title: Pathogenic mechanism and therapeutic intervention of impaired N7-methylguanosine (m7G) tRNA modification [RNA-seq]

overall_design: RNA sequencing was used to study the differentially transcripted genes in the WDR4 mutated and wild type mice brain tissues.


title: Investigating metabolism of artemisinin-resistant falciparum malaria parasites: mitochondrial rather than apicoplast pathways are key targets?

status: Public on Oct 16 2024

city: Toulouse

first: Lucie

last: Paloque

address: 205 route de Narbonne

country: France

institute: CNRS

type: Expression profiling by high throughput sequencing

summary:
In the context of artemisinin resistance, the objective of the project was to evaluate the role of apicoplast and mitochondrion pathways during the parasite quiescent state induced by dihydroartemisinin (DHA) treatment.
We performed gene expression profiling analysis using data obtained from RNA-seq  of artemisinin-resistant parasites in two conditions: DHA treatment or DMSO treatment (as control condition) at the ring stage (obtained by D-sorbitol synchronization).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for F32-ART (artemisinin-resistant) after 6 h treatment with 700 nM DHA compared to the control condition.

first: Thibaud

last: Reyser


title: Targeting PELP1 reduces endometrial cancer progression via attenuation of ribosomal biogenesis

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

country: USA

institute: UT Health Science Center at San Antonio

summary: We examined the mechanisms by which SMIP34 regulates EEC progression. EEC cells (HEC-1-A) were treated with either vehicle or SMIP34 20µM for 24 hours, and total RNA was isolated for RNA-seq analysis. Our results demonstrated that PELP1 inhibition by SMIP34 reduces the expression of genes involved in ribosome biogenesis and translation.

overall_design: Total RNA from HEC-1-A control, and SMIP34-treated cells were isolated using RNeasy mini kit (Qiagen). For whole-genome transcriptome profiling, 2 libraries (3 replicates from each group) were generated using a TruSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol (Illumina Inc.). Samples were sequenced on the Illumina HiSeq 3000 platform (Illumina Inc.) using the 50 base-pair single-read (50SR) sequencing module.

first: Ratna

middle: K

last: Vadlamudi

first: Xue

last: Yang

first: Zhao

last: Lai


title: lncRNA Array of iPSC-ECs treated with and without e-cigarette extraction

city: Macau

first: Ning-Yi

last: Shao

address: University of Macau

department: Faculty of Health Sciences

country: China

institute: University of Macau

summary: Four healthy iPSC lines were differentiated into ECs. iPSC-ECs were then treated with and without e-cigarette extraction for 24 hours.

overall_design: Arraystar Human LncRNA Arrays V5.0 of iPSC-ECs with and without e-cigarette extreation treatment over a period of 24 hours.

first: Won

middle: H

last: Lee


title: White button mushroom intake modulates PMN-MDSCs, T, and NK cells’ function at the single cell level in prostate cancer patients

city: Duarte

first: Shiuan

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

summary: In prostate cancer patients following 3 months of white button mushroom consumption in freeze-dried tablet form, we observed the decline of circulating polymorphonuclear MDSCs (PMN-MDSCs), along with an increase of granzyme B positive CD8+ T cells and NK cells. Furthermore, single immune cell profiling of peripheral blood from WBM-treated patients revealed the transcriptional landscape of circulating immune cells. This methods showed a decrease in overall circulating PMN-MDSCs with suppression on the expression of STAT3/IRF1 and TGFβ signaling. Subclusters of PMN-MDSCs showed transcriptional profiles associated with "response to fungus", "neutrophil chemotaxis", "leukocyte aggregation", and "regulation of inflammatory response", which are associated with enhanced immune-modulated anti-tumor activity.

overall_design: Paired whole blood samples of four patients from timepoint of baseline vs. 3 months treatment were collected and processed based single immune cell profiling protocol. The leukocytes from whole blood were enriched according to 10X standard protocol

first: Xiaoqiang

last: Wang

first: Jinhui

first: Xiwei

last: Wu


title: The prion protein is required for normal responses to light stimuli by photoreceptor and bipolar cells

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: The prion protein, PrPC, is well known as an essential susceptibility factor for neurodegenerative prion diseases, yet its function in normal, healthy cells remains uncertain. A role in synaptic function has been proposed for PrPC, supported by its cell surface expression in neurons and glia.   Here, in mouse retina, we localized PrPC with synaptic proteins EAAT5, CtBP2 and PSD-95, which are present at junctions between photoreceptors and bipolar cells.   PrPC localized most densely with the bipolar cell dendrites synapsing with cone photoreceptor terminals.  In two coisogenic mouse strains, deletion of the gene encoding PrPC, Prnp, significantly altered the scotopic and photopic electroretinographic (ERG) responses of photoreceptor and bipolar cells.  Cone-dominant pathways showed the most significant ERG changes.   Retinal thickness, quantitated by high-resolution optical coherence tomography (OCT), and ribbon synapse morphology were not altered upon deletion of PrPC, suggesting that the ERG changes were driven by functional rather than structural alterations

overall_design: Uninfected mouse retina's were isolated and nuclei used for 10X analysis.

first: James

middle: F

last: Striebel

middle: A

last: Carroll

first: Brent

last: Race

first: Jacqueline

middle: M

last: Leung

first: Cindi

last: Schwartz

first: Emily

middle: D

last: Reese

first: Catherine

middle: B

last: Rickman

first: Bruce

last: Chesebro

first: Mikael

last: Klingeborn


title: Gene editing of colocalized NCF1 loci is associated with homologous recombination and chromosomal rearrangements - CAST-seq

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary: Despite lingering genotoxicity concerns, CRISPR-based genome editing has progressively entered the gene therapy field. Here we report that interactions between nucleotide sequences that are localized on the same chromosome and exhibit a high degree of homology contribute substantially to post-editing chromosomal rearrangements. We successfully employed corrective editing strategies at the NCF1 gene, as well as at the colocalized pseudogenes, NCF1B and NCF1C, in a human cell line model of p47phox-deficient chronic granulomatous disease and in patient-derived human hematopoietic stem cells. Upon genetic manipulation, an improved droplet digital PCR-based method identified cells with altered copy numbers, spanning megabases from the edited loci. We attributed the high aberration frequency to the interaction between repetitive sequences and their predisposition to recombination events. Our findings emphasize the need for careful evaluation of the target-specific genomic context, such as the presence of homologous regions, whose genome instability can constitute a risk factor for chromosomal rearrangements upon genome editing.

overall_design: NCF1B and NCF1C gene loci were simultaneously targeted with Cas9- and Cas12a-RNPs in mobilized peripheral blood human CD34+ cells from a healthy donor. Genotoxicity was assesed via CAST-Seq.

first: Carla

last: Fuster Garcia

first: Toni

last: Cathomen

first: Federica

last: Raimondi

first: Kah

last: Siow

first: Dominik

last: Wrona

first: Oleksandr

last: Pastukhov

first: Michael

last: Schmitz

first: Katja

last: Bargsten

first: Lucas

last: Kissling

first: Daan

middle: C

last: Swarts

first: Ute

last: Modlich

first: Martin

last: Jinek

first: Janine

last: Reichenbach


title: YAP-TEAD complex inhibits photoaging via transcriptional regulation of homologous recombination repair in mouse (smal) - lncRNA-seq

status: Public on Oct 15 2024

city: Kunming

first: Yi hang

last: Huang

state: Yunnan

address: No. 1168 Chunrong West Road, Yuhua Street, Chenggong District, Kunming City

institute: Kunming Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Occurrence and mechanism of photoaging in mouse back skin

overall_design: A total of 6 samples from two groups of mice were subjected to UV irradiation and their transcriptomes were sequenced

first: Jia

last: Xiaorong

first: Yang

last: zhi


title: The therapeutic potential and significance of the PELP1 signaling pathway in hepatocellular carcinoma

first: Yidong

last: Chen

summary: We examined the significance and therapeutic potential of targeting PELP1 in Hepatocellular carcinoma. Total RNA were isolated from HEP3B-control Sh, and HEP3B-PELP1-Sh cells using RNeasy mini kit, and total RNA was isolated for RNA-seq analysis. Our results demonstrated that PELP1 knockdown regulates pathways related to inflammation and interferon signaling and downregulates several pathways including MYC and E2F.

overall_design: Total RNA were isolated from Hep3B-control Sh, and Hep3B-PELP1-Sh using RNeasy mini kit (Qiagen). For whole-genome transcriptome profiling, 2 libraries (3 replicates from each group) were generated using a TruSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol (Illumina Inc.). Samples were sequenced on the Illumina HiSeq 3000 platform (Illumina Inc.) using the 50 base-pair single-read (50SR) sequencing module.

first: Ratna

last: Vadlamudi

first: Uday

middle: P

last: Pratap

first: Zhao

last: Lai


title: Identification of Postn + periosteal stem cells that orchestrate bone regeneration

city: Chendu

first: Fangyuan

last: Shen

state: --- Select a state ---

address: No.29 Jiuyanqiao Wangjiang Road, Chengdu, 610064

institute: Sichuan University

summary: Bone fracture healing requires skeletal stem cells (SSCs), which facilitate intramembranous ossification and endochondral ossification in long bone fractures. Although the periosteum is necessary for bone homeostasis and regeneration, the in vivo origin and regulatory mechanisms of periosteal SSCs (P-SSCs) remain unclear. Here, we identified Postn+ P-SSCs at the cambium layer of the periosteum that actively orchestrate regeneration in response to bone injury. Notably, the Postn+ P-SSCs that arise during bicortical fractures are likely derived from Gli1+ P-SSCs. In addition, Postn+ cell ablation compromises cortical bone homeostasis and bone regeneration. The IGF signal is indispensable in the regulatory effect of Postn+ P-SSCs on bicortical fractures since the genetic deletion of Igf1r in Postn+ cells dampens bone fracture healing. Taken together, adult Postn+ cells are region-specific P-SSCs that contribute to bone homeostasis and regeneration and are partially dependent upon IGF signaling.

overall_design: Bone callus was digested to isolate the periosteal cells within the callus at 7/10/14 day after femoral fracture. A CD45/CD31/Ter119 cocktail was used to exclude hematopoietic and endothelial cells by FACS, and mesenchymal lineages (referred to as the CD45-negative population) were selected for scRNA-seq via the 10x Genomics approach.


title: mgo promotes the expression of a gene cluster that contributes to the survival of Pseudomonas syringae in tomato leaflets

city: East Lansing

first: Qiang

last: Guo

state: MI

address: 612 Wilson Rd

department: MSU-DOE Plant Research Laboratory

institute: Michigan State University

summary: Pseudomonas syringae is an important plant pathogen that infects a wide variety of crops. The mgo (mangotoxin-generating operon) gene cluster produces an extracellular signaling molecule, leudiazen, and is highly conserved in Pseudomonas syringae strains. Here, we genetically removed mgo in Pseudomonas syringae pv. syringae (Pss) UMAF0158 to interrogate its impacts on bacterial infection. Loss of mgo not only alleviated the chlorosis symptom caused by Pss UMAF0158 infection, but also reduced bacterial population in tomato leaflets. Structure-activity relationship revealed that the diazeniumdiolate group and the isobutyl side chain of leudiazen are critical for its signaling activity. Through global transcriptome analysis, we found that mgo regulates the expression of a new gene cluster in addition to mangotoxin biosynthetic operon, namely RS17235-RS17245. This new gene cluster contributes to in planta survival of Pss UMAF0158 and is widely distributed in Pseudomonas syringae strains. Our results demonstrate that chemical signaling systems in plant pathogens play prominent roles in virulence and population increase and set stages for understanding downstream components of mgo-regulated signaling pathways.

overall_design: Analysis of Pss UMAF0158 (wild-type) and Δmgo, with three biological replicates per genotype (six total samples).


title: Spatial Multiomics Reveals Metabolic Reprogramming and Calcification Characteristics of Diabetic Macroangiopathy

city: Zhenjiang

first: Zhongqun

last: Wang

address: Jiefang road 438

institute: Affiliated Hospital of Jiangsu University

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

overall_design: Refer to individual Series


title: The mouse Balbiani body regulates primary oocyte quiescence via RNA storage

city: Columbia

first: Lei

last: Lei

state: MO

address: 920 East Campus Dr

department: of Obstetrics, Gynecology and Women's Health

institute: University of Missouri School of Medicine

summary: In mammalian females, the transition between dormancy in primordial follicles and follicular development is critical for maintaining ovarian function and reproductive longevity. In mice, the quiescent primary oocyte of the primordial follicle contains a Balbiani body (B-body), represented by a spherical aggregate of Golgi complexes. Here we show that the structure of the B-body is maintained by microtubules and actin. The B-body stores mRNA-capping enzyme and 597 mRNAs associated with mRNA-decapping enzyme 1A (DCP1A). Gene ontology analysis results indicate that proteins encoded by these mRNAs function in enzyme binding, cellular component organization and packing of telomere ends. Pharmacological depolymerize microtubules or actin led to B-body disassociation and nascent protein synthesis around the dissociated B-bodies within three hours. An increased number of activated developing follicles were observed in ovaries with prolonged culture and in vivo mouse model. Our results indicate that the mouse B-body is involved in the activation of dormant primordial follicles likely via translation of the B-body-stored RNAs in primary oocytes.

overall_design: To identify the RNAs that interact with DCP1A protein in mouse primary oocytes, we conducted RNA-immunoprecipitation sequencing of postnatal day 8 ovarian cortex tissues using  a DCP1A antibody.


title: Consequences of the perivascular niche remodeling for tumoricidal T-cell trafficking into metastasis of ovarian cancer [scRNA-seq]

city: Buffalo

first: Jianmin

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: We investigated the mechanisms by which inflammatory responses generated by tumor-specific T cells delivered to ovarian tumor-bearing mice alone or after oncolytic vaccinia virus-driven immunogenic cancer cell death affect antitumor efficacy using  scRNA-seq.

overall_design: Tumor draining lymph nodes  in MOVCAR 5009 tumor-bearing SCID mice were analyzed using 10 Genomics single cell RNASeq platfomr 10 days after the treatment.

first: Marta

last: Winkle

first: Danuta

last: Kozb


title: Consequences of the perivascular niche remodeling for tumoricidal T-cell trafficking into metastasis of ovarian cancer [Spatial Transciptomics]

summary: We investigated the mechanisms by which inflammatory responses generated by tumor-specific T cells delivered to ovarian tumor-bearing mice alone or after oncolytic vaccinia virus-driven immunogenic cancer cell death affect antitumor efficacy using spatial transcriptomics.

overall_design: Changes in the perivascular tumor microenvironment within the ovarian cancer metastasis in MOVCAR 5009 tumor-bearing SCID mice were analyzed by Spatial Transcriptomic analysis using 10x Genomic Visium platform 10 days after the treatment.


title: Lymphatic-specific Methyltransferase3-mediated m6A modification drives vascular patterning through prostaglandin metabolism reprogramming

city: Nanjing

first: Lianjun

last: Shi

state: Jiangsu

address: No.138 Hanzhong Road

institute: Eye Hospital, Nanjing Medical University

summary: Lymphangiogenesis plays a pivotal role in the pathogenesis of various vascular disorders, including ocular vascular diseases and cancers. Deregulation of N6-methyladenosine (m6A) modification has been identified as a key contributor to human diseases. However, the specific involvement of m6A modification in lymphatic remodeling remains poorly understood. In this study, we demonstrate that inflammatory stimulation and corneal sutures induce elevated levels of METTL3-mediated m6A modification. METTL3 knockdown inhibits lymphatic endothelial viability, proliferation, migration, and tube formation in vitro. METTL3 knockdown attenuates corneal sutures-induced lymphangiogenesis and intratumoral lymphangiogenesis initiated by subcutaneous grafts, consequently restraining corneal neovascularization, tumor growth, and tumor neovascularization in vivo. Mechanistically, METTL3 knockdown upregulates prostaglandin-endoperoxide synthase 2 (PTGS2) expression through an m6A-YTHDF2-dependent pathway, enhancing the synthesis of cyclopentenone prostaglandins (CyPGs). Aberrant CyPG production in lymphatic endothelial cells impairs mitochondrial oxidative phosphorylation, contributing to pathological lymphangiogenesis. Moreover, selective inhibition of METTL3 with STM2457 reduces m6A levels in lymphatic endothelial cells, effectively suppressing pathological lymphangiogenesis. This study provides compelling evidence that lymphatic-specific METTL3 plays a critical role in vascular patterning through prostaglandin metabolism reprogramming. Thus, METTL3 emerges as a promising target for treating pathological lymphangiogenesis.

overall_design: Examination of transcript expression differences between HLECs with or without METTL3 gene knocked down by shRNA.

first: Shuting

last: Lu

first: Xue

last: Han

first: Fan

last: Ye

first: Xiumiao

last: Li

first: Ziran

last: Zhang

first: Qin

last: Jiang

first: Biao

last: Yan


title: Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer factor-mediated zygotic genome activation [RNA-seq]

city: Madison

first: Melissa

last: Harrison

state: Wisconsin

address: 6204B Biochemical Sciences Building, 440 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin- Madison

summary: Immediately after fertilization the genome is transcriptionally quiescent. Maternally encoded pioneer transcription factors reprogram the chromatin state and facilitate the transcription of the zygotic genome. In Drosophila, transcription is initiated by the pioneer factor Zelda. While Zelda-occupied sites are enriched with histone acetylation, a post-translational mark associated with active cis-regulatory regions, the functional relationship between Zelda and histone acetylation in zygotic genome activation remained unclear. We show that Zelda-mediated recruitment of the histone acetyltransferase CBP is essential for zygotic transcription and embryonic development. CBP catalytic activity is necessary for release of RNA Polymerase II (Pol II) into transcription elongation. However, CBP largely activates zygotic transcription independent of acetylation through Pol II recruitment. Neither acetylation nor CBP are required for the pioneering function of Zelda. Our data suggest that pioneer factor-mediated recruitment of CBP is a conserved mechanism required to activate zygotic transcription but that this role is separable from the function of pioneer factors in restructuring chromatin accessibility.

overall_design: This data set contains single-embryo RNA-seq on embryos precisely staged 15 minutes into nuclear cycle 14 during the maternal-to-zygotic transition. GFP-CBP;his2AV-RFP and GFP-CBP;nos-deGrad/+;his2AV-RFP embryos were used to quantify the effect CBP knockdown has on transcription during zygotic genome activation. To assay the catalytic function of CBP we used an optogenetic line, CRY2-CBP, to inactivate CBP mediated histone acetyltransferase with blue light treatments. CRY2-CBP;his2av-RFP were treated with blue light to inactivate CBP catalytic activity via the CRY2 optogenetic tag or left in the dark as a control to assay the function of CBP mediated acetylation during ZGA. His2AV-RFP control embryos were treated similarly and used to compare to CRY2-CBP;His2avRFP embryos.

first: Audrey

middle: J

last: Marsh

first: Sergei

last: Pirogov

first: Abby

last: Ruffridge

first: Suresh

last: Sajwan

first: Tyler

last: Gibson

first: George

last: Hunt

first: Mattias

last: Mannervik


title: CD38 controls IL-2 production in CD4 T cells

city: Boston

first: Morgane

last: h

state: MA

address: 3 Blackfan Street

department: Rheumatology

institute: BIDMC

summary: CD38 has emerged as a potential therapeutic target for patients with systemic lupus erythematosus (SLE) but it is not known whether CD38 alters CD4+ T cell function. Using primary human T cells and CD38-sufficient and -deficient Jurkat T cells, we demonstrate that CD38 shifts the T cell lipid profile of gangliosides from GM3 to GM2 by upregulating B4GALNT1 in a Sirtuin 1-dependent manner. Enhanced expression of GM2 causes ER stress by enhancing Ca2+ flux through the PLC_1-IP3 pathway. Interestingly, correction of the calcium overload by an IP3 receptor inhibitor, but not by a store-operated calcium entry (SOCE) inhibitor, improves IL-2 production by CD4+ T cells in SLE. This study demonstrates that CD38 affects calcium homeostasis in CD4+ T cells by controlling cell membrane lipid composition that results in suppressed IL-2 production. CD38 inhibition with biologics or small drugs should be expected to benefit patients with SLE.

overall_design: Total RNA was extracted from JurkatControl and JurkatCD38KO using the RNeasy mini kit (QIAGEN) and submitted for RNA sequencing to the Molecular Biology Core Facilities at the Dana-Farber Cancer Institute (DFCI). Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits according to the manufacturer’s protocols. Samples were sequenced on an Illumina NextSeq500 run with single-end 75-bp reads. Data analyses were performed using the VIPER pipeline by the DFCI Core.

first: Eri

last: Katsuyama

last: Tsokos


title: Anti-inflammatory role of low intensity pulsed ultrasound in inhibiting LPS-induced M1 polarization of RAW264.7 via Wnt2b/AXIN/β-catenin

city: Suzhou

first: Juan

last: Yin

address: 80 Tian'e Dang Road

department: Suzhou Key Laboratory of Gut Microecology

institute: The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University

summary: Low-intensity pulsed ultrasound (LIPUS) is a special type of low intensity ultrasound. In periodontal disease, LIPUS was applied as an adjuvant and non-invasive therapeutic treatment. While, the specific mechanism of LIPUS in the treatment of periodontal disease is not quite clear.RAW264.7 cells were induced to M1/M2 macrophage-like polarization by LPS/IL4. LIPUS was performed to stimulate RAW264.7 cells at an intensity of 45 mW/cm2, 25 min, interval 24 h, twice. The polyA mRNA sequencing of LPS induced RAW264.7 cells, LPS induced and LIPUS treated RAW264.7 cells were conducted.Our results suggested that LIPUS played an anti-inflammatory role by inhibiting LPS-induced M1 polarization of RAW264.7 cells in an Wnt2b/AXIN/β-catenin dependent way. LIPUS may inhibit inflammation in periodontal diseases by regulating macrophage differentiation, so as to play a therapeutic role in periodontal diseases.

overall_design: To investigate the specific mechanism of Low-intensity pulsed ultrasound (LIPUS) in periodontal disease. RAW264.7 cells were induced by 100ng/mL LPS to M1 polarization for 48 hours. LIPUS was performed to stimulate RAW264.7 cells at an intensity of 45 mW/cm2, 25 min, interval 24 hours, twice. RAW264.7 cells induced by LPS, or treated with LPS and LIPUS, were analyzed by RNA sequencing to discover differential gene expression profiling. 3 replicates of each group were analyzed by RNA sequencing.

first: Mingxin

last: Xu

first: Hui

last: Xue

first: Xing

last: Yang

first: Yu

last: Bao


title: Intracellular expression of a chimeric antigen reverses resistance to cancer immunotherapy

city: Kyoto

first: kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

country: Japan

institute: Graduate School of Medicine, Kyoto University

summary: The interaction of frameshift mutation-derived cancer neoantigens and cancer immunotherapy remains unknown. We found that live cell adjuvant or cDNA transfection in the muscle, which express MHC-class I and class II-restricted non-self-peptides, generated broad-spectrum anti-tumor immunity. Such chimeric peptides did not need to be tumor-neoantigens, but must be in a single chain (complete T cell antigen: CTA). Long product of frameshift mutation frequently contained CTA and the colon cancer patients with the long frameshift products (>120 amino acids) showed a good prognosis. Mechanistically, live cell adjuvant expressing CTA strengthened crosstalk between dendritic cells and CD8+ T cells in a CD4+ T cells-dependent manner. This cross talk suppressed CD8+ T cell exhaustion and produced stem-cell like progenitor CD8+ T cells in vivo. Combination of the live cell adjuvant conversed unresponsive tumors to responsive to PD-1 blockade therapy. Together, our findings provide a new broad-spectrum cancer immunotherapy, and clarify the type of frameshift neoantigens controlling the efficacy.

overall_design: A total of 4 single cell rna seqence samples, including a pair of tumor-infiltrating CD8+ T cells(CD8 TILs), and a pair of draining lymph node single cells(DLN). Treatment group were MC38 tumor-bearing mice (control),and MC38 tumor-bearing mice receive alive adjuvant Bpmel-SIY-OVAII immunization.(SIY-OVAII)

first: Rongsheng

last: Zhang

first: Yaguchi

last: Tomonori

first: Tasuku

last: Honjo

first: Kenji


title: Pathogenic mechanism and therapeutic intervention of impaired N7-methylguanosine (m7G) tRNA modification [TRAC-Seq]

city: Canton

first: jieyi

last: Ma

state: Guangdong province

address: No.58 Zhong Shan Er Road

department: 1Department of Otolaryngology

institute: the First affiliated hospital of Sun Yat-sen University

type: Methylation profiling by high throughput sequencing

summary: The tRNA N7-methylguanosine (m7G) modification is not essential for yeast growth, but in mammals mis-regulations of tRNA m7G modification cause stem cell defect and developmental disorders. Here we found that homozygous mutated WDR4 caused microcephaly, retardation in motor coordination and spatial learning ability in mice, which mimics the symptom in human patients with WDR4 mutation. Further analysis revealed that homozygous mutation of WDR4 impaired tRNA m7G modification and reduced the translation level of genes involved in mTOR signaling pathway in mouse brain, which further caused endoplasmic reticulum (ER) stress and cell death. Our study uncovered a new layer of translation regulation mechanism mediated by tRNA m7G modification, provided strong evidence to support the important physiological function of mis-regulated tRNA modification in neuron disorders.

overall_design: TRAC-Seq were developed to identify the tRNA m7G methylome in mouse brain.

first: Jieyi

first: Shuibin

last: Lin


title: RNAseq data for COV362 and PEO1 cell lines treated with DMSO (vehicle) or Prexasertib 20 nM

city: Rochester

first: Cristina

last: Correia

state: Minnesota

address: Kellen Bld 3 th Floor, 200 1st street SW

institute: Mayo Clinic

summary: RNAseq data of 12 samples of PEO1 and COV362 cell lines treated with DMSO or Prexasertib (20 nM for 48 h) each in three independent experiments.

overall_design: RNA-Seq

first: Scott

last: Kaufmann


title: TARGETING KRAS SIGNALING AT THREE INDEPENDENT NODES LEADS TO COMPLETE AND DURABLE PANCREATIC CANCER REGRESSION [Methylation array]

city: Madrid

first: Vasiliki

last: Liaki

address: Melchor Fernandez Almagro 3

country: Spain

institute: CNIO

type: Methylation profiling by genome tiling array

summary: Pancreatic ductal adenocarcinoma (PDAC) has one of the lowest cancer survival rates. Although KRAS oncogenes are responsible for the initiation of most PDACs, thus far KRAS inhibitors have not changed their clinical outcome. Here, we describe a therapeutic strategy that combines inhibition of three independent signaling nodes involved in downstream (RAF1), upstream (EGFR) and orthogonal (STAT3) KRAS signaling pathways. Genetic elimination and/or pharmacological inhibition/degradation of these independent nodes in orthotopic mouse tumor models results in their complete and durable regression.  The efficacy of this therapeutic strategy has also been validated in several patient-derived organoid (PDO) and xenograft (PDX) PDAC tumor models using a combination of a Pan-ERBB inhibitor (Afatinib), a selective STAT3 PROTAC (SD36) and a RAF1 shRNA. Importantly, this triple strategy did not induce significant toxicities. These results open the door to the development of novel targeted therapies for PDAC patients.

overall_design: We explanted mouse Pancreatic Ductal Adenocarcinomas (PDACs) in culture from different tumors. All cultures were infected with Adeno-GFP viral particles.  We then bisulphite converted DNA from 12 cell lines and then, they were hybridized to the Illumina Infinium Mouse Methylation BeadChip.

first: Carmen

last: Guerra


title: The unique Legionella longbeachae capsule favors intracellular replication and immune evasion

city: Paris

first: Christophe

last: Rusniok

address: 25, 28 rue du Docteur Roux

department: Genomes et Genetique

institute: Institut Pasteur

summary: To study the gene expression of wild-type L. longbeachae and a mutant in the capsule transporter gene ctrC, we grew each strain to exponential, post-exponential or stationary phase and extracted RNA for RNAseq.

overall_design: L. longbeachae wild-type and ΔctrC were grown in rich yeast medium (BYE) to reach exponential, post-exponential or stationary phase. RNA was isolated from quadruplicate samples and analyzed by RNAseq. Gene expression was compared for wild-type samples between exponential and post-exponential phase, and between wild-type and ΔctrC for exponential and post-exponential phase, respectively.

first: Silke

last: Schmidt

last: Buchrieser


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild and intervertebral disc degeneration mice

city: WuHan

first: Xiao-Jun

last: Yu

address: Jiefang Blvd

department: Department of Orthopedics, Tongji Hospital, Tongji Medical College

institute: Huazhong University of Science and Technology

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived intervertebral disc transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: Methods: Retinal mRNA profiles of 21-day-old Wild and intervertebral disc degeneration mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays


title: IRE1a silences double stranded RNA through RIDD

city: Houston

first: FEI

last: YUAN

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Chemotherapy is often combined with immune checkpoint inhibitor (ICI) to enhance immunotherapy responses. Despite the approval of chemo-immunotherapy in multiple human cancers including triple-negative breast cancer (TNBC), immunologically cold tumors remain largely unresponsive due to weak chemotherapy-stimulated immune responses. The mechanisms determining the immunogenicity of chemotherapy in immunologically cold tumors remain largely unknown. Here, we identify the endoplasmic reticulum (ER) stress sensor IRE1α as a critical checkpoint that restricts the immunogenicity of taxane chemotherapy and prevents the innate immune recognition of immunologically cold TNBC. IRE1α RNase silences chemotherapy-induced double-stranded RNA (dsRNA) through RIDD (Regulated IRE1-Dependent Decay) to prevent NLRP3 inflammasome–dependent pyroptosis. Inhibition of IRE1α RNase activity with a selective RNase inhibitor ORIN1001, currently in Phase I clinical trial, allows taxane chemotherapy to induce extensive dsRNA accumulation and activate NLRP3 inflammasome–dependent gasdermin D (GSDMD) cleavage. This triggers pyroptosis and a highly effective immune response in immunologically cold TNBC.

overall_design: J2-RIP and paired INPUT controls were performed in biological triplicates.

first: Longyong

last: Xu

first: Fei

last: Yuan

first: Xi

last: Chen


title: Effect of Ad-NNMT and Ad-NC Transfection on Histone Modification and Methylation in Human Umbilical Vein Endothelial Cells

city: Beijing

first: Jun

last: Guo

address: Dahua Road

institute: Beijing Hospital

summary: This study investigates the epigenetic impact of Nicotinamide N-methyltransferase (NNMT) overexpression on human umbilical vein endothelial cells (HUVECs). HUVECs were transfected with adenovirus vectors, Ad-NC (negative control) or Ad-NNMT (overexpressing NNMT), for 48 hours. Subsequently, protein was collected for chromatin immunoprecipitation analysis using antibodies against H3K4me3 and H3K27me3 via Cut&Tag technology. To further elucidate the effects on DNA methylation, whole-genome methylation sequencing was performed. The resulting data provide insight into NNMT's regulatory role in histone modifications and methylation patterns.

overall_design: Human umbilical vein endothelial cells (HUVECs) were cultured and transfected with either Ad-NC or Ad-NNMT for 48 hours. Following transfection, chromatin-associated proteins were subjected to Cut&Tag analysis using H3K4me3 and H3K27me3 antibodies to examine histone modifications. Subsequently, DNA methylation sequencing was performed to investigate the effects of NNMT overexpression on the methylation landscape. Comparative analyses were carried out between Ad-NC and Ad-NNMT transfected cells to understand the role of NNMT in epigenetic regulation.

first: Jiameng

last: Yin

first: Jian

last: Li


title: Single-cell atlas of the pregnant equine endometrium before and after implantation.

city: Olsztyn

first: Dawid

last: Tobolski

state: Warmińsko-mazurskie

address: Kazimierza Jaroszyka

department: Department of Large Animal Diseases and Clinic

country: Poland

institute: Institute of Veterinary Medicine, Warsaw University of Life Sciences

summary: Embryo implantation in the mare occurs just over one month after fertilization, coinciding with the production of chorionic gonadotropin. The factors that regulate this late implantation in the mare, and whether they are unique or shared with more invasive embryos, remains poorly understood.  This study aimed to determine and compare the transcriptome and subpopulations of endometrial cells before and after embryo implantation in the horse. Single-cell RNA sequencing was used to characterize the transcriptome of nearly 97 000 endometrial cells collected from biopsies of the endometrium at the beginning (day 33 of gestation) and the end of the embryo implantation (day 42 of gestation) in mares. Sixteen immune and 24 non-immune cell clusters were identified representing all known main cell populations, as well as subpopulations of horse immune cells such as resident innate lymphoid cells and mucosal-associated invariant T cells. Contrary to current knowledge, endometrial natural killer (eNK) cells were the most abundant endometrial leukocyte population during implantation in horses. Moreover, eNK cells not only expressed genes which may interact with fetal MHC I such as LY49F but also exert immunoregulatory functions regardless of MHC I expression such as CD96/TIGIT. Analogous to other species studied, upregulation of CXCR4 was found in several subpopulations of immune cells. Our results suggest that despite distinctive and later placentation compared with humans, horses share some key similarities in the mechanisms of embryo implantation.

overall_design: Endometrial biopsies were collected from pregnant mares at day 33 (N=4) and day 42 (N=4) of pregnancy, cells were enriched over Ficoll and subjected to scRNAseq. In the final analysis 3 samples from each gestational day were retained.

first: Joanna

last: Jaworska

first: Anne

last: Kahler

first: Shebl

last: Salem

first: Izabela

last: Wocławek-Potocka

first: Amanda

last: De Mestre


title: The combination of a microbial and a non-microbial biostimulant increases yield in lettuce (Lactuca sativa) under salt stress conditions by up-regulating cytokinin biosynthesis

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

summary: Salinization poses a significant challenge in agriculture, exacerbated by anthropogenic global warming. Biostimulants, derived from living microorganisms or natural extracts, have emerged as valuable tools for conventional and organic agriculture. However, our understanding of the molecular mechanisms underlying the effects of biostimulants is very limited, especially in crops under real cultivation conditions. In this study, we adopted an integrative approach to investigate the effectiveness of the combined application of plant growth-promoting bacterium (Bacillus megaterium strain BM08) and a non-microbial biostimulant under control conditions (normal watering) and salt stress. After confirming the yield increase under both conditions, we investigated the molecular mechanisms underlying the observed effect by measuring a number of physiological parameters (i.e., lipid peroxidation, antioxidants, chlorophylls, total phenolics and phytohormone content), as well as RNA sequencing and primary metabolite analyses. Our findings reveal that the combined effect of the microbial and non-microbial biostimulants led to a decrease in the antioxidant response and an up-regulation of genes involved in cytokinin biosynthesis under salt stress conditions. This, in turn, resulted in a higher concentration of the bioactive cytokinin, isopentenyladenosine, in roots and leaves and an increase in γ-aminobutyric acid, a non-proteic amino acid related to abiotic stress responses. In addition, we observed a decrease in malic acid, along with an abscisic acid (ABA)-independent up-regulation of SR-kinases, a family of protein kinases associated with abiotic stress responses. Furthermore, we observed that the single application of the non-microbial biostimulant triggers an ABA-dependent response under salt stress; however, when combined with the microbial biostimulant, it potentiated the mechanisms triggered by the BM08 bacterial strain. This comprehensive investigation shows that the combination of two biostimulants is able to elicit a cytokinin-dependent response that may explain the observed yield increase under salt stress conditions.

overall_design: To investigate the effect of the biostimulant Calbio (BS) alone or in combination with microorganisms: A bacterial strain (PGPB) and an arbuscular mycorrhizal fungus (AMF) under normal and saline stress conditions. For this purpose, lettuce plants were grown in greenhouse conditions and 6 treatments were carried out: control (without product), Calbio (BS), Bacteria (PGPB), mycorrhizal fungus (AMF), Calbio with bacteria (BS+PGPB) and Valbio with mycorrhizal fungus (BS+AMF); under two conditions: normal and saline stress. From this, a transcriptomic profile analysis was carried out with the aim of observing the effect of the different treatments on the plant's response to saline stress. To do this, the effect of the different individual treatments (BS, PGPB and AMF) was compared with the combined treatments (BS+PGPB and BS+AMF). For the transcriptomic analysis, three biological replicates of each of the treatments and conditions were used. In addition, to make a more detailed analysis, the expression was analyzed both in root and leaf.

first: Patricia

last: Benito

first: Marina

last: Celdrán

last: Bellón

first: Vicente

last: Arbona

first: Miguel

last: González-Guzmán

first: Rosa

last: Porcel

first: Lynne

last: Yenush

first: José

last: Mulet


title: Transcriptional rearrangements associated with thermal stress and preadaptation in Baikal whitefish (Coregonus baicalensis)

city: Irkutsk

first: Tuyana

last: Sidorova

address: 3, Ulan-Batorskaya

department: Siberian Branch of the Russian Academy of Sciences

country: Russia

institute: Limnological Institute

summary: In this work, we describe the transcriptional profiles of adapted and non-adapted one-month-old Baikal whitefish juveniles after heat shock exposure. Preadapted fish were exposed to a repeated thermal rise of 6 °C above control temperature every 3 days throughout embryonic development. One month after hatching, preadapted and non-adapted larvae were either maintained at control temperatures (12 °C) or exposed to an acute thermal stress (TS) of 12 °C above control temperature. The information on transcriptional profiles will contribute to further understanding of the mechanisms of adaptation of whitefish to the environment.

overall_design:
To study the effects of temperature stress, a transcriptomic analysis of adapted and non-adapted fish was conducted. For these purposes, the fish were divided into 4 groups: 1) a1_C_P Preadapted Control (C_P) in the temperature experiment on Baikal whitefish (Coregonus baicalensis) larvae: eggs adaptation at 30 days after fertilization (two times a week, increased temperature by 6 °C over the control of 3–3.5 °C, then lowering it to baseline values). Preconditioning training lasted for three months in total. In one month after adaptation, the larvae were sampled. 2) a2_AcS_P Preadapted Treatment (AcS_P) in the temperature experiment on Baikal whitefish (Coregonus baicalensis) larvae: eggs adaptation at 30 days after fertilization (two times a week, increased temperature by 6 °C over the control of 3–3.5 °C, then lowering it to baseline values). Preconditioning training lasted for three months in total. In one month after adaptation, larvae were exposed to "acute stress" up to 24 °C for two hours over the control of 12 °C, and sampled. 3) a3_AcS_N Non-adapted Treatment (AcS_NP) in the temperature experiment on Baikal whitefish (Coregonus baicalensis) larvae: One-month-old non-adaptated larvae were exposed to "acute stress" up to 24 °C for two hours over the control of 12 °C, and sampled. 4) a4_C_N Non-adapted Control (C_NP) in the temperature experiment on Baikal whitefish (Coregonus baicalensis) larvae: The temperature in the "control" aquariums remained constant at 12 °C throughout the experiment. One-month-old non-adaptated larvae were  sampled.

Grant ID No.: RSF 23-24-00644 (https://rscf.ru/project/23-24-00644/)
Grant title: Biomarkers of temperature stress and indicators of the well-being of whitefish in the natural environment and in aquaculture for the further use of these biomarkers for monitoring work
Funding source: Russian Science Foundation

first: Yulia

last: Sapozhnikova

first: Anastasiya

middle: G

last: Koroleva

middle: V

first: Sergey

last: Potapov

first: Alexander

last: Epifantsev

first: Evgenia

last: Vakhteeva

first: Lyubov

middle: I

last: Tolstikova

first: Olga

middle: Y

last: Glyzina

first: Vera

last: Yakhnenko

first: Valeria

last: Cherezova

last: Sukhanova


title: Droplet-based scRNA-seq of plasma-positive microglia and plasma-negative microglia from hypothalamus region in young mice

city: Stanford

first: Tony

last: Wyss-Coray

address: 290 Jane Stanford way, RM E365 TWC-Neurology

institute: Stanford University

summary: Microglia are highly responsive to their local environment and signals from the periphery. Blood plasma proteins readily permeate the healthy brain parenchyma. However, whether microglia are responsive to such proteins is unclear. Here, we identify a stable population of microglia takes up plasma proteins in a region-specific manner in healthy brains. To understand these two populations at the single cell transcriptomic level, we sorted plasma-positive microglia and plasma-negative microglia from hypothalamus region of young mice (3-month-old) and perform droplet-based scRNA-seq.

overall_design: Single cell RNAseq of sorted microglia from hypothalamus region of young mice 20 hours after injecting with dye-labeled plasma protein (from multiple pooled mice), using 10x Genomics Drop-seq (v3.1). Microglia are identified as plasma-positive microglia or plasma-negative microglia during FACS sorting step.

first: Nannan

last: Lu


title: YAP-TEAD complex inhibits photoaging via transcriptional regulation of homologous recombination repair in mouse (smal) - miRNA-seq

city: Kunming

first: Yi hang

last: Huang

address: No. 1168 Chunrong West Road, Yuhua Street, Chenggong District, Kunming City

institute: Kunming Medical University

summary: Occurrence and mechanism of photoaging in mouse back skin

overall_design: A total of 6 samples from two groups of mice were subjected to UV irradiation and their transcriptomes were sequenced

first: Jia

last: Xiaorong

first: Yang

last: zhi


title: ATAC-seq comparing CD4CD38low vs CD4CD38high T cells from healthy donors and SLE

first: Morgane

last: h

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Biological triplicates of sorted CD38high and low T cells  from HC and from SLE patients

first: Eri

last: Katsuyama

first: George

last: Tsokos


title: Bulk RNA-seq of primary microglia with LPS stress and ApoA-I treatment

summary: To test the functional role of ApoA-I on microglia in the context of stress, we treated primary microglia with LPS stress with or without ApoA-I protein, and used bulk RNA-seq to evaluate if ApoA-I exhibits an anti-inflammatory role.

overall_design: Primary rat microglia (DIV12) were treated with LPS (100 ng/ml) for 20 hours, with or without adding ApoA-I protein (100 ug/ml) in the culture medium. We have 4 groups in total (Con, LPS, ApoA-I, LPS+ApoA-I) and 4 replicates per group.

last: Wyss-Coary


title: TARGETING KRAS SIGNALING AT THREE INDEPENDENT NODES LEADS TO COMPLETE AND DURABLE PANCREATIC CANCER REGRESSION [RNA-seq]

first: Vasiliki

last: Liaki

overall_design:
We explanted mouse Pancreatic Ductal Adenocarcinomas (PDACs) in culture from 27 different tumors. All 27 cultures were infected with Adeno-GFP viral particles.  We then performed gene expression profiling of the 27 PDAC cultures infected with Adeno-GFP viral particles.
14 of those tumors were also infected with Adeno-CRE viral particles, for the genetic elimination of the floxed alleles Egfr and Raf1. We also performed differential expression analysis of the 14 PDAC cultures treated with Adeno-GFP vs Adeno-CRE viral particles, to detect differences before and after elimination of Egfr and Raf1.

first: Carmen

last: Guerra

first: Ruth

last: Alvarez


title: Location of polyadenylation sites within 3’ untranslated regions is linked to biological function in yeast

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

summary: Expression of a typical yeast gene results in ~50 3’ mRNA isoforms that are distinguished by the locations of poly(A) sites within the 3’ untranslated regions (3’ UTRs).The location of poly(A) sites with respect to the translational termination codon varies considerably among genes, but it is unknown whether this has any functional significance.Using hierarchical clustering of 3’ UTRs, we identify eight classes ofS. cerevisiaegenes based on their poly(A) site locations within 3’ UTRs.Genes involved in related biological functions (GO categories) are uniquely over-represented in six of these classes.Similar analysis ofS. pombegenes reveals three classes of 3’ UTRs, all of which show over-representation of functionally related genes.Remarkably,S. cerevisiaeandS. pombehomologs have similar patterns of poly(A) site locations.These observations suggest that the location of poly(A) sites within 3’ UTRs has biological significance.

overall_design: 3' READS to identify 3' isoforms (arising from alternative polyadenylation) of mRNA extracted from wild-type, exponentially growing S. pombe cells

first: Joseph

last: Geisberg

first: Kevin

last: Struhl


title: Histone H3.3 chaperone HIRA is required for acquired tolerance by rendering stress-responsive genes poised for prospective lethal stresses [RNA-seq]

city: Kyoto-shi

first: Yoshikazu

last: Nagagaki

address: Yoshida-Konoe-cho, Sakyo-ku

institute: Kyoto University

summary: Appropriate responses to environmental challenges are imperative for the survival of all living organisms. Exposure to low-dose stresses is recognized to yield increased cellular fitness, a phenomenon termed hormesis. However, our molecular understanding of how cells respond to low-dose stress remains profoundly limited. Here we report that histone variant H3.3-specific chaperone, HIRA, is required for acquired tolerance, where low-dose heat stress exposure confers resistance to subsequent lethal heat stress. We found that human HIRA activates stress-responsive genes, including HSP70, by depositing histone H3.3 following low-dose stresses. These genes are also marked with histone H3 Lys-4 trimethylation and H3 Lys-9 acetylation, both active chromatin markers. Moreover, depletion of HIRA greatly diminished acquired tolerance, both in normal diploid fibroblasts and in HeLa cells. Collectively, our study revealed that HIRA is required for eliciting adaptive stress responses under environmental fluctuations and is a master regulator of stress tolerance.

overall_design: To investigate thr gene expression profile after low-dose of heat stress (40°C, 2 hr), we performed RNA-seq of samples with or without the stress treatment.

first: Ryuichiro

last: Nakato

first: Fuyuki

last: Ishikawa


title: Identification of a link between splicing and endoplasmic reticulum proteostasis

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

institute: FU berlin

summary: The role of general splicing in endoplasmic reticulum (ER)-proteostasis remains poorly understood. Here, we identify SNRPB, a component of the spliceosome, as a novel regulator of export from the ER. Mechanistically, SNRPB regulates the splicing of components of the ER export machinery, including Sec16A, a regulator of ER exit sites. Loss of function of SNRPB is causally linked to cerebro-costo-mandibular syndrome (CCMS), a genetic disease characterized by bone defects. We show that heterozygous deletion of SNRPB in mice resulted in intracellular accumulation of type-1 collagen as well as bone defects reminiscent of CCMS. Silencing SNRPB inhibited osteogenesis in vitro, which could be rescued by overexpression of Sec16A. This indicates that the role of SNRPB in osteogenesis is linked to its effects on ER export. Finally, we show that SNRPB is a target for the unfolded protein response (UPR), which supports a mechanistic link between the spliceosome and ER-proteostasis. Our work highlights SNRPB as a novel node in the proteostasis network, shedding light on CCMS pathophysiology.

overall_design: HeLa cells were transfected with HiPerFect either with a CTRL siRNA or an siRNA targeting SNRPB. RNA was extracted and analyzed by RNA-Seq.

first: Hesso

last: Farhan


title: Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors [RNA-Seq]

first: Zimu

last: Zhang

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: LIM domain-binding protein 1 (LDB1) is a highly conserved and widely expressed chromatin looping protein that connects enhancer-promoter genes through LIM and LIM homologous domains in various cell types. LDB1 has been confirmed to play a crucial role in various physiological and pathological processes. In our study, we aim to investigate the function and mechanisms of LDB1 in the context of T-cell acute lymphoblastic leukemia (T-ALL). RNA-seq was conducted and the differently expressed genes were revealed in the LDB1-knockdown 6T-CEM and J.gamma1 cells in comparison to control group. Cleavage Under Targets and Tagmentation (CUT&Tag) showed the co-localization of LDB1 with several master transcription factors on chromatin in 6T-CEM cells.

overall_design: mRNA profiles of 6T-CEM and J.gamma1 cells transfected with control shRNA (sh-NC) or sh-LDB1 were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Yan

last: Li

first: Shaoyan

last: Hu

first: Jian

last: Pan


title: Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors [CUT&Tag]

overall_design: CUT&Tag using antibody against LDB1, ERG, ETV6, IRF1, H3K27ac in 6T-CEM cells, antibody against LDB1 in MOLT4 and Loucy cells.


title: Enhancer looping protein LDB1 affects T-ALL cell proliferation by cooperating with master transcription factors

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

overall_design: Refer to individual Series


title: Assessment and Evaluation of Contemporary Approaches for Astrocyte Differentiation from hiPSCs: A Modeling Paradigm for Alzheimer's Disease

city: Brno

first: Martina

last: Zapletalová

address: Kamenice 5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

summary:
Background: Astrocytes have recently gained attention as key players in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease. Numerous differentiation protocols have been developed to study human astrocytes in vitro. However, the properties of the resulting glia are inconsistent, making it difficult to select an appropriate method for a given research question. Therefore, we compared three approaches for the generation of iPSC-derived astrocytes. We performed a detailed analysis using a widely used long serum-free (LSFP) and short serum-free (SSFP) protocol, as well as a TUSP protocol using serum for a limited time of differentiation.
Results: We used RNA sequencing and immunochemistry to characterize the cultures. Astrocytes generated by the LSFP and SSFP methods differed significantly in their characteristics from those generated by the TUSP method using serum. The TUSP astrocytes had a less neuronal pattern, showed a higher degree of extracellular matrix formation, and were more mature. The short-term presence of FBS in the medium facilitated the induction of astroglia characteristics but did not result in reactive astrocytes. Data from cell-type deconvolution analysis applied to bulk transcriptomes from the cultures assessed their similarity to primary and fetal human astrocytes.
Conclusions: Overall, our analyses highlight the need to consider the advantages and disadvantages of a given differentiation protocol for solving specific research tasks or drug discovery studies with iPSC-derived astrocytes.

overall_design:
The differentiation of iPSC-derived NPCs into astrocytes was performed using three different protocols: LSFP method (1), SSFP method (2) and TUSP method (3). For each method of astrocyte differentiation, cell pellet samples were taken after NPC expansion (AE), astrocyte induction (AI) and maturation (AM).
At the end of the maturation phase of the TUSP method of astrocyte differentiation and treatment, cells were treated in triplicate with 500 nM AB42 or 150 uM H2O2.
All collected cellular pellets were analysed with RNASeq.

first: Veronika

last: Juráková

first: Balazs

last: Szeky

last: Zapletalova

first: Anita

last: Feher

first: Melinda

last: Zana

first: Shashank

last: Pandey

first: Radek

last: Kucera

first: Omar

last: Šerý

first: Jiří

last: Hudeček

first: Andras

last: Dinnyes

first: Jan

last: Lochman


title: MYC-rearranged aggressive B-cell lymphoma are molecularly Burkitt Lymphoma despite of morphology.

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

type: Genome variation profiling by genome tiling array


title: MYC-rearranged aggressive B-cell lymphoma are molecularly Burkitt Lymphoma despite of morphology [OncoScan_CNV]

summary: Overall, the genetic profile of aggressive B-cell NHL in CAYA in the spectrum of BL and DLBCL is heterogeneous. MYC-R cases mostly displayed a molecular profile close to BL regardless of their morphology, whereas MYC-non-R had a more heterogeneous genetic landscape resembling DLBCL.

overall_design:
Using an integrated approach, including fluorescence in situ hybridization, targeted gene Next Generation Sequencing (NGS) sequencing, copy number arrays, and gene expression profiling, we characterized 37 B-cell lymphomas in CAYA with intermediate morphological features between DLBCL and BL, blastoid morphology, DLBCL morphology with MYC rearrangements, and BL without MYC rearrangements.
Please note that 'HG9_A_(OncoScan_CNV).CEL' file.(for the GSM8010850 HG9 sample) has been lost and thus is not provided.

first: Sara

last: Mato


title: Cytokine Priming Enhances the Antifibrotic Effects of Mesenchymal Stromal Cells Conditioned Medium Via Fibrogenic Myofibroblasts Elimination and Extracellular Matrix Degradation.

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

summary: Background: Fibrosis is a pathological scarring process characterized by persistent myofibroblasts activation with excessive accumulation of extracellular matrix (ECM). Fibrotic disorders represent an increasing burden of disease-associated morbidity and mortality worldwide for which there are limited therapeutic options. Reversing fibrosis requires the elimination of myofibroblasts, remodeling of the ECM, and regeneration of functional tissue. Multipotent mesenchymal stromal cells (MSC) have antifibrotic properties mediated by secreted factors present in their conditioned medium (MSC-CM). However, there are no standardized in vitro assays to predict the antifibrotic effects of human MSC, and, as a consequence, we lack evidence on the effect of cytokine priming on MSC’s antifibrotic effects. We hypothesize that the MSC-CM promotes fibrosis resolution in vitro and that this effect is enhanced following MSC cytokine priming. Methods: We tested the antifibrotic effects of resting and interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α) primed MSC-CM in three in vitro assays: prevention of fibroblast activation, myofibroblasts deactivation and ECM degradation. Furthermore, we performed transcriptomic analysis of myofibroblasts treated or not with resting- or primed-MSC-CM and proteomic characterization of resting- and primed-MSC-CM. Results: We report that MSC-CM treatment prevented TGF-β induced fibroblast activation and reduced fibrogenic myofibroblasts (i.e. transcriptomic upregulation of apoptosis, senescence, and inflammatory pathways). These effects were higher when primed rather than resting MSC-CM was used. Priming increased the ability of MSC-CM to remodel the extracellular matrix reducing its content of collagen I and fibronectin. Priming increased the following antifibrotic proteins in MSC-CM: DKK1, MMP-1, MMP-3, follistatin and cathepsin S. DKK1 inhibition reduced the anti-fibrotic effects of MSC-CM. Thus, cytokine priming increases antifibrotic factors in the MSC-CM which in turn amplify the anti-fibrotic effects of MSC-CM. Conclusions: In a pro-fibrotic in vitro environment MSC-CM promote fibrosis resolution, an effect enhanced following MSC cytokine priming. Specifically, MSC-CM reduces fibrogenic myofibroblasts through apoptosis, senescence, and inflammatory signals, as well as by enhancing ECM degradation. Future studies will establish the in vivo relevance of MSC priming to fibrosis resolution

overall_design: To investigate the effect of human adipose tissue derived multipotent mesenchymal stromal cell conditioned media [hMSC(AT)-CM] on modulating fibrotic responses in activated fibroblasts, we compared transcriptional responses in (1) resting human fibroblasts, (2) activated human fibroblasts (TGF-β treated, demonstrating a myofibroblast-like profile), and activated human fibroblasts treated with either (3) resting or (4) cytokine-primed (IFN-γ and TNF-α primed) hMSC(AT)-CM.

first: Mathieu

last: Mancini

first: Marianela

last: Brizio

first: Inés

last: Colmegna


title: Bulk RNA-seq of microglia from Apoa1 KO mice injected with ApoA-I protein intravenously

first: Tony

last: Wyss-Coray

summary: We found ApoA-I from blood can be taken up by microglia in the brain. To determine if ApoA-I from circulation is sufficient to restore microglial transcriptomic state to a more wild-type-like state, we performed a rescue experiment by intravenously injecting ApoA-I protein into adult Apoa1 KO mice and sorted microglia with or without ApoA-I uptake for bulk transcriptomic analysis.

overall_design: We intravenously injected ApoA-I protein three times, two days apart, into adult Apoa1 KO mice. One day before taking down the mice, we injected dye-labeled ApoA-I into both wild-type mice and Apoa1 KO mice. We then sorted ApoA1-Pos and ApoA1-Neg microglia from both WT mice and Apoa1 KO mice for bulk RNA-seq analysis. We have 4 groups in total and 4 replicates per groups.

first: Nannan

last: Lu


title: The underlying mechanism of SCNAs-induced lncRNA LOC101927668 overexpressoin facilitating colorectal cancer progression

first: wang

last: zaozao

state: Beijing

address: No. 52 Fucheng Rd., Haidian District

department: Key Laboratory of Carcinogenesis and Translational Research

institute: Peking University Cancer Hospital & Institute

summary: Somatic copy number alterations (SCNAs) are pivotal in cancer progression and patient prognosis. Dysregulated long non-coding RNAs (lncRNAs), modulated by SCNAs, significantly impact tumorigenesis, including colorectal cancer (CRC). Nonetheless, the functional significance of lncRNAs induced by SCNAs in CRC remains largely unexplored. In this study, we elucidate that the overexpression of LOC101927668, driven by SCNAs, facilitates CRC proliferation and metastasis by recruiting hnRNPD, thus perturbing the RBM47/P53/P21 signaling pathway.

overall_design:
To elucidate the underlying mechanism by which LOC101927668 promotes colorectal carcinogenesis, RNA sequencing analysis was employed to identify differentially expressed genes in LOC101927668-overexpressed RKO cells compared to control cells.
Each experimental group includes three biological replicates.

first: ZaoZao

last: Wang

first: ChenXin

last: Wu


title: Long-Read Sequencing of an Advanced Cancer Cohort Resolves Rearrangements, Unravels Haplotypes, and Reveals Methylation Landscapes

city: Vancouver

first: Marco

last: Marra

state: BC

address: 570 W 7th Ave

institute: Canada's Michael Smith Genome Sciences Centre

summary: The Long-read POG dataset comprises a cohort of 189 patient tumours and 41 matched normal samples sequenced using the Oxford Nanopore Technologies PromethION platform. This dataset from the Personalized Oncogenomics (POG) program and the Marathon of Hope Cancer Centres Network includes accompanying DNA and RNA short-read sequence data, analytics, and clinical information. We show the potential of long-read sequencing for resolving complex cancer-related structural variants, viral integrations, and extrachromosomal circular DNA. Long-range phasing of variants facilitates the discovery of allelically differentially methylated regions (aDMRs) and allele-specific expression, including recurrent aDMRs in the cancer genes RET and CDKN2A. Germline promoter methylation in MLH1 can be directly observed in Lynch syndrome. Promoter methylation in BRCA1 and RAD51C is a likely driver behind patterns of homologous recombination deficiency where no driver mutation was found. This dataset demonstrates applications for long-read sequencing in precision medicine, and is available as a resource for developing analytical approaches using this technology.

overall_design:
We sequenced 189 patient tumours and 41 matched normal (blood) samples. We show the potential of long-read sequencing for resolving complex cancer-related structural variants, viral integrations, and extrachromosomal circular DNA by sequencing . Long-range phasing of variants facilitates the discovery of allelically differentially methylated regions (aDMRs) and allele-specific expression. Associated WGS data are available at the European Genome-phenome Archive (EGA) under study accession number: EGAS00001001159. Additional open data and code is available at https://github.com/bcgsc/long_read_pog

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Raw data are available at the European Genome-phenome Archive (EGA) under study accession number: EGAS00001001159.
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title: Aconitate decarboxylase 1 mediates acute airway inflammatory response to environmental exposures

city: Omaha

first: Aaron

last: Schwab

state: NE

address: 42nd and Emile St.

institute: University of Nebraska Medical Center

summary:
Background: Environmental lipopolysaccharide (LPS) and microbial component-enriched organic dusts cause significant lung diseases. These environmental exposures induce the recruitment and activation of distinct lung monocyte/macrophage subpopulations involved in disease pathogenesis. Given monocyte/macrophage activation is tightly linked to metabolism, the objective of these studies was to determine the role of the immunometabolic regulator, aconitate decarboxylase 1 (ACOD1), in environmental exposure-induced lung inflammation.
Methods: Wild-type (WT) mice were intratracheally instilled (I.T.) with 10 ug LPS or saline. Whole lungs were profiled using bulk RNA sequencing or sorted to isolate monocyte/macrophage subpopulations. Sorted subpopulations were then characterized transcriptomically using a NanoString innate immunity multiplex array 48 hours post-exposure. Next, WT and Acod1-/- mice were instilled with LPS, 25% organic dust extract (ODE), or saline with serum, bronchoalveolar lavage fluid (BALF), and lung tissues collected. BALF metabolites of the tricarboxylic acid (TCA) cycle were quantified by mass-spectrometry. Cytokines/chemokines and tissue remodeling mediators were quantitated by ELISA. Lung immune cells were characterized by flow cytometry. Whole body plethysmography was performed 3 hours post-LPS with WT and Acod1-/- mice.
Results: By bulk sequencing, Acod1 was one of the most significantly upregulated genes following LPS (vs. saline) exposure of murine whole lungs. Transcriptomic profiling of sorted lung monocyte/macrophage subpopulations corroborated Acod1 significance. Acod1-/- mice treated with LPS (vs. WT) demonstrated decreased BALF levels of itaconate, TCA cycle reprogramming, decreased BALF neutrophils, increased lung CD4+ T cells, decreased BALF and lung levels of TNF-a, and decreased BALF CXCL1. In comparison, Acod1-/- mice treated with ODE (vs. WT) demonstrated decreased serum pentraxin-2, BALF levels of itaconate, lung total cell, neutrophil, monocyte, and B cell infiltrates with decreased BALF levels of TNF-a, IL-6, and decreased lung CXCL1. Mediators of tissue remodeling (TIMP1, MMP8, MMP9) were also decreased in the LPS-exposed Acod1-/- mice, with MMP-9 also decreased in the ODE-exposed Acod1-/- mice. Lung function assessments demonstrated a blunted response to LPS-induced airway hyper-responsiveness in Acod1-/- mice.
Conclusion: Acod1 is robustly upregulated in the lungs following LPS-exposure and encodes a key immunometabolic regulator. ACOD1 mediates the pro-inflammatory response to acute inhaled, environmental LPS and organic dust exposure-induced lung inflammation.

overall_design: C57BL/6 male mice (between 6 and 8 weeks of age) were purchased from The Jackson Laboratory (Bar Harbor, ME), randomized upon arrival, and allowed to acclimate for 1 week prior to initiation of experiments. Airway inflammation was induced using a singular intratracheal instillation whereby mice were lightly sedated under isoflurane (VetOne, Boise, ID) and received treatment with either 50 ml of sterile saline (CXN) or 10 mg LPS. An intubation laryngoscope (Harvard Apparatus, Holliston, MA) enabled tracheal visualization and access for the intratracheal instillation technique. Biologic triplicates were obtained with animals euthanized 48 hours post-exposure.

first: Jill

last: Poole


title: Tissue-resident memory T cells drive CD103-dependent salivary gland inflammatory infiltration in primary Sjogren's syndrome

city: Woolloongabba

first: Ranjeny

last: Thomas

address: 37 Kent St

country: Australia

institute: University of Queensland Diamantina Institute, Translational Research Institute

summary: Tissue resident memory cells (Trm) are a specialized subset of T cells residing persistently and long-term within specific tissues that contribute to persistent inflammation, tissue damage, and aberrant immune responses. Expansion of Trm in the salivary gland of primary Sjogren’s Syndrome (pSS) and its animal models suggests CD103 determines the tissue localization of Trm. We characterized phenotype and function of Trm and the role of CD103 in pSS.

overall_design: scRNA-seq and scTCR-seq of CD45+ immune cells flow-sorted from PBMC and ST of 5 pSS donors

first: Daniele

last: Mauro

first: Xiang

last: Lin

first: Elena

last: Pontarini

first: Pascale

last: Wehr

first: Giuliana

last: Guggino

first: Chong

last: Deng

first: Saviana

last: Gandolfo

first: Fan

last: Xiao

first: Ke

last: Rui

first: Yuan

last: Tang

first: Enyu

last: Huang

first: Jie

last: Tan

first: Stefania

last: Raimondo

first: Maureen

last: Rischmueller

first: Sarah

last: Downie-Doyle

first: Hendrik

last: Nel

first: Adriana

last: Baz-Morelli

first: Adele

last: Barr

first: Arthur

last: Hsu

first: Eugene

last: Maraskovsky

first: Patrice

last: Hemon

first: Loukas

last: Chatzis

first: Emiliano

last: Boschetti

first: Giuseppe

last: Colella

first: Riccardo

last: Alessandro

first: Aroldo

last: Rizzo

first: Jacques-Olivier

last: Pers

first: Michele

last: Bombardieri

first: Liwei

first: Francesco

last: Ciccia


title: P-bodies dynamics of hESCs by unveiling P-bodies properties of hESC and hESC-derived mesodermal cells

city: 嘉兴市

first: Jin

last: Jiang

state: 浙江省

address: 硖石街道

institute: 浙江大学爱丁堡大学联合学院

summary: Processing bodies (P-bodies) are the membraneless organelles that play a critical role in RNA storage and degradation. P-body abnormalities contribute to diseases and developmental disorders, however, the dynamics of RNA components of P-bodies in human embryonic stem cells during maintenance and differentiation remain elusive. Here, we captured P-bodies during human embryonic stem cells(hESCs) to mesodermal differentiation using flow cytometry, and revealing unique transcriptomic features to other organelles and characterized by lower GC content and reduced M6A modifications. Genes enriched in P-body are cell-specific, mainly associated with translation regulation and the cytoskeleton, long non-coding RNAs in P-body tend to interact with RNAs, whereas cytoplasmic genes are conserved and essential for fundamental processes, and cytoplasmic lncRNAs mostly interact with proteins. During hESC to mesodermal differentiation, both the number of P-bodies and enriched genes were significantly reduced. In addition, P-bodies selectively attracted specific transposable elements in hESCs. Perturbation of P-body gene expression or overexpression of P-body core protein LSM14A could disrupt hESC differentiation but not maintenance. In conclusion, our data elucidate the dynamics of P-body during the differentiation of hESCs to the mesodermal lineage and support the link between P-body and stem cell pluripotency.

overall_design:
To investigate the properties of P-bodies in different cell types, we established tetON-LSM14A-GFP (P-bodies labelling) 293T and hESCs cell lines and purified P-bodies properties from 293T, hESCs, and hESC-derived mesodermal cells by fluorescence-activated cell sorting.
To investigate the linkage of P-body and hESCs differentiation, we treat hESCs with 1μg/ml TGFβi, and analysis the gene expression profiles about the pluripotency markers.
we treat tetON-LSM14A-GFP hESCs and derived mesodermal cells with or without 1μg/ml Doxycycline, and analysis the gene expression profiles of P-body core protein LSM14A overexpression in hESCs and hESC-derived mesodermal cells.
After candidate screen, we construct CRISPRi-SPTAN1 knock-down hESCs, and comparatively analysis the gene expression of SPTAN1-KD in hESCs and hESC-derived mesodermal cells.

first: Sisi

last: Xie

first: Di

last: Chen


title: Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice

first: Tony

last: Wyss-Coray

state: CA

summary: Microglia are highly responsive to their local environment and signals from the periphery. Blood plasma proteins readily permeate the healthy brain parenchyma. However, whether microglia are responsive to such proteins is unclear. Here, we identify a stable population of microglia takes up plasma proteins in a region-specific manner in healthy brains. To understand these microglia at the single cell transcriptomic level and correlate their transcriptome with plasma uptake intensity, we sorted plasma-high, plasma-low, and plasma-negative microglia from young mice (3-month-old) and perform plate-based scRNA-seq.

overall_design: Microglia are isolated from 3-month-old young mice, 20 hours after injecting NHS-Atto647N labeled plasma proteins. Based on the intensity of plasma protein within each cell, microglia were assigned into plasma negative (plasma-neg), plasma-low and plasma-high groups. The sorted microglia were then used to perform plate-based single-cell RNA sequencing (scRNA-seq) using smart-seq2 pipeline.

first: Nannan

last: Lu


title: Clostridium sporogenes-derived metabolites protect against colonic inflammation

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

summary: Purpose: Gut microbiota-derived metabolites play a pivotal role in the maintenance of local gut homeostasis and can even induce systemic effects via accumulation in the bloodstream. Here, we demonstrate that mono-colonization of germ-free (GF) mice with Clostridium sporogenes protects mice from inflamation and death induced by DSS colitis. Method: 8-12-week-old male mice (GF, SPF and GF colonized with C. sporogenes (CS)) were treated with 2.5% DSS in drinking water for 5 days and colon tissue was isolated on day 7. RNA was isolated from the colon tissue and RNA sequenzing was performed. Results:  Mono-colonization of GF mice with Clostridium sporogenes protected the mice from DSS colitis induced death, while producing high amounts of indole-3-propionic acid (IPA), branched chain (BCFA) and short-chain (SCFA) fatty acids. In comparison to CS mice, SPF mice showed much higher levels of inflammatory related genes and a worse histological score. Conclusion: Histological stainings and the RNAseq both showed high levels of protection of C. sporogenes colonized mice in colitis, compared to SPF and GF animals. The data provide evidence for a therapeutic  potential of C. sporogenes for IBD patients.

overall_design: Colon tissue from DSS-treated GF, CS, and SPF mice (n=3 per group) was isolated, and RNA was extracted and sequenced.

first: Felix

last: Krause

first: Alexander

last: Visekruna


title: Bulk RNA-seq of plasma-positive microglia and plasma-negative microglia from hypothalamus region in young mice

summary: Microglia are highly responsive to their local environment and signals from the periphery. Blood plasma proteins readily permeate the healthy brain parenchyma. However, whether microglia are responsive to such proteins is unclear. Here, we identify a stable population of microglia takes up plasma proteins in a region-specific manner in healthy brains. To understand the difference of these two populations at the transcriptomic level, we sorted plasma-positive microglia and plasma-negative microglia from hypothalamus region of young mice (3-month-old).

overall_design: Bulk-RNAseq of sorted microglia from hypothalamus region of young mice 20 hours after injecting with dye-labeled plasma protein (n=4 replicates)


title: RNA-Seq experiment of wild-type mouse livers with mLMRs knockdown and hLMRs rescue

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary:
Rescue experiment in wild-type mice offers a valuable mean to verify the functional similarity of lncRNAs. By suppressing mLMRs in mice and observing the impact on gene regulation, followed by overexpression of hLMRs, we can determine the ability of hLMRs to rescue the loss-of-function effects of mLMRs. Should hLMRs exhibit a reversal of the loss-of-function on transcriptome regulations, this would suggest that they have similar functions to mLMRs.
To do this, we used adenovirus-delivered shRNAs to suppress the expression of mLMRs in the livers of wild-type mice, while overexpressing corresponding hLMRs as a rescue group.

overall_design: Wild-type mice (C57BL6, 12 weeks age) were injected with three groups of viruses, including control viruses for knockdown and overexpression (Lac+pAdv5, control group), mLMR knockdown viruses and control viruses for overexpression (mouse-lncRNA KD+pAdv5, mLMR knockdown group), and mLMR knockdown viruses and hLMR overexpression group (mouse-lncRNA KD+human-lncRNA OE, hLMR rescue group). The adenoviruses were intravenously delivered to  mice at a dose of 5 × 10^8 PFU/mouse for overexpression virus or 1 × 10^9 PFU/mouse for knockdown virus. After a 5-hour fast (~9:00 am to 2:00 pm), the livers  were harvested for RNA-Seq analysis after 7 days.

first: Chengfei


title: The VelB gene is involved in conidiogenesis and secondary metabolism in Penicillium expansum

city: TOULOUSE

first: Olivier

last: PUEL

address: 180 chemin de Tournefeuille

department: TOXALIM UMR 1331

institute: INRAE

summary: The aim of this study was to characterize the role of VelB in Penicillium expansum. For that a null mutant PeΔVelB was generated.

overall_design: PeΔVelB, PeΔLaea, PeΔVeA and WT strains were grown in the same conditions ( 25°C for 5 days in the dark) on MEA medium. The RNAs were extracted and their transcriptomes were analyzed.

first: Nadia

last: Tahtah

first: Chryztian

last: Zetina-Serrano

first: Ophélie

last: Rocher

first: Sophie

last: Lorber

last: Puel

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Gene expression profile at single cell level from mitral valves of wild-type and Fbn1 C1039G/+ mice at 1 month-of-age

city: Cincinnati

first: Katherine

last: Yutzey

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Myxomatous valve disease is the most common form of heart valve disease leading to morbidity and mortality worldwide. It is primarily associated with inherited connective tissue disorders caused by genetic variants in extracellular matrix genes such as Marfan syndrome. Mice with Fibrillin 1 gene variant Fbn1 C1039G/+ recapitulate histopathological features of Marfan syndrome. However, the cell heterogeneity and changes of gene expression at single cell level in Marfan syndrome valves are completed unknown.

overall_design: Mitral valves from 5 wild-type and 3 Fbn1 C1039G/+ mice at 1 month-of-age were dissected separately and pooled together by genotype for subsequent single-cell dissociation and single-cell RNA sequencing.

last: Xu

middle: E


title: Pathogenic mechanism and therapeutic intervention of impaired N7-methylguanosine (m7G) tRNA modification

city: Canton

first: jieyi

last: Ma

address: No.58 Zhong Shan Er Road

institute: the First affiliated hospital of Sun Yat-sen University

summary: Mutations of tRNA modification enzymes including the tRNA m7G methyltransferase complex component WDR4 were frequently found in patients with neural disorders, while the pathogenic mechanism and therapeutic intervention strategies are poorly explored. In this study, we revealed that patient-derived WDR4 mutation leads to temporal and cell-type-specific neural degeneration, and directly causes neural developmental disorders in mice.

overall_design: TRAC-Seq were used to identify the tRNA m7G methylome in mouse brain. RNC-seq was used to identified genes with different translation efficiency in mouse brain upon WDR4 mutation.RNA-seq was used to study the differential gene expression in the mice brain between Wdr4 point mutation and control mice. snRNA-seq were performed for the analysis of cellular components in brain.

first: Ma

last: Jieyi

first: Zheng

last: Siyi

first: Lin

last: Shuibin


title: DNA methylation profiling of lung transplant recipients

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

summary: Targeted bisulfite sequencing  data of peripheral blood mononuclear cells (PBMCs) from participants pre- and post- lung transplant(Tx) was generated to study 1) methylation difference between pre- and postTx, 2) methylation difference between cytomegalovirus (CMV) seropositive and seronegative in preTx, and 3) immune response regarding Tx and immunosuppression prophylaxes.

overall_design: We collected  PBMC for targeted bisulfite sequencing  from 135  kidney transplant patients with samples collected before and then 3 months after transplantation.

first: Rashmi

last: Mohanty

first: John

middle: R

last: Greenland

first: Matteo

last: Pellegrini


title: Histone H3.3 chaperone HIRA is required for acquired tolerance by rendering stress-responsive genes poised for prospective lethal stresses [ChIP-seq]

first: Yoshikazu

last: Nagagaki

address: Yoshida-Konoe-cho, Sakyo-ku

summary: Appropriate responses to environmental challenges are imperative for the survival of all living organisms. Exposure to low-dose stresses is recognized to yield increased cellular fitness, a phenomenon termed hormesis. However, our molecular understanding of how cells respond to low-dose stress remains profoundly limited. Here we report that histone variant H3.3-specific chaperone, HIRA, is required for acquired tolerance, where low-dose heat stress exposure confers resistance to subsequent lethal heat stress. We found that human HIRA activates stress-responsive genes, including HSP70, by depositing histone H3.3 following low-dose stresses. These genes are also marked with histone H3 Lys-4 trimethylation and H3 Lys-9 acetylation, both active chromatin markers. Moreover, depletion of HIRA greatly diminished acquired tolerance, both in normal diploid fibroblasts and in HeLa cells. Collectively, our study revealed that HIRA is required for eliciting adaptive stress responses under environmental fluctuations and is a master regulator of stress tolerance.

overall_design: To investigate thr gene expression profile after low-dose of heat stress (40°C, 2 hr), we performed RNA-seq of samples with or without the stress treatment.

first: Ryuichiro

last: Nakato

first: Fuyuki

last: Ishikawa


title: SUMOylation-Induced Membrane Localization of TRPV1 Suppresses Proliferation and Migration in Gastric Cancer Cells

city: Taizhou

first: Yang

last: Yang

address: 366 Taihu Road

institute: Taizhou People’s Hospital Affiliated to Nanjing Medical University

summary: Gastric cancer (GC) remains a significant health challenge due to its high mortality rate and the limited efficacy of current targeted therapies. A critical barrier in developing more effective treatments is the lack of understanding of specific mechanisms driving GC progression. This study investigates the role of Transient Receptor Potential Vanilloid 1 (TRPV1), a non-selective cation channel known for its high Ca2+ permeability and tumor-suppressive properties in gastrointestinal cancers. Specifically, we explore the impact of SUMOylation—a dynamic and reversible post-translational modification—on TRPV1's function in GC. We demonstrate that SUMOylation of TRPV1 inhibits cell proliferation and migration in MGC-803 and AGS gastric cancer cells. By mutating amino acids near TRPV1's existing SUMO motif (slKpE), we created a bidirectional SUMO motif (EψKψE) that enhances TRPV1 SUMOylation, resulting in further suppression of GC cell proliferation and migration. In vivo studies support these findings, showing that TRPV1 SUMOylation prevents spontaneous tumorigenesis in a mouse gastric cancer model. Further investigation reveals that TRPV1 SUMOylation increases the protein's membrane expression by inhibiting its interaction with the adaptor-related protein complex 2 mu 1 subunit (AP2M1). This elevated membrane expression leads to increased intracellular Ca2+ influx, activating the AMP-activated protein kinase (AMPK) pathway, which in turn inhibits the proliferation and migration of GC cells. In conclusion, our study elucidates a novel mechanism wherein TRPV1 SUMOylation promotes its membrane expression and activates the TRPV1-Ca2+-AMPK signaling pathway, thereby inhibiting GC cell proliferation and migration. These findings enhance our understanding of the molecular dynamics in gastric cancer and could provide a new theoretical basis for clinical treatment strategies.

overall_design: To explore the signaling pathway and possible regulatory molecules that affect the changes of TRPV1 SUMOylation on cell proliferation and migration, RNA lysate of gastric cancer MGC-803 cells with stable Flag-TRPV1WT and Flag-TRPV1K823R were extracter, and performed RNA-Seq


title: Molecular, anatomical, and functional organization of lung interoceptors

city: Stanford

first: Yin

last: Liu

address: 279 Campus Dr.

institute: Stanford University

summary: Interoceptors are the sensory neurons that monitor internal organs and states, essential for physiological homeostasis and generating interoception.Here, we describe a comprehensive, high-quality molecular atlas of interoceptors of the mouse lung, identifing 10 molecular subtypes, which differ in developmental origin, myelination, receptive fields, and cell contacts in the organ. Each subtype expresses a unique but overlapping combination of sensory receptors that detect diverse physiological and pathological stimuli, and each can signal to distinct sets of lung cells including immune cells, forming an intricate local neuroimmune interaction network. Functional interrogation of two mechanosensory subtypes reveals exquisitely-specific homeostatic roles in breathing, one regulating inspiratory time and the other inspiratory flow. These suggest that lung interoceptors encode diverse and dynamic sensory information rivaling that of canonical exteroceptors, and this information is used to drive myriad local cellular interactions and enable precision control of breathing, while providing only vague perceptions of oragn states.

overall_design: Vagal ganglia from adult mice instilled with fluorescent conjugated wheat germ agglutinin into the lung were dissociated, and single labeled sensory neurons were mannually picked and analyzed by single-cell RNA sequencing using SmartSeq2 method.

first: Mark

last: Krasnow


title: Gene Expression of Cardiogenic Shock Patients under Extracorporeal Membrane Oxygenation

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
Prognosis for cardiogenic shock patients under ECMO was our study goal. Success defined as survived more than 7 days after ECMO installation and failure died or had multiple organ failure in 7 days. Total 34 cases were enrolled, 17 success and 17 failure.
Peripheral blood mononuclear cells collected at ECMO installation 0hr, 2hr and removal were used analyzed.

overall_design: Analysis of the cardiogenic shock patients at extracorporeal membrane oxygenation treatment by genome-wide gene expression. Transcriptomic profiling between successful and failure groups were analyzed.

first: Tsai-Hsia

last: Hong

first: Yi-Jing

last: Hsiao

first: Yan-Ming

last: Chen

first: Hsuan-Yu

first: Sun-Liang


title: Histone H3.3 chaperone HIRA is required for acquired tolerance by rendering stress-responsive genes poised for prospective lethal stresses

city: Kyoto-shi

institute: Kyoto University

overall_design: To test the effects of knocking down the histone chaperone HIRA on whole transcripts, total RNA was extracted from HIRA-knockdown (shHIRA) and control (shLuc) cells and hybridyzed on Affymetrix microarrays. We sought to obtain differentially expressed genes between those cells.

first: Yuji

last: Kozakura


title: NMN ameliorates brain ischemia reperfusion injury after MCAO by reducing apoptosis and neutrophil extracellular trap formation in rats

status: Public on Oct 14 2024

city: Changchun

first: Daoyu

last: Zhang

address: Xinzhu street 1977

institute: Jilin University

summary: Ischemia reperfusion injury (IRI) is a common disease encountered in clinical practice, especially in the management of patients experiencing shock and the treatment of patients with cerebral infarction, and it is also an important factor in the poor prognosis of patients with cardiopulmonary resuscitation or stroke. Therefore, in this study, we constructed rat MCAO models and treated them with NMN. The tissues was collected for RNAseq to explore the gene expression and pathways influenced by NMN. We detected the neutrophil content by flow cytometry, apoptosis was detected by TUNEL staining and flow cytometry, the formation of NETs was evaluated by quantification of NE-DNA, and qPCR and Western blotting were performed to detect the expression of related genes. Our results showed there were fewer apoptotic cells after NMN treatment, and the ROS production was decreased. Importantly, the neutrophil was decreased and NETs were reduced after NMN treatment. Meanwhile, we observed the levels of p-ERK and p-p38 were decreased. Our findings indicated that NMN reduced cerebral ischemia reperfusion injury in rat MCAO model. NMN treatment decreased neutrophil and reduced NETs formation. The mechanism was referred to as the inhibition effect of ROS and ERK/p38 signaling.

first: Di

last: Wu


title: Cardiogenic Shock Patients under Extracorporeal Membrane Oxygenation

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

overall_design: Refer to individual Series


title: Single cell genomic analysis of PBMCs cells from a primary myelofibrosis patient

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

country: Italy

institute: University of Modena and Reggio Emilia

summary: We performed single cell DNA sequencing by means of Tapestri platform on a mix of Peripheral Blood Mononuclear Cells (PBMCs) and CD34+ hematopoietic stem/progenitor cells (HSPCs) from a primary myelofibrosis (PMF). The main purpose of this project was to reconstruct the clonal composition of the neoplastic population by analyzing the mutational profile at the single-cell level.

overall_design: CD34+ cells were isolated through immunomagnetic selection from frozen PBMCs coming from a PMF patient. PBMCs and CD34+ cells were subjected to Tapestri analysis through a custom DNA panel.

first: Chiara

last: Carretta

first: Sandra

last: Parenti

first: Filippo

last: Badii

last: Bertesi

first: Sebastiano

last: Rontauroli

first: Lara

last: Tavernari

first: Elena

last: Genovese

first: Samantha

last: Sperduti

last: Enzo

first: Margherita

last: Mirabile

first: Francesca

last: Pedrazzi

last: Pessina

first: Ilaria

last: Colugnat

first: Barbara

last: Mora

first: Monica

last: Maccaferri

last: Tenedini

first: Silvia

last: Martinelli

first: Ruggiero

last: Norfo

first: Elisa

last: Bianchi

first: Livio

last: Casarini

first: Leonardo

last: Potenza

first: Mario

last: Luppi

first: Enrico

last: Tagliafico

first: Paola

last: Guglielmelli

first: Manuela

last: Simoni

first: Francesco

last: Passamonti

first: Alessandro

last: Vannucchi


title: 3D Model Enhances Human Glia conversion to Neurons with Dopaminergic Functional and Molecular Traits Or: 3D Model Enhances Human Glia conver-sion to Induced Dopamine Neurons?

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

summary: Parkinson’s disease (PD), a prevalent neurodegenerative disorder, is primarily characterized by progressive loss of ventral midbrain dopamine (DA) neurons. This focal degeneration makes PD suitable for cell replacement therapies and clinical trials using stem cell derived-DA neurons are ongoing. An emerging alternative to cell transplantation for brain repair is in vivo reprogramming, where resident glia is converted into neurons directly inside the brain. While functional neurons with potential therapeutic effects can be obtained via in vivo conversion in rodent studies, translating this to relevant human pre-clinical models has been limited to two-dimensional (2D) cultures. To mimic three-dimensional (3D) complexity and approximate in vivo-like conversion, we developed a 3D model for human glia conversion. Our model promotes neural conversion and generates functionally mature DA neurons at a faster pace than in 2D. Molecular profiling, single-nucleus transcriptomics and lineage tracing mapped glia heterogeneity, provided mechanistic insights of the reprogramming process and defined neuronal identity after conversion. Our results emphasize the advantages of utilizing 3D models as a reproducible and con-sistent platform for reprogramming studies.

overall_design:
Single-nuclei RNA-seq of stem cell derived glial progenitors and converted neurons
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Authors state "Due to privacy concerns we are unable to submit raw data and has hence only uploaded count matrices."

first: Malin

last: Parmar

first: Jessica

last: Giacomoni


title: Microbiota-dependent early life programming of gastrointestinal motility

city: Chicago

first: Mary

last: Frith

state: Illinois

address: 900 E 57th St

department: Medicine

institute: University of Chicago

summary: Gastrointestinal microbes modulate peristalsis and stimulate the enteric nervous system (ENS), whose development, as in the central nervous system (CNS), continues into the murine postweaning period. Given that adult CNS function depends on stimuli received during critical periods of postnatal development, we hypothesized that adult ENS function, namely motility, depends on microbial stimuli during similar critical periods. We gave fecal microbiota transplantation (FMT) to germ-free mice at weaning or as adults and found that only the mice given FMT at weaning recovered normal transit, while those given FMT as adults showed limited improvements. RNAseq of colonic muscularis propria revealed enrichments in neuron developmental pathways in mice exposed to gut microbes earlier in life, while mice exposed later – or not at all – showed exaggerated expression of inflammatory pathways. These findings highlight a microbiota-dependent sensitive period in ENS development, pointing to potential roles of the early life microbiome in later life dysmotility.

overall_design: Microbe-lacking (“germ-free”, GF) mice, were given fecal microbiota transplantation (FMT) at weaning (4wC) or as adults (12wC). Gene expression was evaluated from RNAseq of colonic muscularis propria of adult 4wC and 12wC mice at least 4 weeks after FMT and of adult GF and conventional (SPF) mice.

first: Purna

last: Kashyap

first: David

last: Linden

first: Betty

last: Theriault

first: Eugene

last: Chang


title: MYC-rearranged aggressive B-cell lymphoma are molecularly Burkitt Lymphoma despite of morphology [CYTOSCAN]

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

summary: Overall, the genetic profile of aggressive B-cell NHL in CAYA in the spectrum of BL and DLBCL is heterogeneous. MYC-R cases mostly displayed a molecular profile close to BL regardless of their morphology, whereas MYC-non-R had a more heterogeneous genetic landscape resembling DLBCL.

overall_design: Using an integrated approach, including fluorescence in situ hybridization, targeted gene Next Generation Sequencing (NGS) sequencing, copy number arrays, and gene expression profiling, we characterized 37 B-cell lymphomas in CAYA with intermediate morphological features between DLBCL and BL, blastoid morphology, DLBCL morphology with MYC rearrangements, and BL without MYC rearrangements.

first: I

first: S

last: Mato