CTRL, elevated cytokines/chemokines, and growth factors were observed in LOPE, whereas EOPE primarily showed decreased levels. Using ICS, we observed more monocytes producing IL-12, TNF, and IL-1 (all p<0.05) in LOPE vs CTRL. At the transcriptomic level, we found differentially expressed genes (DEGs) between EOPE and CTRL, predominantly related to upregulation of immune activation pathways. Lastly, EOPE peripheral blood mononuclear cells (PBMCs) induced heightened endothelial activation in vitro observed by increased ICAM-1 and ET-1 (p<0.05), whereas LOPE PBMCs required LPS stimulation. While significant proteomic changes are observed in the LOPE group, the EOPE displayed changes mostly at the transcriptomic levels and could induce endothelial activation in vitro.

overall_design: Peripheral blood mononuclear cells (PBMC) were isolated from patients blood and analyzed using scRNAseq

first: Elsa

last: Bernier

first: Camille

last: Couture

last: Borchers

first: Marie-Eve

last: Brien

first: Charles

middle: H

last: Graham


title: Transfer of mitochondrial DNA into the nuclear genome during gene editing  [PEM-Seq MT stress]

first: Jinchun

last: Wu

summary: Mitochondria serve as the cellular powerhouse, and their distinct DNA makes them a prospective target for gene editing to treat genetic disorders. However, the impact of genome editing on mitochondrial DNA (mtDNA) stability remains a mystery. Our study reveals previously unknown risks of genome editing that both nuclear and mitochondrial editing cause broad transfer of mitochondrial DNA segments into the nuclear genome in various cell types including human cell lines, primary T cells, and mouse embryos. Furthermore, drug-induced mitochondrial stresses and mtDNA breaks exacerbate this transfer of mtDNA into the nuclear genome. Notably, we observe that mitochondrial targeting editors, mitoTALEN and recently developed base editor DdCBE, can also induce widespread mtDNA integrations. However, we provide a practical solution to suppress mtDNA transfer by co-expressing TREX1 or TREX2 exonucleases during DdCBE editing. These findings also shed light on the origins of mitochondrial-nuclear DNA segments.

first: Yang

last: Liu

first: Liqiong

last: Ou

first: Tingting

last: Gan

first: Zhengrong

last: Zhangding

first: Shaopeng

last: Yuan

first: Xinyi

first: Mengzhu

first: Jiasheng

last: Li

first: Jianhang

last: Yin

first: Changchang

last: Xin

first: Ye

last: Tian

first: Jiazhi

last: Hu


title: Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [ATAC-Seq]

first: J

last: Ruby

overall_design: Human fetal lung cells in culture were analyzed by ATAC-seq

first: Alyssa

last: Kaiser


title: Single-cell sequencing of human induced pluripotent stem cell-derived ventral midbrain astrocytes

city: Cardiff

first: Zongze

country: United Kingdom

summary: Regional specificity of stem cell-derived astrocytes is believed to be an important prerequisite for their applications in disease modelling and cell-based therapies. The regional identity of these astrocytes is often defined by the positional characteristics of their antecedent, stem cell-derived neural progenitors patterned to a fate of interest, with the assumption that the positional specification is to be preserved by the derived astrocytes. Using a human iPSC line designed for tracing midbrain floor plate derivatives, here we show that lineage composition of the derived astrocytes is not a faithful recapitulation of the founder progenitor population, as demonstrated by the loss of floor plate differentiated progeny in the final astrocyte products. Using deep single cell RNA sequencing, we identified distinct transcriptomic signatures of midbrain floor plate-derived astrocytes. Our study highlights the need for rigorous characterisation of PSC-derived regional astrocytes and provides a valuable resource for assessing midbrain floor plate-derived human astrocytes.

overall_design: Human induced pluripotent stem cell-derived astrocytes and neurons isolated for CD49f by fluorescence activated cell sorting or unisolated were analysed using single cell RNA sequencing.

first: Lucia

last: Cardo

first: Michal

last: Rokicki

first: Caleb

last: Webber

first: Meng


title: Transfer of mitochondrial DNA into the nuclear genome during gene editing [target sequencing]

first: Jinchun

first: Yang

first: Liqiong

first: Tingting


title: Transfer of mitochondrial DNA into the nuclear genome during gene editing [mitoTALEN_ND4 PEM-seq]

first: Zhengrong

first: Shaopeng

first: Xinyi

first: Mengzhu


title: Transfer of mitochondrial DNA into the nuclear genome during gene editing [ND5.1 PEM-seq]

first: Jiasheng

first: Jianhang

first: Changchang

first: Ye


title: Scar management through modulation of the fibrotic microenvironment by CAR-Trem2-macrophages

city: Chongqing

first: Wen

last: Zeng

address: Gaotanyan street

department: Department of Cell Biology

institute: Army Medical University

summary: Dipeptidyl peptidase 4 (Dpp4) plays a pivotal role in fibrotic and nonfunctional scar development following skin injury and is present in a subset of fibroblasts implicated in scar formation. Simultaneously, heterogeneous vascular endothelial cells (ECs) retain their capacity to drive tissue regeneration and repair within scarred areas. Effective strategies for inhibiting scar-associated fibroblasts and regulating EC subtypes in the scar microenvironment remain unclear. Here, we engineered CAR-Trem2-Ms capable of targeting DPP4+ fibroblasts and modulating EC phenotypes within the scar microenvironment to effectively prevent and treat scarring. Furthermore, compared to those in normal control samples, DPP4 expression levels were higher in both clinical scar databases and samples from scar patients. We transferred a CAR gene specifically targeting Dpp4+ fibroblasts into macrophages, which were then induced into CAR-Trem2-Ms with 1,25-dihydroxycholecalciferol (an active form of VD, VD3). Hydrogel micropore microneedles (mMNs) were employed to deliver CAR-Trem2-Ms to effectively alleviate scar formation. Single-cell transcriptome sequencing and analysis revealed that CAR-Trem2-Ms could modify EC phenotypes and regulate fibrosis by suppressing the profibrotic gene Lrg1. CAR-Trem2-Ms effectively inhibited fibrosis in fibroblasts induced by high EC LRG1 expression in vitro, further revealing the underlying mechanism by which CAR-Trem2-Ms exert their antifibrotic effects. Our findings offer a promising approach for treating post-traumatic scarring and provide novel insights into the pathological mechanisms underlying fibrosis.

overall_design: We detected transcriptome differences between the two groups of cells CAR-Ms  and CAR-Trem2-Ms

first: Min

first: Xin

last: Zhou


title: Transfer of mitochondrial DNA into the nuclear genome during gene editing [ND5.3 PEM-seq]

last: Wu

last: Liu

first: Jiazhi


title: Scar management through modulation of the fibrotic microenvironment by CAR-Trem2-macrophages (scRNA-seq)

summary: Dipeptidyl peptidase 4 (Dpp4) plays a pivotal role in fibrotic and nonfunctional scar development following skin injury and is present in a subset of fibroblasts implicated in scar formation. Simultaneously, heterogeneous vascular endothelial cells (ECs) retain their capacity to drive tissue regeneration and repair within scarred areas. Effective strategies for inhibiting scar-associated fibroblasts and regulating EC subtypes in the scar microenvironment remain unclear. Here, we engineered CAR-Trem2-Ms capable of targeting DPP4+ fibroblasts and modulating EC phenotypes within the scar microenvironment to effectively prevent and treat scarring. Furthermore, compared to those in normal control samples, DPP4 expression levels were higher in both clinical scar databases and samples from scar patients. We transferred a CAR gene specifically targeting Dpp4+ fibroblasts into macrophages, which were then induced into CAR-Trem2-Ms with 1,25-dihydroxycholecalciferol (an active form of VD, VD3). Hydrogel micropore micro

overall_design: scRNA-seq for skin tissues at 14 days after treatment with mMN-loaded CAR-Ms and CAR-Trem2-Ms，combined with POD group.


title: Transfer of mitochondrial DNA into the nuclear genome during gene editing [PEM-Seq mtDNA breaks]

last: Ou

last: Gan


title: Transfer of mitochondrial DNA into the nuclear genome during gene editing [CBE_ND4 PEM-seq]

last: Zhangding

last: Yuan


title: Transfer of mitochondrial DNA into the nuclear genome during gene editing [PEM-seq]

last: Yin


title: CENPA as a reader of m6A-modified centromeric RNA to ensure centromere integrity in cancer cells [RIP-Seq]

first: Jun

address: Haidian District

department: School of Life Sciences

summary: Maintaining centromere integrity is crucial for genome stability and proper chromosome segregation during mitosis. CENPA, a conserved histone H3 variant, is localized at the centromeres and plays an essential role in preserving centromere integrity and function. However, the mechanisms that retain CENPA at centromeres remain an enigma. In this study, we identified CENPA as an m6A reader of centromeric RNA (cenRNA), which is essential for its centromeric localization and function in maintaining centromere stability. We discovered a higher level of m6A modification on cenRNA in cancerous cells compared to normal cells. CENPA preferentially binds the cenRNAs with m6A modification, which stabilizes its localization in centromeric regions during the S phase of the cell cycle. We then identified two residues in CENPA responsible for m6A recognition. Mutations in these CENPA residues or removal of m6A on cenRNAs leads to the loss of centromere-bound CENPA during the S phase, thereby resulting in abnormal chromosome separation during mitosis and increased genomic instability. Consequently, this impairment in centromere integrity hindered cancer cell proliferation and tumor growth. Our findings unveiled a novel m6A reading mechanism by CENPA that epigenetically governs centromere integrity in cancer cells, providing potentially new targets for cancer therapy.

overall_design: RNA immunoprecipitation sequencing (RIP-seq) for CENPA in control A375 cells, as well as CENPA knockdown cells followed by expressing wild-type CENPA  or double mutant CENPA.

first: Zihong

last: Kang

first: Ruimeng

last: Li


title: CPEB2-activated Prdm16 translation promotes brown adipocyte function and prevents obesity

city: Taipei

first: Yi-Shuian

last: Huang

address: 128 Sec. 2, Academia Rd. Nankang

country: Taiwan

institute: Institute of Biomedical Sciences, Academia Sinica

summary:
Objective
Brown adipose tissue (BAT) plays an important role in mammalian thermogenesis through the expression of uncoupling protein 1 (UCP1). Our previous study identified cytoplasmic polyadenylation element binding protein 2 (CPEB2) as a key regulator that activates the translation of Ucp1 with a long 3′-untranslated region (Ucp1L) in response to adrenergic signaling. Mice lacking CPEB2 or Ucp1L exhibited reduced UCP1 expression and impaired thermogenesis; however, only CPEB2-null mice displayed obesogenic phenotypes. Hence, this study aims to investigate how CPEB2-controlled translation impacts body weight.
Methods
Body weight measurements were conducted on mice with global knockout (KO) of CPEB2, UCP1 or Ucp1L, as well as those with conditional knockout of CPEB2 in neurons or adipose tissues. RNA sequencing coupled with bioinformatics analysis was used to identify dysregulated gene expression in CPEB2-deficient BAT. The role of CPEB2 in regulating PRD1-BF1-RIZ1 homologous-domain containing 16 (PRDM16) expression was subsequently confirmed by RT-qPCR, Western blotting, polysomal profiling and luciferase reporter assays. Adeno-associated viruses (AAV) expressing CPEB2 or PRDM16 were delivered into BAT to assess their efficacy in mitigating weight gain in CPEB2-KO mice.
Results
We validated that defective BAT function contributed to the increased weight gain in CPEB2-KO mice. Transcriptomic profiling revealed upregulated expression of genes associated with muscle development in CPEB2-KO BAT. Given that both brown adipocytes and myocytes stem from myogenic factor 5-expressing precursors, with their cell-fate differentiation regulated by PRDM16, we identified that Prdm16 was translationally upregulated by CPEB2. Ectopic expression of PRDM16 in CPEB2-deprived BAT restored gene expression profiles and decreased weight gain in CPEB2-KO mice.
Conclusions
In addition to Ucp1L, activation of Prdm16 translation by CPEB2 is critical for sustaining brown adipocyte function. These findings unveil a new layer of post-transcriptional regulation governed by CPEB2, fine-tuning thermogenic and metabolic activities of brown adipocytes to control body weight.

overall_design: RNA-seq from CPEB2-WT or -KO BAT with/without virus (GFP or PRDM16) injection

first: Wen-Hsin

last: Lu

first: Chai Ling

last: Lim

first: Pei-Chih

last: King


title: Serine/Threonine Phosphorylation of RUNX1 Promotes Megakaryocytic Fate in Megakaryocyte-Erythroid Progenitors (Primary Human Bulk mRNA-seq)

city: New Haven

first: Evrett

middle: Nathanial

last: Thompson

state: CT

address: 333 Cedar Street

department: Cell Biology

institute: Yale School of Medicine

summary: The differentiation of primary human megakaryocyte-erythroid progenitors (MEP) into  megakaryocytic (Mk) or erythroid (E) progenitors is critical for maintaining the blood  system, yet the mechanisms that regulate this fate specification remain unclear. Here,  we analyzed RNA-seq data and found that RUNX1 is a key regulator of differential gene  expression in MEP fate specification. Through viral transduction of primary MEP with  RUNX1, we demonstrated that overexpression of RUNX1 promotes Mk over E  specification, whereas pan-RUNX inhibition promotes E fate specification over Mk. We  found that although the levels of total RUNX1 do not differ between MkP and ErP, MkP  have higher levels of RUNX1 phosphorylated serine residues, and that serine/threonine  phosphorylation of RUNX1 dramatically increases its effectiveness. We used human  erythroleukemia (HEL) cell lines with expression of HA-tagged WT RUNX1,  phosphomimetic (RUNX1-4D) and non-phosphorylatable (RUNX1-4A) mutants to model  their effects on MEP. Although the chromatin association was not informative, the three  forms of RUNX1 caused differential expression of 2,625 genes. Approximately 40% of  these differentially expressed genes (DEGs) showed an increase with both RUNX1-WT  and RUNX1-4D while another 40% showed a decrease with both RUNX1-WT and  RUNX1-4D. We compared these DEGs with DEGs from primary human MEP, Mk  progenitors (MkP), and E progenitors (ErP), and found that the genes upregulated by  WT and RUNX1-4D in HEL cells overlapped significantly with the genes upregulated in  MkP vs. MEP, whereas genes downregulated by WT and RUNX1-4D in HEL cells  overlapped significantly with the genes downregulated in MkP vs. MEP. These results  suggest that phosphorylation of RUNX1 enhances RUNX1’s function to activate or  repress transcription of target genes that are up/downregulated during MEP fate  specification.

overall_design: Total RNA was extracted from each cell population isolated via FACS from CD34-selected mobilized peripheral blood. Four separate donors were used to prepare sequencing from CMP, MEP, and ERP. Two separate donors were used to prepare sequencing from MKP. Two additional replicates from donors three and four were prepared from additional FACS isolations.

first: Nayoung

last: Kwon

first: Yi-Chien

middle: N

first: Lin

last: Wang

first: Ping-Xia

last: Zhang

first: Diane

last: Krause

first: Rubia

last: Mancuso


title: Serine/Threonine Phosphorylation of RUNX1 Promotes Megakaryocytic Fate in Megakaryocyte-Erythroid Progenitors (HEL Cell Line Bulk mRNA-seq)

overall_design: Total RNA was extracted from HEL cell lines expressing HA-tagged WT RUNX1, RUNX1-4A, RUNX1-4D, along with an empty vector control HEL cell line. RNA was prepared from two biological replicates of each cell line.


title: Serine/Threonine Phosphorylation of RUNX1 Promotes Megakaryocytic Fate in Megakaryocyte-Erythroid Progenitors (CUT&RUN)

overall_design: CUT&RUN was performed using anti-HA antibody on HEL cell lines expressing HA-tagged WT RUNX1, RUNX1-4A, RUNX1-4D, and an empty vector control HEL cell line. The empty vector control cell line was used as a background control for peak calling. CUT&RUN libraries were prepared from two biological replicates of each cell line.


title: Serine/Threonine Phosphorylation of RUNX1 Promotes Megakaryocytic Fate in Megakaryocyte-Erythroid Progenitors

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

overall_design: Refer to individual Series


title: CENPA as a reader of m6A-modified centromeric RNA to ensure centromere integrity in cancer cells [ChIRP-seq]

last: Liu

overall_design: To strengthen the potential link between centromere RNA (cenRNA) methylation and centromere regions, we applied chromatin isolation by RNA purification (ChIRP) to cenRNA followed by high-throughput sequencing in both control and METTL3 knockdown A375 cells.


title: CENPA as a reader of m6A-modified centromeric RNA to ensure centromere integrity in cancer cells [MeRIP-seq]

overall_design: m6A-methylated RNA immunoprecipitation sequencing (MeRIP-seq) for A375 cells upon METTL3 knockdown or with dCas13b-FTO targeting.  m6A-methylated RNA immunoprecipitation sequencing (MeRIP-seq) for control HEK293T cells.


title: m6A-modified cenRNA stabilizes CENPA to ensure centromere integrity in cancer cells


title: Selective translation of nuclear mitochondrial respiratory proteins reprograms succinate metabolism in AML development and chemoresistance. [Ribo-seq]

city: wuhan

first: Haojian

state: Hubei

address: Donghu Rd

department: Medical Research Institute

institute: Wuhan university

summary: Here we identify a novel RAS-responsive element binding protein 1 short isoform, RREB1α, as a key in governing mitochondrial complex II translation to promote stemness and drug resistance of cancer stem cells of acute myeloid leukemia

overall_design: This dataset contains Ribo-seq experiments of leukemia stem cells isolated fromWT or Rreb1-KO mice.leukemia stem cells were isolated from the bone marrow for Ribo-seq analysis with two biological replicates.

first: Guoqiang

last: Han


title: CENPA as a reader of m6A-modified centromeric RNA to ensure centromere integrity in cancer cells [CHIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3.3 and CENPA during the S phase of A375 cells upon METTL3 knockdown or with dCas13b-FTO targeting.


title: Selective translation of nuclear mitochondrial respiratory proteins reprograms succinate metabolism in AML development and chemoresistance.


title: Selective translation of nuclear mitochondrial respiratory proteins reprograms succinate metabolism in AML development and chemoresistance. [RNA-seq]

overall_design: [RNA-seq] This dataset contains RNA-seq experiments of leukemia stem cells isolated fromWT or Rreb1-KO mice.leukemia stem cells were isolated from the bone marrow for RNAseq analysis with two biological replicates.


title: In vivo expansion of gene-targeted hepatocytes through transient inhibition of an essential gene

status: Public on Sep 23 2024

city: Houston

first: Jong

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Homology directed repair (HDR)-based genome editing is an approach that could permanently correct a broad range of genetic diseases. However, its utility is limited by inefficient and imprecise DNA repair mechanisms in terminally differentiated tissues. Here, we tested “Repair Drive”, a platform technology for selectively expanding HDR-corrected hepatocytes in vivo. Repair Drive involves transient conditioning of the liver by knocking down an essential gene – Fumarylacetoacetate hydrolase (Fah), and delivery of an untargetable version of the essential gene in cis with a therapeutic transgene. We show that Repair Drive dramatically increases the percentage of correctly targeted hepatocytes, up to 25%. This resulted in a five-fold increased expression of a therapeutic transgene – human Factor IX (FIX). Repair Drive was well-tolerated and did not induce toxicity or tumorigenesis in long-term follow up. This approach will broaden the range of liver diseases that can be treated with somatic genome editing.

overall_design: To investigate the hepatocyte population expanded through Repair Drive we isolated nuclei from ~100 mg of frozen liver samples. The liver samples were homogenized using Dounce homogenizers. Nuclei were isolated by using strainers and sucrose gradient centrifugation. Nuclei samples were diluted to obtain 15000 - 18000 nuclei for single cell library construction according to the 10X single cell gene expression workflow. Libraries were sequenced on an Illumina NovaSeq 6000 instrument.

first: Marco

last: De Giorgi

first: Rich

last: Gang Li

first: James

last: Martin

first: William

last: Lagor


title: Selective translation of nuclear mitochondrial respiratory proteins reprograms succinate metabolism in AML development and chemoresistance.[ChIP-seq]

summary: Here we identify a novel RAS-responsive element binding protein 1 short isoform, RREB1S, as a key in governing mitochondrial complex II translation to promote stemness and drug resistance of cancer stem cells of acute myeloid leukemia

overall_design: This dataset contains input and ChIP-seq experiments of leukemia stem cells isolated from WT or Rreb1-KO mice. Leukemia stem cells were isolated from the bone marrow for ChIP-seq analysis with two biological replicates.


title: MAPseq data of mouse corticospinal neurons with respect to laterality

city: New York

first: Benjamin

last: Fait

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: The spinal cord receives inputs from the cortex via corticospinal neurons (CSNs). While predominantly a contralateral projection, a less-investigated minority of its axons terminate in the ipsilateral spinal cord. We analyzed the spatial and molecular properties of these ipsilateral axons and their post-synaptic targets in mice and found they project primarily to the ventral horn, including directly to motor neurons. Barcode-based reconstruction of the ipsilateral axons revealed a class of primarily bilaterally-projecting CSNs with a distinct cortical distribution. The molecular properties of these ipsilaterally-projecting CSNs (IP-CSNs) are strikingly similar to the previously described molecular signature of embryonic-like regenerating CSNs. Finally, we show that IP-CSNs are spontaneously regenerative after spinal cord injury. The discovery of a class of spontaneously regenerative CSNs may prove valuable to the study of spinal cord injury. Additionally, this work suggests that the retention of juvenile-like characteristics may be a widespread phenomenon in adult nervous systems. This data set comprises the MPASeq experiment.

overall_design: MAPseq sindbis barcode was injected into the caudal forelimb area of the mouse motor cortex. Both sides of the cervical spinal cord were dissected, along with the injection site, olfactory bulbs, and contralateral cortex for barcode reverse transcription and sequencing.

first: Eric

last: Schmidt


title: Viral TRAP RNAseq Data from Ipsilateral and Contralateral Corticospinal Neurons in Mouse

summary: The spinal cord receives inputs from the cortex via corticospinal neurons (CSNs). While predominantly a contralateral projection, a less-investigated minority of its axons terminate in the ipsilateral spinal cord. We analyzed the spatial and molecular properties of these ipsilateral axons and their post-synaptic targets in mice and found they project primarily to the ventral horn, including directly to motor neurons. Barcode-based reconstruction of the ipsilateral axons revealed a class of primarily bilaterally-projecting CSNs with a distinct cortical distribution. The molecular properties of these ipsilaterally-projecting CSNs (IP-CSNs) are strikingly similar to the previously described molecular signature of embryonic-like regenerating CSNs. Finally, we show that IP-CSNs are spontaneously regenerative after spinal cord injury. The discovery of a class of spontaneously regenerative CSNs may prove valuable to the study of spinal cord injury. Additionally, this work suggests that the retention of juvenile-like characteristics may be a widespread phenomenon in adult nervous systems. This TRAP sequencing data was used to determine the molecular similarity to regenerating and embryonic CSNs.

overall_design: To determine the molecular characteristics of ipsilateral and contralateral CSNs, we used retrograde viral TRAP in CSNs and sequenced both input mRNA and TRAP immunoprecipitated RNA from 5 paired biological replicates of three animals each


title: Differentiation of SH-SY5Y cells by 9 cis retinoic acid

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

summary: The RNA seq analysis aims to determine the changes in gene expression between undifferentiated and differentiated SH SY5Y neuroblastoma cells following differentiation with 9 cis retinoic acid.

overall_design: SH-SY5Y cells were differentiated by incubation with 1 micromolar 9-cis retinoic acid for 7 days.

first: Caroline

last: Austin


title: Gene expression profile of B lymphocytes from GPR40 KO and WT mice

city: Huzhou

first: Yunliang

last: Yao

state: Zhejiang

address: 759 East Second Ring Road

department: Medical School

institute: Huzhou University

summary: GPR40 deficiency in B cells was shown to result in enhanced B cell activation and proliferation, antibody production, germinal center formation, and class switch recombination. We used whole transcriptome sequencing to analyze B cells isolated from the spleens of both GPR40-WT and GPR40-BKO mice.

overall_design: B lymphocytes from  GPR40-WT and GPR40-BKO mice were separated by B cell isolation kit and analyzed using RNAseq.

first: Anqi

last: Li


title: Retinoic acid, an essential component of the RP organizer, promotes the spatio-temporal segregation of dorsal neural fates

city: Jerusalem

first: Chaya

last: Kalcheim

address: Hadassah Medical School

department: Medical Neurobiology

country: Israel

institute: The Hebrew University in Jerusalem

summary: Dorsal neural tube-derived retinoic acid promotes the end of neural crest production and transition into a definitive roof plate. Here we analyze how this impacts the segregation of central and peripheral lineages, a process essential for tissue patterning and function. Localized in-ovo inhibition of retinoic acid activity followed by single cell transcriptomics unraveled a comprehensive list of differentially expressed genes relevant to these processes. Importantly, progenitors co-expressed neural crest, roof plate and di1 interneuron markers indicating a failure in proper lineage segregation. Furthermore, we found that separation between roof plate and dI1 interneurons is mediated by Notch activity downstream of retinoic acid, highlighting their critical role in establishing the roof plate-dI1 boundary. Within the peripheral branch, where absence of retinoic acid resulted in neural crest production and emigration extending into the roof plate stage, sensory progenitors failed to separate from melanocytes leading to formation of a common glia-melanocyte cell with aberrant migratory patterns. Together, we uncover and characterize a molecular mechanism responsible for segregation of dorsal neural fates during development.

overall_design: To enrich for dorsal NT cell types, quail E2.5 neural tubes were electroporated at the flank region of the axis with Msx1-Citrine combined with either a control vector, or RARa403, a dominant negative retinoic acid receptor. For each group, ten neural tubes with associated mesoderm were mechanically microdissected at E4 and single cell suspensions prepared. Fluorescent cells were then sorted and subjected to droplet-based scRNA-seq (10x Genomics Chromium) to generate a gene expression profile of control and treated dorsal neural tube cells

first: Dina

last: Rekler

first: Shai

last: Ofek

first: Sarah

last: Kagan

first: Gilgi

last: Friedlander


title: High-throughput sequencing analysis of mRNA and lncRNA in wild-type mouse bone marrow-derived macrophages after deoxycholic acid treatment

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

summary: At the epigenetic level, lncRNAs play an important role in cell differentiation and function. We investigated the global programme of gene expression in detail using high-throughput sequencing and identified different classes of up- or down-regulated genes in deoxycholic acid-treated wild-type mouse BMDMs.

overall_design: BMDMs were treatment with 100 µM DCA for 24h. One days later, all cells with or without DCA treatment were collected for RNA extraction. Total RNA was extracted using an RNeasy mini kit (QIAGEN, CA). RNA-seq libraries were prepared with the TruSeq sample preparation kit (Illumina, CA).


title: Gene expression in Phf6-deleted and Phf6-intact foetal mouse cortical neurons and foetal mouse cortex assessed by RNA-seq

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: This study assessed the impact of germline Phf6-deletion on gene expression in the E15.5 mouse cortex and the impact of Nestin-cre mediated Phf6-deletion on gene expression in cultured E16.5 mouse cortical neurons

overall_design: Cortex and Cultured Cortical Neuron (CCN) cells were isolated from individual mice. Of the cortex samples, three are wild type (WT) and five are Phf6 deleted. For the CCN samples, three are WT and four are Phf6 deleted.

first: Helen

last: McRae

first: Anne

last: Voss

first: Tim

last: Thomas

first: Gordon

middle: K

last: Smyth


title: Expression data from Sos1 and Sos2-depleted (individually or combined) mouse primary fibroblasts

city: Salamanca

first: Fernando

last: Baltanas

address: Campus Miguel de Unamuno

institute: Centro de Investigacion del Cancer

summary: Sos1 and Sos2 are guanine-nucleotide exchange factors for Ras and Rac small GTPases, which are involved in a wide range of cellular responses including proliferation and migration. We have previously shown that Sos1 and Sos2 have different effects on cell migration, but the underlying mechanisms are not clear. Here, we examined the role of Sos1 and Sos2 in the overall transcriptional profile of mouse primary fibroblasts in order to unveil the specific functions of these Ras/Rac activators in regulating migration.  We used microarrays to detail the impact of Sos1/2 depletion (individual or combined) in the transcriptional signature of mouse primary keratinocytes

overall_design: Mouse primary fibroblasts (WT, Sos1KO, Sos2KO and Sos1/2DKO) at actively growing conditions 4-hydroxytamoxifen-treated for 12 days were selected for RNA extraction and hybridization on Affymetrix microarrays. RNA was isolated and hybridated following manufacturer's recommendations.

first: Eugenio

last: santos


title: Redirecting the pioneering function of FOXA1 with covalent small molecules [ATAC-Seq]

city: La Jolla

first: Yuxiang

last: Zhang

address: 10550 N. Torrey Pines Rd.

department: Chemistry

institute: The Scripps Research Institute

summary: Pioneer transcription factors (TFs) exhibit a special ability to bind to and open closed chromatin, facilitating engagement by other regulatory factors involved in gene activation or repression. Chemical probes are lacking for pioneer TFs, which has hindered their mechanistic investigation in cells. Here, we report electrophilic small molecules that stereoselectively and site-specifically bind the pioneer TF, FOXA1, at a cysteine (C258) within the forkhead DNA-binding domain. We show that these covalent ligands react with FOXA1 in a DNA-dependent manner and rapidly remodel its pioneer activity in prostate cancer cells reflected in redistribution of FOXA1 binding across the genome and directionally correlated changes in chromatin accessibility. Motif analysis supports a mechanism where the covalent ligands relax the canonical DNA binding preference of FOXA1 by strengthening interactions with suboptimal ancillary sequences in predicted proximity to C258. Our findings reveal a striking plasticity underpinning the pioneering function of FOXA1 that can be controlled by small molecules.

overall_design: ATAC-seq experiments for profiling the impact of stereoprobes treatments on chromatin accessibility in 22Rv1 cells gene-edited to express C1111S-SF3B1.

first: Michael

last: Erb

first: Benjamin

last: Cravatt

first: Sang

last: Won

first: Lauren

last: Hargis


title: PRDM9 drives the location and rapid evolution of recombination hotspots in salmonids

city: Montpellier

first: Bernard

last: de Massy

address: 141, rue de la Cardonille

country: France

institute: Institute of Human Genetics - UMR9002 CNRS

summary: In many eukaryotes, meiotic recombination occurs preferentially at discrete sites, called recombination hotspots. In various lineages, recombination hotspots are located in regions with promoter-like features and are evolutionarily stable. Conversely, in some mammals, hotspots are driven by PRDM9 that targets recombination away from promoters. Paradoxically, PRDM9 induces the self-destruction of its targets and this triggers an ultra-fast evolution of mammalian hotspots. PRDM9 is ancestral to all animals, suggesting a critical importance for the meiotic program, but has been lost in many lineages with surprisingly little effect on meiosis success. However, it is unclear whether the function of PRDM9 described in mammals is shared by other species. To investigate this, we analyzed the recombination landscape of several salmonids, the genome of which harbors one full-length PRDM9 and several truncated paralogs. We identified recombination initiation sites in Oncorhynchus mykiss by mapping meiotic DNA double-strand breaks (DSBs). We found that DNA DSBs clustered at hotspots positioned away from promoters, enriched for the H3K4me3 and H3K36me3 marks and the location of which depended on the genotype of full-length Prdm9. We observed a high level of polymorphism in the zinc finger domain of full-length Prdm9, indicating diversification driven by positive selection. Moreover, population-scaled recombination maps in O. mykiss, Oncorhynchus kisutch and Salmo salar revealed a rapid turnover of recombination hotspots caused by PRDM9 target motif erosion. Our results imply that PRDM9 function is conserved across vertebrates and that the peculiar evolutionary runaway caused by PRDM9 has been active for several hundred million years.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the recombinase DMC1 as well as the histone modifications H3K4me3 and H3K36me3 in rainbow trout testes.

first: Marie

last: Raynaud

first: Paola

last: Sanna

first: Julien

last: Joseph

first: Julie

last: Clément

first: Yukiko

last: Imai

first: Jean-Jacques

last: Lareyre

first: Audrey

last: Laurent

first: Nicolas

last: Galtier

first: Frédéric

last: Baudat

first: Laurent

last: Duret

first: Pierre-Alexandre

last: Gagnaire


title: Comparative characterization of the seven H3K4 methyltransferases in Arabidopsis thaliana

city: Davis

first: Satoyo

last: Oya

address: 1 Shields Ave, Plant_ Enviro Sci, RM 1210, 387 N Quad (MS11665)

department: Plant Sciences

institute: UC Davis

summary: Methylation of H3 lysine 4 (H3K4me) marks transcribed elements of eukaryotic genome, and their distribution alters dynamically through developmental stages and environmental change. These dynamic regulations are likely achieved by combinatorial work of H3K4me writers, which multi-cellular organisms carry multiple copies of. To better understand the chromatin targeting mechanisms of H3K4 methyltransferase in plants, here we comparatively characterized the seven H3K4 methyltransferases in model plants Arabidopsis. This work clarified, in combination with previous results, ATX1-5 (TRX/TRR-type methyltransferase) localizes on loci with specific sets of chromatin modifications and DNA motifs. Notably, ATX3 localizes to binding motifs of ASR3 and RAP2.11 transcriptional factors and also directly interacts with those TFs. ATXR7(SET1-type) and ATXR3 (non-canonical H3K4 methyltransferase) seemed co-transcriptional. Interestingly, ATXR3, the major H3K4me3 methyltransferase in Arabidopsis, was not associated with COMPASS, which suggests H3K4me3 regulation in plants and animals is divergent. Our work provides a foundation for understanding the regulation of H3K4 methyltransferases in plants.

overall_design: Experimental design; This study contains several data series as described below. 14 ~15 dai seedling of MS plate grown Arabidopsis thaliana were used for all of the data series;  1. ChIP-seq targeting the seven H3K4 methyltransferase proteins in *Arabidopsis thaliana.* Plants expressing epitope (3x-FLAG) tagged ATX1, ATX2, ATX3, ATX4, ATX5, ATXR7 and ATXR3 were generated and their genomic localization were determined in by ChIP-seq. In duplicates for ATX3, ATX4, ATX5 and ATXR3, of which a prior study is unavailable, and single replicate for ATX1, ATX2 and ATXR7, of which ChIP-seq profiles were described previously. 2. H3, H3K4me2 and H3K4me3 ChIP-seq in WT, *atx3-1, atx4/atx5* and *atx3-1/atx4/atx5* mutants, in two replicates. 3. Transcriptome for chromatin-bound, immature RNA  in WT and *atxr3* mutant. 4. H3K4me3 ChIP-seq for WT and *cdkc2*. 5. Transcriptome Start Site Sequencing 2 (TSS-seq2) for WT and atxr3 in duplicates.

first: Soichi

last: Inagaki


title: Redirecting the pioneering function of FOXA1 with covalent small molecules

first: Yuxiang

last: Zhang

overall_design: SLAM-seq experiments for profiling the transcriptomic changes in 22Rv1 C1111S-SF3B1 cells after stereoprobe (20 uM, 3h) or PladB treatments (10 nM, 3h)

first: Michael

last: Erb

first: Benjamin

last: Cravatt


title: S7, E7 peptide action on BMSCs II

city: 南充市

first: Cai-Ping

last: Yan

state: sichuan

address: No. 1 The South of Maoyuan Road

department: orthopedics

institute: North sichuan medical college

summary: Recruitment and regulation of cellular Mitochondrial Respiratory Chain of  BMSCs by E7 and SS31 peptides

overall_design:
Blank group, SS31 group, E7 group, SS31+E7 group
Buy PROCELL cell line


title: Neural and molecular mechanisms underlying paraventricular hypothalamus as a visceral and somatic pain sorting center

city: Suzhou

first: Li

last: Yong-Chang

address: Renai road 199

institute: Soochow university

summary: Distinct representation of visceral and somatic pain by unique PVH neuronal ensembles and suggested that PVH as a pain sorting center that distinctly processes visceral and somatic pain, providing a new framework for comprehending how the brain processes nociceptive information and identifying potential molecular targets for specific pain processing.

overall_design: Analysis of differential genes in three groups of CRD-labeled, VFF-labeled and CRD & VFF labeled cells by RNA-Seq

first: Yong-Chang

last: Li

first: Fu-Chao

first: Di

first: Guang-Yin

last: Xu


title: Exploring Epigenetic Changes in the Development of Gemcitabine Resistance [SW1990R_vs_SW1990_ATACseq]

city: Shanghai

first: Boshi

last: Wang

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

summary: To elucidate the epigenetic events, particularly the dynamic alterations in chromatin accessibility during the development of gemcitabine resistance in pancreatic cancer cells, both the parental SW1990 cells and the gemcitabine-resistant counterparts, SW1990R cells, were employed for mapping of the chromatin accessibility landscape. The ATAC-seq technology was used for precise detection of  chromatin accessibility.

overall_design: To establish gemcitabine-resistant (Gem-R) PDAC cell lines, a progressive exposure to increasing concentrations of gemcitabine was employed. High-throughput epigenome technique ATAC-seq was utilized for comprehensive exploration of epigenetic landscapes.

first: Dianhui

last: Wei


title: Exploring Transcriptional alterations in the Development of Gemcitabine Resistance [SW1990R_vs_SW1990_RNAseq]

summary: To investigate the transcriptional alterations that occur during the development of gemcitabine resistance in pancreatic cancer cells, we established gemcitabine-resistant SW1990 cells, referred to as SW1990R. We then employed RNA-seq to explore the transcriptome changes between the gemcitabine-resistant cells and their parental counterparts.

overall_design: To establish gemcitabine-resistant (Gem-R) PDAC cell lines, a progressive exposure to increasing concentrations of gemcitabine was employed.  We utilized RNA-seq to explore changes in the transcriptome.


title: Exploring Epigenetic Changes in the Development of Gemcitabine Resistance [SW1990R_vs_SW1990_CUTTAG]

summary: To elucidate the epigenetic events, particularly the dynamic alterations in chromatin states during the development of gemcitabine resistance in pancreatic cancer cells, both the parental SW1990 cells and the gemcitabine-resistant counterparts, SW1990R cells, were employed for mapping of the histone modification landscape. The CUT&Tag-seq technology was used for precise detection of histone marks, including H3K4me1 (associated with enhancers), H3K27ac (related to active enhancers and promoters), H3K4me3 (linked to PolII-bound and CpG-rich promoters), H3K9me3 (associated with heterochromatin regions), and H3K27me3 (indicative of Polycomb inhibition).

overall_design: To establish gemcitabine-resistant (Gem-R) PDAC cell lines, a progressive exposure to increasing concentrations of gemcitabine was employed. High-throughput epigenome technique CUT&Tag-seq was utilized for comprehensive exploration of epigenetic landscapes.


title: Exploring Transcriptional alterations in the Development of Gemcitabine Resistance [AsPC1R_vs_AsPC1_RNAseq]

summary: To investigate the transcriptional alterations that occur during the development of gemcitabine resistance in pancreatic cancer cells, we established gemcitabine-resistant AsPC1 cells, referred to as AsPC1R. We then employed RNA-seq to explore the transcriptome changes between the gemcitabine-resistant cells and their parental counterparts.


title: A two-step de-differentiation and maturation of primary human hepatocytes in vitro with efficient metabolic and regenerative capacities

city: luzhou

last: Jiang

address: Zhong Shan Road

institute: SWMU

summary: Hepatocytes hold significant promise for applications in drug screening, disease modeling, and clinical cell transplantation. Generating large amouts of hepatocyte in vitro for those application is still challenging. We have previously established a 5C medium for long-term culture and functional maintanace human primary hepatocytes (PHHs) in vitro. However, 5C condtion could not support hepatocyte expansion, which limited its application. In this study, we established a new hepatocyte expansion medium (NHEM) for efficient hepatocyte expansion, which turned the PHHs into hepatic progenitor-like cells (HPLCs). We also generated an optimized 6C condtion for HPLCs maturation. Overall, this study provide a new strategy to generate large amounts of hepatocytes in vitro.

overall_design: Total of 24 samples were analyzed, which included fresh  primary human hepatocytes (PHHs) and PHHs cultured in different condition in vitro. To figure out whether NHEM induce PHHs into proliferative hepatic progenitor-like cells (HPLCs), we conducted RNA-seq of PHHs cultured in NHEM from different donors. We also analyzed the 5C_PHHs and 6C_HHs to characterize their transcriptome as matured hepatocytes.

first: Bingqing

last: Xie


title: Exploring Epigenetic Changes in the Development of Gemcitabine Resistance [SW1990R_vs_SW1990_RRBS]

type: Methylation profiling by high throughput sequencing

summary: To elucidate the DNA methylation alterations during the development of gemcitabine resistance in pancreatic cancer cells, we utilized both the parental SW1990 cells and their gemcitabine-resistant derivatives, SW1990R cells, to examine DNA methylation patterns. We employed reduced representation bisulfite sequencing (RRBS) assays to uncover the specific CpG methylation profiles.

overall_design: To establish gemcitabine-resistant (Gem-R) PDAC cell lines, a progressive exposure to increasing concentrations of gemcitabine was employed. RRBS experiment was utilized for exploration of CpG methylation landscapes.


title: Exploring Changes in the Development of Gemcitabine Resistance

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

overall_design: Refer to individual Series


title: Exploring Epigenetic Changes in the Development of Gemcitabine Resistance [AsPC1R_vs_AsPC1_CUTTAG]

summary: To elucidate the epigenetic events, particularly the dynamic alterations in chromatin states during the development of gemcitabine resistance in pancreatic cancer cells, both the parental AsPC1 cells and the gemcitabine-resistant counterparts, AsPC1R cells, were employed for mapping of the histone modification landscape. The CUT&Tag-seq technology was used for precise detection of histone marks, including H3K4me1 (associated with enhancers), H3K27ac (related to active enhancers and promoters), H3K4me3 (linked to PolII-bound and CpG-rich promoters), H3K9me3 (associated with heterochromatin regions), and H3K27me3 (indicative of Polycomb inhibition).


title: 3D-printed Scaffolds to Regulate the Translational Balance between Vascularization and Bone Metabolism

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: The single-cell Atlas of Cellular Heterogeneity and The Immunosuppressive Microenvironment of Brain Metastasis from laryngeal squamous cell carcinoma

city: Guangzhou

first: Xiaobing

state: Guangdong Province

address: Sun Yat-Sen University

institute: Sun Yat-sen University Cancer Center

summary: Brain metastasis (BM) from laryngeal squamous cell carcinoma (LSCC) is rare but with poor prognosis. Here, we reported a rare case with two BMs from LSCC, which were removed surgically. Despite treated with radiotherapy, chemotherapy and a PD-1 inhibitor, a new brain lesion was found and resected again. The three lesions were analyzed with single-cell RNA-seq.

overall_design: Two samples from primary brain metastasis (one left, another right). One sample from recurrence brain metastasis after radiotherapy, chemotherapy and a PD-1 inhibitor.

first: Yunzhi

last: Zou


title: S7, E7 peptide action on EPCs

summary: Pro-vascular differentiation and adhesion of EPCs by S7 and E7 peptides

overall_design: Blank group, S7 group, E7 group, S7+E7 group


title: The identification of Stat92E target genes in Drosophila testis by ChIP-seq [Stat-ChIP]

city: Beijing

first: Ruiyan

last: Kong

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

institute: Capital Normal University

summary: To identify the target genes of Stat92E in adult Drosophila testis cyst cells, the testes of c587ts;UAS-Stat92E were dissected and cross-linked to conduct chromatin immunoprecipitation(ChIP) assay and ChIP-high throughput sequencing.

overall_design: JAK/STAT signaling was over-expressed in testis cyst cells by c587ts;UAS-Stat92E.The testis with 1 day at 29℃ was used for ChIP-seq, followed by deep sequencing analysis.

first: Zhouhua


title: The identification of Stat92E target genes in Drosophila testis by ChIP-seq [CG-ChIP]

summary: To identify the target genes of Stat92E in adult Drosophila testis cyst cells, the testes of control (c587ts) and c587ts;UAS-upd were dissected and cross-linked to conduct chromatin immunoprecipitation(ChIP) assay and ChIP-high throughput sequencing.

overall_design: JAK/STAT signaling was over-expressed in testis cyst cells by c587ts;UAS-upd. The testis with 2 day at 29℃ was used for ChIP-seq, followed by deep sequencing analysis.


title: Human iPSC-derived liver co-culture spheroids to model liver fibrosis

city: Brussels

first: Stefaan

last: Verhulst

address: Laarbeeklaan 103, D022

department: BMWE

country: Belgium

institute: Vrije Universiteit Brussel

summary: The lack of adequate human in vitro models that recapitulate the cellular composition and response of the human liver to injury hampers the development of anti-fibrotic drugs. The goal of this study was to develop a human spheroid culture model to study liver fibrosis by using induced pluripotent stem cell (iPSC)-derived liver cells. iPSCs were independently differentiated towards hepatoblasts (iHepatoblasts), hepatic stellate cells (iHSCs), endothelial cells (iECs) and macrophages (iMΦ), before assembly into free floating spheroids by culturing cells in 96-well U-bottom plates and orbital shaking for up to 21 days to allow further maturation. Through transcriptome analysis, we show further maturation of iECs and iMΦ, the differentiation of the iHepatoblasts towards hepatocyte-like cells  (iHeps) and the inactivation of the iHSCs by the end of the 3D culture. Moreover, these cultures display a similar expression of cell-specific marker genes (CYP3A4, PDGFRβ, CD31 and CD68) and sensitivity to hepatoxicity as spheroids made using freshly isolated primary human liver cells. Furthermore, we show the functionality of the iHeps and the iHSCs by mimicking liver fibrosis through iHep-induced iHSC activation, using acetaminophen. In conclusion, we have established a reproducible human iPSC-derived liver culture model that can be used to mimic fibrosis in vitro as a replacement of primary human liver derived 3D models. The model can be used to investigate pathways involved in fibrosis development and to identify new targets for chronic liver disease therapy

overall_design: To evaluate the maturity of the iPSC-liver spheroids, we performed RNA sequencing on spheroids on day 1 after seeding in 3D and 21 days after seeding. In order to look further into iHep maturity, we looked at transcription factor activity of spheroids 21 days after seeding and compared it to iPSC cells, primary human hepatocytes and iHepatoblasts.


title: The identification of Stat92E target genes in Drosophila testis by ChIP-seq


title: S7, E7 peptide action on BMSCs

summary: Pro-vascular differentiation and adhesion of  BMSCs by S7 and E7 peptides


title: Reactive astrocytes with inflammatory signature in CCM disease in hypoxia and normoxia conditions

first: Miguel

middle: Alejandro

last: Lopez-Ramirez

state: Ca

address: 9500 Gilman Dr

department: Medicine

institute: University of California, San Diego

summary: The CCM endothelium is hypersensitive to angiogenesis and can induce a hypoxic program associated with changes in angiogenesis, inflammation, and endothelial-cell metabolism under normoxic conditions. However, the role of active drivers of angiogenesis as CCM disease modifiers in human disease remains unclear. To assess whether CCM reactive astrocytes with neuroinflammatory capacity respond to hypoxia-induced CCM exacerbation, we employed the astrocyte-specific (Aldh1l1-EGFP/Rpl10a) Translational Ribosome Affinity Purification (TRAP) system in combination with a CCM mouse model (Pdcd10BECKO;Aldh1l1-EGFP/Rpl10a). TRAP protocol was performed using Slco1c1-iCreERT2;Pdcd10fl/fl;Aldh1l1-EGFP/Rpl10a mice to isolate ribosomes from astrocytes as previously described. Astrocyte-TRAP mRNAs were from cerebral tissue of mice age P50 exposed to hypoxia or normoxia conditions.

overall_design: Brain endothelial cell-specific conditional Pdcd10-knockout mice were generated by crossing a brain endothelial tamoxifen-regulated Cre recombinase (Slco1c1-iCreERT2) strain with loxP-flanked Pdcd10 (Slco1c1-iCreERT2; Pdcd10fl/fl). To perform Translational Ribosome Affinity Purification (TRAP) in astrocytes we generated Slco1c1-iCreERT2;Pdcd10fl/fl;Aldh1l1-EGFP/Rpl10a and controls littermate Pdcd10fl/fl;Aldh1l1-EGFP/Rpl10a. On a postnatal day 1 (P1), mice were administered 50 μg of 4-hydroxy-tamoxifen (H7904, Sigma-Aldrich) by intragastric injection to induce genetic inactivation of endothelial CCM3 gene in littermates with Slco1c1-iCreERT2;Pdcd10fl/fl; Aldh1l1-EGFP/Rpl10a (Pdcd10BECKO; Aldh1l1-EGFP/Rpl10a) and Pdcd10fl/fl;Aldh1l1-EGFP/Rpl10a mice were used as littermate controls. Non-injected animals with Cre recombinase were also used as littermate controls, whose gene expression and histology were the same as in Pdcd10fl/fl; Aldh1l1-EGFP/Rpl10a mice. Hypoxic conditions consisted in 12% O2,  for seven days and normoxic conditions consisted in 21% O2.TRAP mRNAs from astrocytes was perform using the protocol and instructions as previously described. Astrocyte-TRAP mRNAs were from brains of mice age P57. Total RNA was assessed for quality using an Agilent Tapestation 4200, and 50 nanograms of RNA from samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA-seq libraries using the Illumina® Stranded mRNA Prep (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions.

first: Eduardo

last: Frias-Anaya

first: Brendan

last: Gongol

first: Helios

last: Gallego-Gutierrez

first: Catherine

last: Lai


title: Neuroinflammation and immunothrombosis transcriptional patterns in CCM lesions revealed by spatial transcriptomics

summary: Cerebral cavernous malformation (CCM) immunothrombosis is the connection between immune cells, platelet activation, coagulation cascades and astrocyte-CCM endothelium interaction, and its excessive activation may contribute to neurological disabilities in CCM disease.  We characterized the spatial organization of CCM immunothrombosis observed in Pdcd10BECKObrains under normoxic conditions using the murine 10X Genomics Visium Spatial Gene Expression platform.

overall_design: Brain endothelial cell-specific conditional Pdcd10-knockout mice were generated by crossing a brain endothelial tamoxifen-regulated Cre recombinase (Slco1c1-iCreERT2) strain with loxP-flanked Pdcd10 (Slco1c1-iCreERT2; Pdcd10fl/fl). On a postnatal day 1 (P1), mice were administered 50 μg of 4-hydroxy-tamoxifen (H7904, Sigma-Aldrich) by intragastric injection to induce genetic inactivation of endothelial CCM3 gene in littermates with Slco1c1-iCreERT2;Pdcd10fl/fl (Pdcd10BECKO) and Pdcd10fl/fl mice were used as littermate controls. P65 Pdcd10BECKO mice, with exacerbated lesions under normoxic conditions was used for analysis.


title: Gene expression changes associated with loss of Foxc1 in meningeal tissue of E14.5 mouse embryos

city: Edmonton

first: Serhiy

last: Havrylov

state: Alberta

address: 8-29 Medical Sciences Building

department: Medical Genetics

country: Canada

institute: University of Alberta

summary: To identify gene expression changes associated with loss of Foxc1, we examined meningeal tissue of E14.5 wildtype and Foxc1 null embryos.

overall_design: Comparative gene expression analysis of RNA-seq data for meningeal tissue isolated from wildtype and Foxc1 null E14.5 mouse embryos.

first: Fred

last: Berry

first: Ordan

last: Lehmann


title: Stress response in Escherichia coli following sublethal phenalene-1-one mediated antimicrobial photodynamic therapy: an RNA-Seq study

city: Tuebingen

first: Stefan

last: Czemmel

address: Auf der Morgenstelle 10

department: University of Tuebingen

country: Germany

institute: Quantitative Biology Center (QBiC)

summary: Since the molecular mechanisms behind adaptation and the bacterial stress response toward antimicrobial photodynamic therapy (aPDT) are not entirely clear yet, the aim of the present study was to investigate the transcriptomic stress response in Escherichia coli after sublethal treatment with aPDT using RNA sequencing (RNA-Seq).  Planktonic cultures of stationary phase E. coli were treated with aPDT using a sublethal dose of the photosensitizer SAPYR. After treatment, RNA was extracted, and RNA-Seq was performed on the Illumina NextSeq 500. Differentially expressed genes were analyzed and validated by qRT-PCR.   The analysis of the differential gene expression following pathway enrichment analysis revealed a considerable number of genes and pathways significantly up- or down-regulated in E. coli after sublethal treatment with aPDT. Expression of 1018 genes was up-regulated and of 648 genes was down-regulated after sublethal treatment with aPDT as compared to irradiated controls. Analysis of differentially expressed genes and significantly de-regulated pathways showed regulation of genes involved in oxidative stress response and bacterial membrane damage.   In conclusion, the results show a transcriptomic stress response in E. coli upon exposure to aPDT using SAPYR and give an insight into potential molecular mechanisms that may result in development of adaptation

overall_design: Escherichia coli treated with aPDT using a sublethal dose of the photosensitizer SAPYR.

first: Fabian

last: Cieplik

first: Denise

last: Muehler

first: Silvia

last: Morini


title: Hypoxia increases neuroinflammation and angiogenesis gene programs in CCM disease

summary: The CCM endothelium is hypersensitive to angiogenesis and can induce a hypoxic program associated with changes in angiogenesis, inflammation, and endothelial-cell metabolism under normoxic conditions. However, the role of active drivers of angiogenesis as CCM disease modifiers in human disease remains unclear. To examine if hypoxia, a driver of angiogenesis, may contribute to CCM exacerbation, we performed bulk RNA-seq of brain tissue from P50 Pdcd10BECKO mice under normoxia and hypoxia. P50 Pdcd10fl/fl littermate controls under normoxia and hypoxia were used as controls.

overall_design: Brain endothelial cell-specific conditional Pdcd10-knockout mice were generated by crossing a brain endothelial tamoxifen-regulated Cre recombinase (Slco1c1-iCreERT2) strain with loxP-flanked Pdcd10 (Slco1c1-iCreERT2; Pdcd10fl/fl). On a postnatal day 1 (P1), mice were administered 50 μg of 4-hydroxy-tamoxifen (H7904, Sigma-Aldrich) by intragastric injection to induce genetic inactivation of endothelial CCM3 gene in littermates with Slco1c1-iCreERT2;Pdcd10fl/fl (Pdcd10BECKO) and Pdcd10fl/fl mice were used as littermate controls. Non-injected animals with Cre recombinase were also used as littermate controls, whose gene expression and histology were the same as in Pdcd10fl/fl mice. Hypoxic conditions consisted in 12% O2,  for seven days and normoxic conditions consisted in 21% O2.  Total RNA from cerebral tissue was isolated by TRIzol method according to the manufacturer’s instructions (Thermo Fisher Scientific). Total RNA was assessed for quality using an Agilent Tapestation 4200, and 50 nanograms of RNA from samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA-seq libraries using the Illumina® Stranded mRNA Prep (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions.


title: Improvement of MASLD and MASH by suppression of hepatic N-Acetyltransferase 10 (RIP-Seq)

status: Public on Sep 22 2024

city: Shanghai City

first: Yanying

last: Yang

state: Shanghai City

address: Shanghai

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH) are characterized by excessive triglyceride accumulation in the liver. However, due to an incomplete understanding of its pathogenesis, more efforts are still needed to identify specific and effective treatments. N4-acetylcytidine (ac4C) is a newly discovered RNA modification to regulate mRNA stability post-transcriptionally. N-acetyltransferase 10 (NAT10), the sole enzyme catalyzing mRNA acetylation, has not been fully explored in human diseases, especially in MASLD and MASH. In the current study, abundant RNA acetylation was found in lipid metabolism-related genes in the livers of leptin receptor-deficient (db/db) mice. Besides, hepatic NAT10 expression is significantly increased in multiple mouse models of MASLD and MASH. NAT10 expression is also elevated in patients with MASLD and positively correlated with clinical characteristics. Genetic NAT10 knockdown protects against diet-induced hepatic steatosis and steatohepatitis in mice, while its overexpression exacerbates steatosis. Mechanistically, NAT10 could bind to Srebp-1c mRNA to promote its stability and expression, thereby upregulating lipogenic enzymes. In addition, the translational significance of our findings is that treatment of Remodelin, an NAT10 inhibitor, could improve liver steatosis and dyslipidemia in a preclinical mouse model. Together, these findings highlight the significance of ac4C modification and NAT10 in MASLD and MASH, offering a potential therapeutic target for disease treatment.

overall_design: RNA immunoprecipitation sequencing (RIP-Seq)  for mice injected with AAV-GFP/AAV-NAT10.

first: Bing

last: Zhou

first: Xiaojing

last: Ma

first: Yan

last: Lu


title: Gene expression of wild-type or GC-A knockout mouse glomeruli treated with high salt diet and aldosterone infusion after uninephrectomy.

city: Kyoto

first: Takuya

last: Ishimura

state: Kyoto

address: Sakyo-ku Syogoinkawaharatyo 54

department: Nephrology

institute: Kyoto University

summary:
Podocytes are integral to maintaining the glomerular filtration barrier and preventing proteinuria. Our previous research underscored the crucial role of podocyte guanylyl cyclase-A (GC-A) in the pathogenesis of severe albuminuria in both systemic and podocyte-specific GC-A knockout mice.
In this study, we demonstrate that matrix metalloproteinase-10 (MMP-10) is highly expressed in the glomeruli of GC-A knockout mice and in the kidneys of patients with glomerulonephritis.

overall_design: Systemic GC-A knockout and wild-type mice were performed uninephrectomy before aldosterone infusion and high salt diet for 3 weeks. Total glomerular RNA from these mice was subjected to microarray assay

first: Keisuke

last: Osaki

first: Yoshihisa

last: Ogawa

first: Hideki

last: Yokoi


title: D(+)-Raffinose pentahydrate targeting PI3K/AKT pathway inducing apoptosis to inhibit pancreatic carcinoma proliferation

city: Wenzhou

first: Bangjie

last: He

state: Zhejiang Province

address: Nanbaixiang Street

institute: the first affiliated hospital of wenzhou medical university

summary: Our study confirmed the D(+)-Raffinose pentahydrate have the inhibitory effect on pancreatic cancer cells from different methods. By RNA-seq and q-PCR, we detected that D(+)-Raffinose pentahydrate could induce apoptosis via PI3K/Akt signaling pathway. Together, our findings presented a potential therapeutic effect of D(+)-Raffinose pentahydrate for human pancreatic cancer cells.

overall_design: PANC-1 cells treated with or withoutD(+)-Raffinose pentahydrate (50 uM) for 24 hours

first: Gang

last: Chen

first: Jiuyi

last: Zheng

first: Ke

last: Xu


title: Multi-omics Analysis Identifies Glioblastoma Dependency on H3K9me3 Methyltransferase Activity [ChIP-seq]

city: Bloomington

first: QIQI

last: XIE

state: IN

address: 3209 E 10th St Apt E6

department: Biology

institute: Indiana University Bloomington

summary: Purpose: Enzymes catalyzing histone H3 lysine 9 (H3K9) methylation, such as SUV39H1, SUV39H2, SETDB1, SETDB2, EHMT1, and EHMT2, are individually linked to cancer progression. However, a comprehensive comparison and understanding of their characteristics and mechanisms in cancers is lacking. This study aims to fill this knowledge gap and explore its translational implications. Experimental Design: We conducted multi-omics analyses, including gene expression, mutations, copy number variations, and DNA methylation, to assess the expression patterns, regulation, and prognostic relevance of H3K9 methyltransferases across tumor types. This led to the development of "H3K9me3 MtSig", incorporating SUV39H1, SUV39H2, and SETDB1, with a focus on GBM. Correlations with signaling pathways were explored using gene set enrichment analysis (GSEA) and single-cell expression analyses. ChIP-sequencing was employed to detect H3K9me3 genomic binding sites in GBM cells. We validated the dependency of H3K9me3 MtSig in GBM using patient-derived samples through western blot, immunohistochemistry, immunofluorescence, cell growth, and quantitative PCR. Clinical prediction modeling and drug susceptibility screening were utilized to identify potential therapeutic avenues. Results: H3K9 methyltransferases display diverse expression patterns across cancers, influenced by mutations, CNVs, and DNA methylation associated with the genes. The unique H3K9me3 MtSig signature shows prognostic implications and associations with signaling pathways, particularly in GBM. Elevated H3K9me3 MtSig levels in GBM cells correlate with the G2/M cell cycle positively and immune responses negatively. H3K9me3-mediated repetitive sequence silencing contributes to these phenotypes, with inhibiting it suppressing proliferation and enhancing immune responses. Clinically, H3K9me3 MtSig could act as an independent prognostic factor, and drug susceptibility screening identifies potential GBM biomarkers and therapeutics. Conclusions: H3K9me3 MtSig has the potential to elucidate novel prognostic markers, therapeutic targets, and predictors of treatment response in GBM and other cancer types for clinical intervention.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K9me3 in GSC3565 cells, which originated from a GBM stem cell (GSC) model established using cells obtained from a 32-year-old male GBM patient at University Hospitals, Cleveland, in Dr. Jeremy Rich's lab.

first: Qiqi

last: Xie

first: Yuanning

last: Du

first: Leng

last: Han

first: Jia

last: Shen


title: Mast Cells Proliferate in the Peri-Hippocampal Space During Early Development and Modulate Local and Peripheral Immune Cells

city: Baltimore

first: Margaret

last: McCarthy

state: Maryland

address: 670 W Baltimore St

institute: University of Maryland, Baltimore

summary: Brain development is a non-linear process of regionally specific epochs occurring during windows of sensitivity to endogenous and exogenous stimuli. We have discovered an epoch in the neonatal rat brain defined by a transient population of peri-hippocampal mast cells (phMCs) that are abundant from birth through 2-weeks postnatal but absent thereafter. The phMCs are maintained by proliferation and harbor a unique transcriptome compared to mast cells residing in the skin, bone marrow or other brain regions. Pharmacological activation of this population broadly increases blood-brain-barrier permeability, recruits peripheral immune cells and stunts local microglia proliferation. Examination of the post-mortem human brain revealed mast cells in the peri-hippocampal region of a newborn but not an older child, suggesting a similar developmental period exists in humans. Mast cells specifically and early life inflammation generally, have been linked to heightened risk for neurodevelopmental disorders and these results reveal a plausible source of that risk.

overall_design: We perfused PN2 and PN7 neonates and dissected the hippocampus, hypothalamus, bone marrow and skin. Each replicate contains cells pooled from 6 animals. We sorted mast cells using flow cytometry for CD45 high, CD11b- and FcERI+ cells. We performed bulk gene RNA-seq of each sample using SMART-Seq v4 UltraLow Input RNA Sequencing.

first: Alexa

last: Blanchard

first: Anna

last: Maximova

first: Taylor

last: Phillips-Jones

first: Matthew

last: Bruce

first: Pavlos

last: Anastasiadis

first: Christie

middle: V

last: Dionisos

first: Kaliroi

last: Engel

first: Erin

last: Reinl

first: Aidan

last: Pham

first: Sonia

last: Malaiya

first: Nevil

last: Singh

first: Seth

last: Ament


title: The Role of Orm2 in Ferroptosis Regulation and Iron Homeostasis During Acute Liver Injury and Multi-Organ Protection

first: Hongyi

last: Tang

address: Chongqing Nan Road 280

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University School of Medicine

summary: Acute liver failure is a critical clinical issue in liver diseases, characterized by extensive hepatocyte death involving various mechanisms, including apoptosis, necroptosis, and ferroptosis. Ferroptosis, an iron-dependent form of non-apoptotic cell death marked by significant lipid peroxidation, plays a crucial role in the pathogenesis of multiple liver disorders.This cell death results in elevated levels of acute phase proteins synthesized and secreted by the liver. While previous studies indicated that the ORM2 protein does not directly influence apoptotic signaling pathways, our findings reveal that its knockout in acute liver injury models significantly worsens damage and reduces the median survival time of mice. In contrast, liver-specific overexpression of Orm2 markedly mitigates acute liver injury.We found that Orm2 exerts its protective effects by non-competitively binding to NCOA4, inhibiting ferroautophagy, and reducing iron ion accumulation, thereby decreasing ferroptosis during acute liver injury. Additionally, interference with TAX1BP1 gene expression compensates for the increased sensitivity to ferroptosis resulting from Orm2 knockdown. Importantly, ORM2 infusion therapy protects against acute damage in various organs, including the liver. Mechanistically, ORM2 in plasma enters damaged cells via endocytosis, regulating iron homeostasis and alleviating acute injury caused by ferroptosis.In summary, Orm2 is a potential protective factor against abnormal iron accumulation and ferroptosis, reducing acute organ damage. These findings suggest that acute phase proteins may play a role in cellular resistance to death during organ injury and offer a potential adjunctive therapeutic strategy for acute organ damage caused by ferroptosis.

overall_design: WT and Orm2 KO mice were injected with APAP or PBS, and liver tissues were collected 24 hours later for RNA-seq.

first: Xuxu

last: Sun

first: Yan

last: Lu


title: Improvement of MASLD and MASH by suppression of hepatic N-Acetyltransferase 10 (acRIP-Seq)

first: Yanying

last: Yang

overall_design: Genome-wide acetylated RNA immunoprecipitation sequencing (acRIP-Seq)  for db/db mice and lean control mice.

first: Bing

last: Zhou

first: Xiaojing

last: Ma


title: CRISPR activation screens identify the SWI-SNF ATPases as suppressors of ferroptosis [NGS3719_ATAC]

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

summary: Ferroptosis is an iron-dependent cell death mechanism characterized by an accumulation of toxic lipid peroxides and membrane rupture. The glutathione dependent enzyme, GPX4 (glutathione peroxidase 4), prevents ferroptosis by reducing these lipid peroxides into non-toxic lipid alcohols. Ferroptosis induction by GPX4 inhibition has emerged as a vulnerability of cancer cells, thus highlighting the need to identify ferroptosis regulators that may be exploited therapeutically. Through genome-wide screens and a series of genetic, genomic, and quantitative imaging approaches, we identify the SWI-SNF ATPases BRM and BRG1 as ferroptosis suppressors. Mechanistically, they directly bind to and catalytically increase chromatin accessibility at NRF2 target loci, thus boosting NRF2 transcriptional output. This primes cells to counter lipid peroxidation and confers resistance to GPX4 inhibition and ferroptosis. Importantly, we demonstrate that the BRM/BRG1-ferroptosis connection can be leveraged to enhance the paralog dependency of BRG1-mutant lung cancer cells on BRM, especially in lines that are less sensitive to BRM inhibition or degradation. Our data reveal ferroptosis induction as a potential avenue for broadening the efficacy of BRM degraders/inhibitors and define a specific genetic context for exploiting GPX4 dependency.

overall_design: Bulk ATAC seq

first: Kamakoti

middle: P

last: Bhat

first: Xin

last: Ye

last: hafner

first: Musaddeque

last: Ahmed

first: Michal

last: Kabza

first: Jinchu

last: Vijay


title: Targeting tumor-intrinsic N7-methylguanosine tRNA modification inhibits MDSC recruitment and improves anti-PD-1 efficacy

first: Haining

last: Liu

address: Zhongshan road 2

institute: The first affiliated hospital of sun yat-sen university

summary: We found that PMN-MDSCs level is elevated in the advanced ICCs tissues and is positively associated with the METTL1 and m7G tRNA modification levels. We further showed that impaired m7G tRNA modification impedes the PMN-MDSCs infiltration and inhibits ICC progression. Mechanistically, METTL1-mediated m7G tRNA modification selectively regulates the translation of human CXCL8 and mouse Cxcl5 transcripts, which facilitates the migration of PMN-MDSCs via binding to their cognate receptor CXCR2. Co-blockade of METTL1 and CXCR2 significantly enhances the efficacy of anti-PD-1 treatment in ICC. Taken together, our study reveals the cellular and molecular basis of crosstalk between ICC cells and MDSCs in shaping TIME and affecting ICIs efficacy, which enables reasonable design of new combined therapy targeting dysregulated mRNA translation and suppressive TIME.

overall_design: TRAC-Seq was developed to identify the tRNA m7G methylome in mouse intrahepatic cholangiocarcinoma tissues. RNA-seq was used to study the differential translated genes in the Mettl1 knockdown and control human cell lines and mouse cell lines

first: Ming

last: Kuang


title: CRISPR activation screens identify the SWI-SNF ATPases as suppressors of ferroptosis [NGS3752_RNA]

overall_design: Bulk RNA-Seq


title: Multi-omics Analysis Identifies Glioblastoma Dependency on H3K9me3 Methyltransferase Activity

first: QIQI

last: XIE

summary: Histone H3 lysine 9 dimethylation or trimethylation (H3K9me2 or H3K9me3) marks more than half of the human genome, particularly in heterochromatin regions and specific genes within euchromatic regions. Enzymes catalyzing the methylation of H3K9 have individually been associated with the modulation of gene expression patterns involved in cancer progression, including suppressor of variegation 3–9 homologue 1 (SUV39H1), SUV39H2, SET domain bifurcated 1 (SETDB1), SETDB2, euchromatic histone-lysine N-methyltransferase 1 and 2 (EHMT1/2). However, a comprehensive comparison and understanding of the characteristics and mechanisms of these chromatin-modifying enzymes in cancers remains incompletely understood. In this study, we demonstrated that these six H3K9 methyltransferases differentially expressed in tumors and correlated expression with somatic copy number variations (CNVs) and DNA methylation patterns. Through integrative multi-omics analyses, we identified SUV39H1, SUV39H2, and SETDB1 as the key players among the six H3K9 methyltransferases that exhibited the most significant associations with cancer phenotypes. By incorporating SUV39H1, SUV39H2, and SETDB1, we developed a novel signature termed “H3K9me3 MtSig” (H3K9me3 methyltransferases signature). H3K9me3 MtSig was unique for various tumor types, had prognostic implications and was linked to significant signaling pathways, particularly in glioblastoma (GBM). Furthermore, elevated H3K9me3 MtSig was confirmed in GBM patient-derived cells and tissues. In addition, single-cell expression analysis of H3K9me3 MtSig in GBM tissues demonstrated a pattern related to the G2/M cell cycle and was negatively correlated with immune responses. H3K9me3-mediated repetitive sequence silencing by H3K9me3 MtSig, determined using ChIP-sequencing, contributed to these phenotypes, and inhibiting H3K9me3 MtSig in patient-derived GBM cells suppressed proliferation and increased immune responses. Translationally, H3K9me3 MtSig performed as an independent prognostic factor in a clinical prediction model, and drug susceptibility screening integrating H3K9me3 MtSig identified potential biomarkers and therapeutics for GBM. In summary, H3K9me3 MtSig has the potential to elucidate novel prognostic markers, therapeutic targets, and predictors of treatment response in GBM and other cancer types for clinical intervention.

overall_design: Total RNA was isolated from GSC3565 cells with control knockdown (Ctrl KD) or SUV39H1 knockdown (SUV39H1 KD) and subjected to RNA-seq analysis at Novogene Corporation.

first: Qiqi

last: Xie

first: Yuanning

last: Du

first: Sugata

last: Ghosh

first: Jia

last: Shen


title: Correlating BRG1 binding with histone methylation and acetylation

overall_design: Cut and Run


title: CRISPR activation screens identify the SWI-SNF ATPases as suppressors of ferroptosis