title: The Skin Microbiome of Mycosis fungoides

summary: The skin Microbiome stratifies Patients with CTCL into two subgroups. One subgroup has a balanced microbiome, while the other subgroups has a skin dybiosis with S. aureus outgrow. This is accompanied by impaired TCR repertoir and poor clinical outcome.

overall_design: 20 Patients with Mycosis fungoides were enrolled from two study sites in Germany (Mainz and Frankfurt am Main). From each patient, up to two samples from lesional skin were obtained. Nonlesional skin from the contralateral site of lesional samples served as controls. Whole Metagenome sequencing was performed and taxonomic profiles were generated successfully for a total of N = 65 metagenomic samples.  Moreover, in a subset of patients peripheral blood was drawn and skin punch biopsies were obtained from the same lesions. T cell receptor sequencing (TCRseq) was performed on n = 21 samples.


title: PNP mediated guanosine induced gene expression

status: Public on Dec 01 2023

city: shanghai

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

country: China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

type: Expression profiling by high throughput sequencing

summary: We find guanosine supplementation can induce metabolic stress on cells. To evaluate this effect we use RKO-NC and RKO-shPNP cells for experiment.

overall_design: RKO-NC and RKO-shPNP cell were stimulated by 4 mM guanosine for 6 hours and after that total RNA were used for gene expression analysis.

first: Cheng‘e

last: Tu


title: RNA sequencing  Facilitates Quantitative Analysis of luteolin or quercetin on adipogenesis Transcriptomes

city: Zhenjiang

first: Jue

last: Jia

address: No.438, Jiefang Road

institute: the Affiliated Hospital of Jiangsu University

summary: We report the use of transcriptome sequencing in the intervention of luteolin or quercetin in adipogenesis. We constructed the adipogenic differentiation model of mouse embryonic fibroblasts and obtained the differential genes of luteolin or quercetin regulating adipocyte differentiation by transcriptomic sequencing. We identified 2085 differentially expressed lipogenesis response genes, 181 luteolin response genes and 574 quercetin response genes. This study provides a framework for the network regulation mechanism of luteolin or quercetin inhibiting preadipocyte differentiation.

overall_design: Examination of luteolin or quercetin on adipose differentiation of 3T3-L1 preadipocytes

first: Ruoshuang

first: Zhicong

last: Zhao


title: Identification of SNHG15-associated microRNAs in SNHG15 overexpression BT549 cells using miRNA-Seq

city: Shantou

first: Zhou

last: Yanchun

state: Guangdong

address: Xinling Road

department: Pathophysiology

institute: Shantou University Medical College

type: Non-coding RNA profiling by high throughput sequencing

summary: LncRNAs have been shown to act as molecular sponges for miRNAs, and hence functionally affect the activity of other RNA transcripts targeted by the sponged miRNAs.  SNHG15 is an oncogenic lncRNA in a variety of cancers including breast cancer, lung cancer, and hepatocellular carcinoma.

overall_design:
In the present study, we used MS2 pulldown and miRNA-Seq to characterize microRNAs that associated with SNHG15 in SNHG15 overexpression BT549 cells.
Cell lysates were prepared from cultured BT549-SNHG15-MS2 cells and then incubated with Amylose resin coated with MBP-MCP (MS2 coat protein) or Amylose resin at 4°C for 5 h with gentle rotation. After incubation, the supernatant was removed by a short centrifugation and the Amylose beads were washed three times in lysis buffer，the co-precipitated RNAs were eluted with 100 µl lysis buffer containing 20 mM maltose. miRNAs associated with SNHG15 were extracted and analyzed by miRNA-seq.

first: Shaoying

last: Chen

first: Yanchun

last: Zhou

first: Wei

last: Gu


title: NCAPG promotes the proliferation and migration of endometrial cancer via the PI3K/AKT/mTOR signaling pathway

city: Changsha

first: Chun

last: Fu

state: hunan

address: No.139 Renmin Road

department: Department of Obstetrics and Gynecology

institute: the Second Xiangya Hospital, Central South University

summary: To investigate the function NCAPG in the regulation in endometrial cancer, we established HEC-1-A cell lines in which NCAPG has been knocked down by RNAi.

overall_design: Construct knockdown NCPAG and corresponding empty vector control cell line in HEC-1-A cell line, and obtain mRNA profile

first: Zhen

last: Ren

first: Chunying

last: Zheng

first: Xiaohan

last: Li


title: T cell receptor repertoire of the skin of Mycosis fungoides patients

city: Mainz

first: Philipp

last: Licht

address: Langenbeckstrasse 1

department: Dept. of Dermatology

country: Germany

institute: University Medical Center Mainz

summary: The skin Microbiome stratifies Patients with CTCL into two subgroups. One subgroup has a balanced microbiome, while the other subgroups has a skin dybiosis with S. aureus outgrowth. This is accompanied by impaired TCR repertoire and poor clinical outcome.

overall_design:
20 Patients with Mycosis fungoides were enrolled from two study sites in Germany (Mainz and Frankfurt am Main). From each patient, up to two samples from lesional skin were obtained. Nonlesional skin from the contralateral site of lesional samples served as controls. Whole Metagenome sequencing was performed and taxonomic profiles were generated successfully for a total of N = 65 metagenomic samples.  Moreover, in a subset of patients peripheral blood was drawn and skin punch biopsies were obtained from the same lesions. T cell receptor sequencing (TCRseq) was performed on n = 21 samples.
TCRseq libraries were generated from the same RNA extraction as the RNAseq libraries. Samples were taken at the same visit and from the same body site sampled for WMS.


title: Single-cell analysis reveals dynamic changes of A549 cells in monolayer, A549 xenografts in nude mice, and xenografts after exposure to dacomitinib

city: Shanghai

first: Yu

last: Yangziwei

state: Shanghai

address: 上海市浦东新区周祝公路279号

institute: Shanghai University of Medicine and Health Science

summary: The in vitro A549 cells, and A549 xenografts in nude mouse were two classic and commonly used models for anti-cancer drug discovery. Here dynamic changes of the A549 models, and also A549 xenografts after exposure to dacomitinib were revealed by single-cell transcriptome analysis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A549 cells in monolayer, A549 xenografts in nude mice, and xenografts after exposure to dacomitinib were digested and processed for single-cell RNA seqencing. Then bioinformatics analysis were performed basing on the transcriptome data.

first: Xiaoyan

first: Yangziwei

last: Yu

first: Haoyang

first: Mengjing

last: Yang

first: Qianqian

last: Cai

first: Weiguo

last: Zhang

first: Feixiang

last: Jiang

first: Yanmei

last: Zhu

first: Linlin

last: Ma

last: Xie

first: Hedi

first: Tianbiao

first: Gang

last: Huang

first: Zhaoli


title: Transcriptomic changes of lung ECs following bleomycin induced pulmonary fibrosis, unilateral pneumonectomy, in WT mouse and the effect of Kitl deletion in Apln+ cells

city: Daejeon

first: Myung Jin

country: South Korea

institute: Institute for Basic Science

summary: To investigate transcriptomic changes of lung ECs following bleomycin induced pulmonary fibrosis and pneumonectomy, lung ECs from CT, Bleomycin induced model, and pneumonectomy model mouse were FACS sorted and single-cell RNA seqs were performed

overall_design: Lung ECs from CT, Bleomycin, and pneumonectomy model from WT (tdT) or Kitl(iΔApln+) deleted mouse were sorted and single-cell libraries were made

first: Gou

middle: Y

last: Koh

first: Myung

middle: J


title: The post-translational modifications and translation-regulatory role of METTL14 in 5-fluorouracil-resistant colorectal cancer

city: Nanjing

first: Shukui

last: Wang

address: No.68, Changle Road, Nanjing

institute: Nanjing First Hospital

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

overall_design: Refer to individual Series


title: The post-translational modifications and translation-regulatory role of METTL14 in 5-fluorouracil-resistant colorectal cancer [mRNA-seq]

summary: 5-fluorouracil (5‑FU)  based chemotherapy is the first-line chemotherapy scheme for CRC, whereas acquired drug resistance poses a huge obstacle to curing CRC patients and the mechanism is still obscure. METTL14 is a core subunit of the m6A methyltransferase complex and has been reported to regulate the drug resistance of cancers. Here, we demonstrated that METTL14 is significantly downregulated in 5-FU-resistant CRC and METTL14 overexpression inhibits the proliferation and 5-FU resistance of CRC cells in vitro and in vivo. In addition, we found that MIB1 catalyzes the K63-linked ubiquitination of METTL14 and induces its degradation through the autolysosome pathway, while AURKA-mediated phosphorylation enhances METTL14 stability by inhibiting its ubiquitination. Moreover, we first discovered that METTL14 functions in 5-FU-resistant CRC cells by directly participating in the translation initiation of non-m6A-modified mRNAs independently of METTL3, rather than cooperating with METTL3 to methylate adenosine residues of targets. Further analysis indicated that METTL14 regulates the cell cycle process in 5-FU-resistant CRC cells. Collectively, our study not only identified METTL14 as a potential therapeutic target for 5-FU resistance in CRC but also revealed a novel translation-facilitating role of METTL14.

overall_design: METTL14 overexpression plasmids and negative control plasmids were transfected into 5-FU-resistant HCT-8 cells, respectively. Then cells were treated with 100ug/mL CHX and implemented to the transcription sequencing. Experiments were performed twice independently.

first: Xiangxiang

last: Liu

first: Yuqin

last: Pan

first: Jian

last: Qin


title: The post-translational modifications and translation-regulatory role of METTL14 in 5-fluorouracil-resistant colorectal cancer [Ribo-seq]

overall_design: METTL14 overexpression plasmids and negative control plasmids were transfected into 5-FU-resistant HCT-8 cells, respectively. Then cells were treated with 100ug/mL CHX and implemented to the Ribosome-sequencing. Experiments were performed twice independently.


title: Effect of long-term exposure of platinum nanopariticles on gene expression of Pseudomonas aeruginosa PAO1

city: Hangzhou,Zhejiang

first: Yulu

last: Lian

state: Zhejiang

address: Hangzhou

institute: Zhejiang Gongshang University

summary:
Previous synthesized Pt NPs were selected to evaluate the influences on bacterial resistance, and a typical pathogenic microbe P. aeruginosa was chosen as model bacteria.
After 60-day PtNPs exposure, we found under 12.5 μg/mL of platinum nanoparticles (PtNPs) exposure for ~7200 generations, the IC50 of evolved Pseudomonas aeruginosa PAO1 to imipenem (IPM) and ciprofloxacin (CIP) reduced 77.0% and 87.8%, respectively. Interestingly, long-term of PtNPs exposure arose the bacterial susceptibility on antibiotics. We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type strains (WT), non-exposed but evolved PAO1 (CK), and 60-day PtNPs exposed and evolved PAO1 (ES)

first: Meizhen


title: Tubuloside B (Tub B) inhibits migration of HCC cells by inhibiting Hippo-YAP pathway

city: wuhan

first: Jie

last: Yao

state: 湖北

address: wuhan hubei province

institute: wuhan university

summary:
Purpose: To date, the biological activity of Tub B has not been fully investigated. We set out to analyze how Tub B regulates gene expression in HepG2 cells.
Conclusions: Tub B reduced the expression of Hippo pathway downstream target genes in HepG2 cells.

overall_design: Methods: RNA-seq was performed with two repetitions in HepG2 followed by treatment with DMSO and 80 μM Tub B for 48 h.

first: Chenyan

last: Shi


title: Mouse lung and brain LCM-ATACseq

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In situ transposition followed by laser capture microdissection was applied to lung and brain mouse tissue sections to demonstrate feasibility of LCM-based spatial chromatin accessibility analysis of regions of interest.

overall_design: Fresh frozen lung and brain tissue sections from C57BL/6J WT mice were tagmented in situ to assess chromatin accessibility. LCM was employed to collect a mini bulk of randomly captured nuclei. Two mini-bulk sizes were investigated: 50 single-captured nuclei or 10 larger captured-areas composed each of roughly 20 nuclei, for a total of ~200 nuclei. This was applied both on brain and lung samples, at least in technical duplicates.

first: Caterina

last: Carraro

first: Adem

last: Saglam

middle: L


title: Single-cell transcriptomics implicate the alteration of peripheral immune cells and interaction with renal macrophages driven by T2DM

city: nanjing

first: XU

last: Ying

state: jiangsu

address: xuanwu district

institute: Nanjing university

summary: The alternation of peripheral immune cells in diabetes is complicated. We performed scRNA-seq on db/db mice to explore the cellular changes in T2DM.

overall_design: peripheral immune cells of  db/db  or wt mice were isolated and analyzed using scRNAseq.

first: Ying

last: Xu

first: Zhaohong

last: Chen


title: Nitric Oxide controls shoot meristem activity controlling DNA methylation in Arabidopsis thaliana

city: Heidelberg

last: Zeng

address: Im Neuenheimer Feld 230

department: Department of Stem Cell Biology

institute: Heidelberg University

type: Methylation profiling by high throughput sequencing


title: Nitric Oxide controls shoot meristem activity controlling DNA methylation in Arabidopsis thaliana (EM-Seq)

summary: Despite the importance of Nitric oxide (NO) in both plant and animal development, the regulatory and mechanism of NO function remain elusive. Here, we show that NO promotes Arabidopsis shoot stem cell differentiation via the RNA directed DNA Methylation (RdDM) pathway. Knocking out of the components of the RdDM pathway causes meristematic defects, and at least in part could block the stem cell and niche-specific genes responding to the NO signaling. Moreover, the homeobox WUSCHEL protein, known to control stem cell pool, has been found to interact with the ARGONAUTE protein, thus mediating NO signaling in the shoot apical meristem (SAM) is crucial for the stem cell fate. Our results reveal an important mechanism that NO is key to stem cell maintenance and differentiation.

overall_design: Methylation profiling by high throughput sequencing

first: Jan

middle: U

last: Lohmann

first: Xin'Ai

last: Zhao

first: Zhe

last: Liang


title: Nitric Oxide controls shoot meristem activity controlling DNA methylation in Arabidopsis thaliana (RNA-Seq)

overall_design: Expression profiling by high throughput sequencing


title: RCCD1 also Resides in Mitochondria to Regulate mtDNA Dynamics and Mitochondrial Homeostasis

city: Beijing

first: Yani

last: Peng

state: State...

address: Xueyuan load number 38

institute: Peking University

summary: Regulator of chromosome condensation domain-containing protein 1 (RCCD1) plays an important role in chromosome segregation and microtubule stability in the nucleus and has been identified recently as a potential driver for breast cancer. We report here that, unexpectedly, RCCD1 is also localized in mitochondria. We show that RCCD1 resides in the mitochondrial inner membrane, where it interacts with the mitochondrial contact site/cristae organizing system (MICOS) and mitochondrial DNA (mtDNA) to regulate mitochondrial nucleoid organization, thereby influencing mtDNA transcription, oxidative phosphorylation, and the production of reactive oxygen species. Interestingly, RCCD1 is upregulated under hypoxic conditions, leading to decreased generation of reactive oxygen species and alleviated apoptosis favoring cancer cell survival. We show that RCCD1 promotes breast cancer cell proliferation in vitro and accelerates breast tumor growth in vivo. Indeed, RCCD1 is overexpressed in breast carcinomas, and its level of expression is associated with aggressive breast cancer phenotypes and poor patient survival. Our study reveals an additional dimension in RCCD1 functionality, indicating RCCD1 is an essential regulator of mtDNA dynamics and mitochondrial homeostasis, whose dysregulation inflicts pathologic states such as breast cancer.

overall_design: The mammary adenocarcinoma MCF-7 cells were infected with lentivirus carrying FLAG-RCCD1 construction or control vector.

first: Xinhua


title: RRBS of TET2-mutant human neutrophils

city: London

first: Dominique

last: Bonnet

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Somatic mutations acquired by hematopoietic stem cells (HSCs) are commonly found over the course of a lifespan. Some of these clones will outgrow through a process known as clonal hematopoiesis (CH) and produce mutated immune cell progeny, which will shape host immunity. Individuals with CH are asymptomatic but have increased risk of developing leukemia, cardiovascular and pulmonary inflammatory diseases, and severe infections. Despite the key role that neutrophils play in the development of such diseases, little is known about how these prevalent somatic mutations affect neutrophil functionality. In this work, we describe how mutations in TET2, one of the most common mutated genes in individuals with CH, affect human neutrophil biology.

overall_design: Using CRISPR-mediated genetic engineering of human HSCs and transplantation in immunodeficient mice, we have sorted and analyzed the methylation status of the DNA of TET2 mutant (TET2Mut) neutrophils coming from 2 biological replicates.

first: Hector

last: Huerga Encabo

first: Manuel

last: Garcia-Albornoz

first: Miriam

last: Llorian Sopena


title: Comprehensive analysis of aberrantly expressed circRNAs, mRNAs and lncRNAs in patients with nasopharyngeal carcinoma

city: Shenzhen

first: Feifan

last: Guo

address: No. 33, Zhongyuan Road

institute: Medical Laboratory of the third affiliated hospital of Shenzhen university

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

summary:
The location of nasophryngeal cancer is hidden,so ti is difficult to diagnose at an early stage.In this study,we aimed to investigate expression profiles of circRNAs,mRNAs and IncRNAs and to provide some basis for further study.The expression profiles of circRNAs, mRNAs and lncRNAs were analyzed by microarray technology. The differentially expressed ncRNA was calculated by bioinformatics.
Our study characterized the landscape of circRNAs, mRNAs and lncRNAs in NPC tissue and provided novel insights into the molecular mechanisms of NPC.

overall_design: We collected fresh tissue samples of NPC (n =4) and the chronic inflammation of the nasopharyngeal mucosa tissues (n =4).Total RNA was extracted from the frozen tissue specimens using TRIzol reagent (Invitrogen, Grand Island, NY, USA) according to the manufacturer’s instructions, and purified by using a RNeasy Mini Kit (Qiagen, GmBH, Germany).Total RNA was checked for a RNA integrity number (RIN) to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).    The quality and amount of RNA were assessed using a NanoDrop ND-2000 spectrophotometer (Thermo Scientific, Rockford, IL, USA).

first: Dayang

first: Zengyan

last: Zong

first: Wei

last: Wu

first: Chan

last: Mo

first: Zhou

last: Zheng

first: Jian

last: Li

first: Xiuming

last: Zhang

first: Dan

last: Xiong


title: ATAC-seq, RNA-seq and RRBS of TET2-mutant human neutrophils


title: RNASeq of TET2-mutant human neutrophils

overall_design: Using CRISPR-mediated genetic engineering of human HSCs and transplantation in immunodeficient mice, we have sorted and analyzed the transcriptome of TET2 mutant (TET2Mut) neutrophils from 4 biological replicates.


title: Rapid PTEFb-dependent transcriptional reorganization underpins the glioma adaptive response to radiotherapy [ATAC-Seq]

city: Aurora

first: Nathan

middle: A

last: Dahl

state: CO

department: Pediatrics

country: USA

institute: University of Colorado School of Medicine

summary: This study examines the reorganization of transcriptionally active chromatin that underlies the adaptive response of glioblastoma cells to radiotherapy.

overall_design: ATACSeq were conducted in the DIPG4 cell line in the presence or absence of AZD or DMSO as control and subjected or not to radiation.

first: Lays

middle: M

last: Sobral

first: Faye

last: Walker

first: Etienne

last: Danis


title: Rapid PTEFb-dependent transcriptional reorganization underpins the glioma adaptive response to radiotherapy


title: Granulocyte-monocyte progenitor (GMP) RNA-seq in wild type and MST1-deficient mice.

first: Anna

last: Jia

address: Beijing Normal University

institute: BNU

summary: We sorted granulocyte-monocyte progenitor from wild-type and MST1-deficient mice by flow cytometry and performed transcriptome sequencing, analysis of differentially expressed genes, signaling pathways, metabolic pathways, etc. in the absence of MST1.

overall_design: Wild type and MST1-deficiency group contain two samples separately (named WT1, WT2, KO1, KO2), each sample contains granulocyte-monocyte progenitor isolated from bone marrow of ten mice.


title: ATACSeq of TET2-mutant human neutrophils

first: Dominique

last: Bonnet

overall_design: Using CRISPR-mediated genetic engineering of human HSCs and transplantation in immunodeficient mice, we have sorted and analyzed the chromatin conformation of TET2 mutant (TET2Mut) neutrophils coming from 4 biological replicates.

first: Hector


title: Transcriptional units form the elementary constraining building blocks of the bacterial chromosome

city: Paris

first: Amaury

last: Bignaud

address: 28 Rue du Docteur Roux

country: France

institute: Institut Pasteur

summary: Transcription generates local topological and mechanical constraints along the DNA fiber, driving for instance the generation of supercoiled chromosomal domains in bacteria. However, the global impact of transcription-based regulation of chromosome organization remains elusive. Notably, the scale of genes and operons in bacteria remains well below the resolution of chromosomal contact maps generated using Hi-C (~ 5 - 10 kb), preventing to resolve the impact of transcription on genomic organization at the fine-scale. Here, we combined sub-kb Hi-C contact maps and chromosome engineering to visualize individual transcriptional units (TUs) while turning off transcription across the rest of the genome. We show that each TU forms a discrete, transcription-induced 3D domain (TIDs). These local structures impose mechanical and topological constraints on their neighboring sequences at larger scales, bringing them closer together and restricting their dynamics. These results show that the primary building blocks of bacteria chromosome folding consists of transcriptional domains that together shape the global genome structure.

overall_design: ChIP-seq method described in Cockram et al. 2015 doi: 10.1073/pnas.142426911

first: Charlie

last: Cockram

first: Eric

last: Allemand

first: Julien

last: Mozziconnacci

first: Olivier

last: Espeli

first: Romain

last: Koszul


title: Microglia care for neurons through tunneling nanotubes

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

institute: University Hospital Bonn

overall_design: Refer to individual Series


title: Microglia care for neurons through tunneling nanotubes [Dataset 2 Microglia mRNA-seq]

summary: We report the transfer of alpha-s-ynuclein aggregates from neurons to microglia and examined transcriptomic changes following protein extraction. By obtaining RNA samples, we performed differential expression analysis and generated gene ontology enrichment and network analysis.

overall_design: mRNA sequencing of Microglia from mice cocultured in the presence of murine neurons treated with and without aSyn

first: Hannah

last: Scheiblich

first: Frederik

last: Eikens

first: Lena

last: Wischhof

first: Sabine

last: Opitz

first: Kay

last: Jüngling

first: Csaba

last: Cserép

middle: V

first: Tracy

last: Bellande

first: Balázs

last: Pósfai

first: Charlotte

last: Geck

first: Jasper

last: Spitzer

first: Alexandru

last: Odainic

first: Stephanie

last: Schwartz

first: Donato

last: Di Monte

first: Daniele

last: Bano

first: Ádám

last: Dénes

first: Eike

last: Latz

first: Ronald

last: Melki

first: Hans-Christian

last: Pape

first: Michael

middle: T

last: Heneka


title: Rapid PTEFb-dependent transcriptional reorganization underpins the glioma adaptive response to radiotherapy [ChIP-Seq]

first: Nathan

last: Dahl

overall_design: H3K27ac ChIPs were conducted in the DIPG4 cell line in the presence or absence of AZD or DMSO as control and subjected or not to radiation.

first: Lays

last: Sobral

first: Faye

last: Walker

first: Etienne

last: Danis


title: F. nucleatum-derived succinic acid induces tumor resistance to immunotherapy in colorectal cancer

first: Yile

last: Xie

address: 145 Middle Shandong Road

institute: Renji Hospital, Shanghai Jiao Tong University School of Medicine

summary: At present, the mechanisms underlying the association between gut microbiota metabolites and immunotherapy in CRC remain unknown. Here, we conducted a multiomics analysis of a cohort of patients with mCRC and found that F.nucleatum was more abundant in patients who did not respond to immunotherapy. We also found that F. nucleatum diminished the sensitivity to anti-PD-1 mAb through its metabolite succinic acid. Accordingly, patients with lower serum succinic acid levels achieved a better response to immunotherapy. Mechanistically, F.nucleatum-derived succinic acid suppressed the cGAS-interferon-β pathway, consequently dampening the antitumor response by limiting CD8+ T-cell trafficking to the tumor microenvironment in vivo. Treatment with metronidazole reduced intestinal F.nucleatum abundance and thereby decreased serum succinic acid levels, thus resensitizing the tumors to immunotherapy in vivo. Collectively, our findings indicate that F. nucleatum and its metabolite succinic acid induce tumor resistance to immunotherapy and offer new insights into microbiota-metabolite-immune crosstalk in CRC.

overall_design: We investigated the effect of Fusobacterium nucleatum on anti-PD-1 therapy in Germfree C57B/L6 MC38-tumor bearing mice.  Tumor 11, 17, 18 and 19 were subcutaneous tumor  from anti-PD-1 group;tumor 36, 37, 39,40 were subcutaneous tumor  from anti-PD-1 + F. nucleatum group.

first: Jing-Yuan

last: Fang

first: Shanshan

last: Jiang


title: Microglia care for neurons through tunneling nanotubes [Dataset 1 Neurons mRNA-seq]

first: Susanne

last: Schmidt

overall_design: mRNA sequencing of Neurons from mice treated with and without aSyn cocultured in the presence of microglia

first: Hannah

last: Scheiblich

first: Frederik

last: Eikens

first: Lena

last: Wischhof

first: Sabine

last: Opitz

first: Kay

last: Jüngling

first: Csaba

last: Cserép

first: Tracy

last: Bellande

first: Balázs

last: Pósfai

first: Charlotte

last: Geck

first: Jasper

last: Spitzer


title: Transcriptome and chromatin changes during CRC organoid outgrowth as proxy for metastatic outgrowth [bulkRNAseq_AKP]

city: Utrecht

first: Maria

middle: Christine

last: Heinz

address: Heidelberglaan 100

department: Molecular Cancer Research

country: Netherlands

institute: University Medical Center Utrecht

summary: Human engineered CRC organoids were equipped with the intestinal stem cell reporter STAR reflecting transcriptional activity of ASCL2. Bulk RNA-sequencing was performed on STAR+ and STAR- cells after 5 days and after 12 days.

overall_design: Organoids were grown from STAR+ cells (APCKO/KO; KRASG12D/-; TP53KO/KO (AKP)). After 5 days and after 12 days, organoids were harvested, dissociated to single cells, and between 10-20 k STAR+ and STAR- cells were collected in technical replicates for bulk RNA-seq.

middle: C

first: Rik

middle: G

last: Lindeboom

first: Koen

last: Oost

first: Lisa

last: van Voorthuijsen

first: Michiel

last: Vermeulen

first: Hugo

last: Snippert


title: Transcriptome and chromatin changes during CRC organoid outgrowth as proxy for metastatic outgrowth [bulkRNAseq_AKPS]

summary: Human engineered CRC organoids were equipped with the intestinal stem cell reporter STAR reflecting transcriptional activity of ASCL2. Bulk RNA-sequencing was performed on STAR populations after 5 days and after 12 days of plating single STAR+ or STAR- cells.

overall_design: Organoids were grown from single STAR+ or STAR- cells (APCKO/KO; KRASG12D/-; TP53KO/KO; SMAD4 KO/KO (AKPS)). After 5 days and after 12 days, organoids were harvested, dissociated to single cells, and between 10-20 k STAR+ and STAR- cells were collected in technical replicates for bulk RNA-seq.


title: Transcriptome and chromatin changes during CRC organoid outgrowth as proxy for metastatic outgrowth

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


title: Transcriptome and chromatin changes during CRC organoid outgrowth as proxy for metastatic outgrowth [bulkATACseq_AKPS]

summary: Human engineered CRC organoids were equipped with the intestinal stem cell reporter STAR reflecting transcriptional activity of ASCL2. Bulk ATAC-sequencing was performed on STAR populations after 5 days and after 12 days of plating single STAR+ or STAR- cells.

overall_design: Organoids were grown from single STAR+ or STAR- cells (APCKO/KO; KRASG12D/-; TP53KO/KO; SMAD4 KO/KO (AKPS)). After 5 days and after 12 days, organoids were harvested, dissociated to single cells, and between 75-100 k STAR+ and STAR- cells were collected in technical replicates for bulk ATAC-seq.


title: Single cell RNA sequencing of mouse male and female liver cells with and without acetaminophen-induced injury

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: We performed transcriptomic profiling of mouse whole liver cells perfused in situ with collagenase and then mechanically dissociated into single cell suspensions, to garner about 40% hepatocytes and 60% non-parenchymal cells. Cells were isolated from male and female C57BL/6J mice that received either PBS vehicle control, or 400 mg/kg acetaminophen (APAP) and perfused 48 hours after injury.

overall_design: Global transcriptomic profiling at single cell resolution of murine liver cells. 4 samples: 1) Male PBS vehicle control, 2) Female PBS vehicle control, 3) Male APAP-Injured, 4) Female APAP-Injured. Cells were isolated on two days, with 48 hours between, but sequenced all together on the same chip.

first: Elissa

last: Everton

first: Carlos

last: Villacorta-Martin

last: Singh Bawa

first: Jonathan

last: Lindstrom-Vautrin

first: Valerie

last: Gouon-Evans


title: Genome-wide analysis of circulating tumor DNA methylation profiles in cerebrospinal fluid: a clinical trial of oncolytic virus for glioblastoma [MeDIP-Seq]

first: Lixin

last: Ma

address: Haidian District

department: Neurosurgery

institute: Sanbo Brain Hospital

summary: Background: Glioblastoma (GBM) is a common malignant tumor of the central nervous system (CNS) with a poor prognosis and short survival period. A novel tumor lysing virus, Ad-TD-nsIL-12, has demonstrated good anti-tumor properties in preclinical studies. However, there is still a gap in the treatment of GBM with Ad-TD-nsIL-12. Methods: We collected cerebrospinal fluid (CSF) and tumor tissues from patients injected with Ad-TD-nsIL-12 at different times and analyzed CSF circulating tumor DNA (ctDNA) methylation profiles and expression profiles. The differential genes were screened by Lasso Cox regression analyses, and Cox regression analyses. The CIBERSORT algorithm was used to assess the abundance of glioma immune cell infiltration in the TCGA dataset. The role of hub genes in diagnosis, prognosis, and immune cell correlation was analyzed using R software, SPSS software, and Graphpad Prism. Results: By observing the trend of methylation levels in different samples, 3631 differential methylation regions (DMRs) were up-regulated and 497 DMRs were down-regulated after Ad-TD-nsIL-12 injection, and these DMRs recovered their methylation levels within 70-82 days. Combined with the TCGA dataset, eight hub genes were screened to construct diagnostic and prognostic models. There was a significant correlation between hub genes and immune cells. Conclusions: This study analyzed the approximate therapeutic concentrations, doses, and cycles of Ad-TD-nsIL-12 for GBM. Revealed that the hub genes in CSF can be used as a biomarker for the diagnosis and prognosis of GBM, as well as boldly speculated the effect of the hub gene on the immune mechanism of Ad-TD-nsIL-12.

overall_design: In this study, circulating tumor DNA (ctDNA) was extracted and whole-genome methylation sequenced from a cohort of normal cerebrospinal fluid (CSF) samples and five CSF samples collected at different time from a patient with recurrent glioblastoma. CSF samples from this patient were collected before oncolytic virus injection, after the first oncolytic virus injection, 70 days after the first oncolytic virus injection, after the second oncolytic virus injection, and 82 days after the second oncolytic virus injection. Meanwhile, we collected glioblastoma tissue samples from this patient for mRNA sequencing at the time of the first injection of oncolytic virus and the second injection of oncolytic virus. In addition, we additionally collected a normal brain tissue sample for mRNA sequencing.

first: Lin

last: Dai


title: Genome-wide analysis of circulating tumor DNA methylation profiles in cerebrospinal fluid: a clinical trial of oncolytic virus for glioblastoma [mRNA-Seq]


title: DJ-1 governs airway progenitor cell/eosinophil interactions to promote allergic inflammation

city: Tianjin

first: Kuan

last: Li

address: Jingu road 890

institute: Department of Basic Medicine, Haihe Hospital, Tianjin University

summary: DJ-1 is an antioxidant protein known to regulate mast cell mediated allergic response, but its role in airway eosinophilic interactions and allergic inflammation is not known.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different treatment lung cells


title: Genome-wide analysis of circulating tumor DNA methylation profiles in cerebrospinal fluid: a clinical trial of oncolytic virus for glioblastoma


title: Utilizing Omomyc to Target MYCN-Amplified Diffuse Intrinsic Pontine Gliomas

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Genomic studies have shown that several types of pediatric brain tumors have dysregulation of MYC family members (c-MYC and MYCN). In fact, it has been estimated that about 50% of all human cancers have increased MYC, and this is correlated with tumor aggression and poor survival. Here we focus on targeting the MYCN oncogene in diffuse intrinsic pontine glioma (DIPG). DIPG has the worst prognosis of any pediatric brain tumor and is in desperate need of viable treatment options. Here we demonstrate that using a 90-amino acid peptide, termed “Omomyc” we are able to down-regulate endogenous MYCN and inhibit growth of MYCN overexpressing DIPG cells. Furthermore, Omomyc binds to promoter regions normally occupied by MYCN to affect transcription of a subset of genes including PLK1 and LDHA, among others. In vivo expression of Omomyc in DIPG cells implanted in mice slows disease progression, suggesting that MYCN targets are important for driving rapid tumor growth and may offer insight into potential targets for treatment of MYCN driven DIPGs.

overall_design: RNASeq was performed on four different samples. Each sample was prepared as a singleton. Three samples are controls/references (1-SM-vumc-GFP_S1, 2-SM-vumc-GFP-dox_S2, 3-SM-vumc-omo_S3) and one sample is treated/test (4-SM-vumc-omo-dox_S4).

first: Shelli

last: Morris

first: Jay

last: Sarthy

first: Brian

last: Freie

first: Patrick

last: Carroll


title: KAT5 activity regulates quiescent-like states in human gliomas [crispr screen]

summary: In solid tumors, quiescent/G0 cell populations likely play important roles in maintaining cellular heterogeneity and promoting recurrence after stand of care. However, little is known about the mechanisms of tumor cell G0 ingress and egress. To discover regulators of G0-like states for glioblastoma (GBM), we performed a genome-wide CRISPR-Cas9 screen in patient-derived GBM stem-like cells (GSCs) for genes that when inhibited trap cells in G0-like states. We identify the protein acetyltransferase KAT5 as a key regulator of G0 and cell cycle dynamics in GSCs and GSC-derived tumors. In primary gliomas, KAT5low cells display quiescent properties, while overall KAT5 activity increases as tumors become more aggressive.  Further, we find that KAT5 activity suppresses the emergence of non-dividing subpopulations with oligodendrocyte progenitor and radial glial cell characteristics both in vitro and in a GSC tumor model. These results reveal that KAT5 activity regulates transitions between non-dividing, neurodevelopmental, and proliferative states in GBM tumors.

overall_design: CRISPR-Cas9 screens include 3 replicates for p27Hi (sorted and unsorted) samples in glioblastoma stem cell line (GSC827)

first: Anca

last: Mihalas

first: Samantha

last: Oconnor

first: John

last: Bassett

first: Christopher

last: Plaisier

first: Anoop

last: Patel

last: Paddison


title: Decipher heterogeneity of cervical squamous cell carcinoma and adenocarcinoma with different HPV status: combining scRNA and TCR-seq with 3D organoid

city: Shanghai

first: Xinyu

last: Qu

address: 419 Fangxie Road

department: Department of Gynecology

institute: Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University

summary: Although adenocarcinoma of the cervix (ADC) exhibits a more malignant phenotype and poorer prognosis than squamous cell carcinoma (SCC), they are treated identically. This clinical dilemma calls for deeper investigation into differences between SCC and ADC. We studied 3 human papillomavirus (HPV)-positive SCC, 3 HPV-associated (HPVA) and 2 non-HPV-associated (NHPVA) ADC samples with single-cell RNA and T cell receptor sequencing plus 3D organoid verification. Notably, we revealed the malignant origin of epithelial cells characterized by stemness and poor differentiation and the potential mechanism of HPVA and NHPVA oncogenesis, deciphering differences between SCC and ADC. Additionally, we discovered the key role of tip cells in sprouting angiogenesis, the protumoral effects of cancer-associated fibroblasts and the functional dysregulation of T lymphocytes. We highlighted tumor microenvironment differences between different histologic subtypes through cellular interaction analysis. Importantly, we discovered novel precise treatment strategies specifically for HPV-positive SCC, HPVA and NHPVA-ADC, providing tremendous clinical value.

overall_design: We performed scRNA-seq and TCR-seq of 8 cervical cancer samples including 3 HPV-positive SCC  samples, 3 HPVA ADC samples and 2NHPVA ADC samples

first: Junjun

last: Qiu

first: Li

last: Wang

first: Xiaoyan

last: Tang

first: Yumeng

first: Chenyan

last: Guo

first: Bin

last: Lv

first: Qian

last: Jiang

first: Wentao

last: Su

first: Keqin

last: Hua


title: RBM4 regulates esophageal cancer progression

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: In order to profile the transcription events that were regulated by RBM4, mRNA-seq was performed on KYSE150_shRBM4 and KYSE150_ctl which based on KYSE150 cells

overall_design: This study includes a total of 2 profiling samples,KYSE150_shRBM4 was generated as a RBM4 knocked down esophageal cancer cells . KYSE150_ctl was generated as a control esophageal cancer cells .

first: Chen

last: Lei

first: Qi

last: Yangfan


title: Pathogenic variants in PRDM16 impair cardiomyocytes maturation and cause cardiomyopathy phenotypes in mice

city: salt lake city

first: Sihem

last: Boudina

state: Utah

department: Nutrition and Integrative Physiology

institute: University of Utah

summary: Loss of the PR domain 16 (PRDM16) genetic locus has been suggested as the needed trigger for the development of left ventricular non-compaction cardiomyopathy (LVNC) and dilated cardiomyopathy (DCM) in patients with 1p36 deletion syndrome. Furthermore, lack of Prdm16 in the murine heart has recently been shown to cause a spectrum of cardiomyopathy phenotypes. In spite of these advances, our understanding of the downstream transcriptional pathways regulated by PRDM16 that lead to these cardiac phenotypes is limited. OBJECTIVE: to unveil the downstream transcriptional pathways involved in the development of cardiomyopathy phenotypes associated with PRDM16 mutations/deletion in human and mice. METHODS AND RESULTS: We hypothesized that PRDM16 acts as an upstream regulator of key transcriptional pathways involved in cardiac maturation. Induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) from a patient with a PRDM16 variant, cardiac tissue from mice expressing the human variant, mice with cardiac-specific deletion of Prdm16 and in vitro gain and loss of Prdm16 function were employed. Here we show that de novo pathogenic variants in PRDM16 are sufficient to cause LVNC in humans. In contrast, haploinsufficiency or complete deletion of Prdm16 in cardiomyocytes in mice led to pathological hypertrophy and dilated cardiomyopathy respectively. We demonstrated that PRDM16 regulates cardiac maturation through the maintenance of estrogen-related receptors (ERRs) expression. By contrast, PRDM16 acts as a supressor of transforming growth factor beta (TGFB) signaling. CONCLUSIONS:  PRDM16 is a novel regulator of cardiac maturation acting upstream of ERRs and their regulators, and a suppressor of fibrotic signaling including TGFB.

overall_design: Mice with cardiomyocytes-specific deletion of Prdm16 (cPrdm16 KO) at embryonic date 17 (E17) were used. Whole heart tissue was used to perform RNA sequencing.

first: Andrew

middle: P

last: Landstrom


title: Pathogenic variants in PRDM16 impair cardiomyocytes maturation and cause cardiomyopathy phenotypes in humans and mice


title: Loss of LSM14b affects the meiosis process of mouse oocytes

city: Nanjing

first: zhang

middle: hui

last: ru

address: 101 Longmian Avenue

institute: Nanjing Medical University

summary: RNA-Seq can comprehensively and quickly obtain almost all transcripts and information of specific cells in rustic states.Here,we compared up-regulated genes in GV and MII oocytes from LSM14b deficient mice and wild-type mice by RNA-Seq,highlighting the important role of LSM14b in meiosis of mouse oocytes.

overall_design: GV and MII oocytes from 5-week-old WT and LSM14b-KO females. RNA profiling data form four groups was collected from three biological replicates.

first: Huiru

last: Zhang

first: Xin

last: Wu


title: Pathogenic variants in PRDM16 impair cardiomyocytes maturation and cause cardiomyopathy phenotypes in humans

overall_design: Induced pluripotent stem cells (iPSCs) were prepared from periferal blood of a control subject and a subject with PRDM16Q187X variant. iPSCs were differentiated into cardiomyocytes (iPSC-CMs) before performing the RNAseq


title: In situ Growth of ZIF-8 Nanoparticles on Graphene Oxide Nanosheets: A Multifunctional Nanoplatform for Combined Ion‐interference and Photothermal Therapy

city: Jinan, Shandong

first: Wenyan

last: Kang

address: No. 44-1 Wenhua Road West

institute: Shandong university

summary: In summary, highly stability and dispersed BSArGO@ZIF8 NSs were prepared by a simple electrostatic interaction method. According to the delivery effect of BSArGO@ZIF8 NSs, we found that BSArGO@ZIF8 NSs possess higher lethality to cancer cells. Furthermore, under NIR irradiation, BSArGO@ZIF8 NSs-mediated PTT could further kill cancer cells, and the increased temperature caused by photothermal conversion accelerated the Fenton reaction rate, enhancing the efficiency of BSArGO@ZIF8 NSs cell lethality. RNA-seq analysis confirmed that. BSArGO@ZIF8 NSs could promote cancer death through activate bim-mediated mitochondrial apoptotic events, induce disruption of microtubule function, loss of integrity of the nuclear membrane, DNA flagmentation, and change pro-apoptptic genes expression.

overall_design: Total RNA of Cal27 from 3 different experiments treated with or without BSArGO@ZIF-8 NSs at 6 h were collected and RNA-seq was used to analyze the whole genome expression at LC Sciences through the Illumina X10 platform

first: Baojin

last: Ma


title: Gastrointestinal B-cells license metabolic T-cell activation in NASH microbiota/antigen-independently and contribute to fibrosis by IgA-FcRγ signaling

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary:
Purpose: Aim of the study was to identify transcriptional changes in the intestinal B cells of NASH-affected mice versus healthy mice.
Results: RNA-Seq analysis in both sorted CD19+/CD20+ and sorted B220+ cells, revealed increased expression levels in genes involved in lipid metabolism, and in antigen presentation, BCR signaling, B cells activation and proliferation.
Conclusion: Mice bearing NASH (both WT and μMT choline-deficient high-fat diet (CD-HFD) fed mice) display altered B cells in the gastrointestinal tract towards an activated phenotype and increased proliferation induced by the CD-HFD.

overall_design: RNAseq analysis of sorted CD19+/CD20+ and of B220+ cells from small intestines of WT normal diet (ND), WT CD-HFD, and μMT CD-HFD fed mice for 6-months.

first: Mathias

last: Heikenwälder

first: Elena

last: Kotsiliti

first: Valentina

last: Leone

first: Rupert

last: Öllinger

first: Roland

last: Rad


title: Biallelic variant in LEF1 are associated with a new syndrome combining ectodermal dysplasia and limb malformations through altered WNT signalling

city: Cologne

first: Muhammad Sajid

last: Hussain

address: Weyertal 115b

department: Cologne Center for Genomics

institute: University of Cologne

summary: We found a homozygous duplication of three base pairs in LEF1 (c.69_71dupGAT; p.M23_I24insM) in patient manifesting ectrodactyly ectrodermal dysplasia syndrome without cleft lip/palate. We aim to elucidate the consequences of this homozygous LEF1 varinat on transcriptome profiling of the patient compared to age matched control. Collectively, we observed differential expression of genes involved in the the canonical WNT pathway. Interestingly, 30 out of 39 known HOX genes were significantly differentially expressed.

overall_design: We concluded that the identified LEF1 variant disturb the canonical WNT signaling pathway.

first: Salem

last: Alawbathani

first: Prerana

last: Wagle

first: Peter

last: Nürnberg

first: Muhammad

middle: S


title: LncRNA RP3-340N1.2 affects the progression of lung adenocarcinoma cell lines by targeting miR-134-5p

city: Jinan

first: Wei

last: Li

state: Shandong

address: Wenhuaxi Road NO.44

institute: Shandong University

summary: We found lncRNA RP3-340N1.2 is highly expressed in LUAD and relatived with the progression of LUAD through high-throughput sequencing. Our results showed that the expression level of RP3-340N1.2 was upregulated significantly in three LUAD cell lines (A549, NCI_x001E_H1299, and NCI-H1975) and lentivirus-mediated knockdown of RP3-340N1.2 inhibited the differentiation, proliferation, migration, invasion, cell cycle, and other biological processes of tumor cells significantly. Bioinformatic software predicted the downstream target of RP3-340N1.2, which was verified using dual luciferase assays and other methods. We found that RP3-340N1.2 can competitively bind miR-134-5p in LUAD, and this microRNA has a significant regulatory effect on the expression of epidermal growth factor receptor (EGFR), which leads to increased migration and invasion of LUAD cells. This discovery provided a possible mechanism by which RP3-340N1.2 participates in the development of LUAD. In conclusion, our results showed that lncRNA RP3_x001E_340N1.2 regulates the expression of EGFR indirectly by targeting miR-134-5p and promotes the progression of LUAD. Therefore, RP3-340N1.2 may become a valuable biomarker and therapeutic target in LUAD.

overall_design: Examination of lncRNAs in lung adenocarcinoma cell lines.

first: Chuanxi

last: Wang


title: Developing high throughput single-cell single-nucleotide in situ pairwise sequencing for macromolecule spatail-omics

city: Wuhan

first: Weize

last: Xu

state: Hubei

address: shizishan street No.1

institute: Huazhong Agricultural University

summary: To identified the method which can differentiate in situ SNP modification, we constructed an RNAseq library to identify SNPs in the C6 cell line and parent-specific SNPs in the PVN of C57. Design probes for these SNPs for in situ SNP detection and was applied to detect tumor driver genes mutation and allele specific expression of parental genes.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Characteristically distributed SNPs in C6 glioma sections, and at the same time obtained parent-specific SNP in situ maps in orthogonal progeny

first: Chengchao

first: Zhongchao

first: Yue


title: Transcriptomic characterization of the 4T1-4T07. cells

city: Montreal

first: Jean-Francois

last: Cote

state: Quebec

address: 110 pine avenue

country: Canada

institute: IRCM

summary: Purpose: 1) define the differentially expressed genes between the 4T1-4T07 cells 2) Correlate the transcriptomic profile of these two lines with human breast cancer cell lines to help define their molecular subtype in an unbiased manner

overall_design: 4T1 or 4T07 cells grown in triplicates, RNA extracted and processed for RNA-Seq

first: Jean-François

last: Côté


title: RNA-seq for mRNA expression profile in the cochlea of coffee or green tea extract treated  and control mice

city: Binzhou

first: Xiuzhen

last: Liu

address: No.661, Second Huanghe Road

institute: Binzhou Medical University Hospital

summary: Our experiments showed that long-term coffee or green tea(GTE) extract supplementation( from 3 months old to 12 months old) ameliorates age-related hearing loss (ARHL) in mice. Then we explored the possible underlying mechanisms through comparing the cochlear transcriptome profiling (RNA-seq) of the coffee or GTE treated mice to the control mice.

overall_design: Cochlear mRNA profiles of the coffee or GTE treated and control mice


title: Chromomal translocations induced by CRISPR-Cas9 persist in expanded T cells

city: Beijing

first: Yang

address: Yiheyuan Road, No. 5

institute: School of life sciences, Peking University

summary: Chromosomal translocations cause various lymphoid cancers and are prevalent in CRISPR-Cas9-meidated gene editing. However, the fate of gene editing-induced translocations remains elusive in vivo. Here, we found that translocations in engineered T cells experience clonal expansion after transferring into recipients for three weeks and remains comparable level with edited T cell before transfer, arguing against the notion that translocations would be gradually lost during cell proliferation due to growth retardation.

overall_design: Examination of the fate of chromosomal translocation induced by gene editing in T cells

first: Jinchun

last: Wu

first: Jiazhi

last: Hu


title: Partial epithelial-to-mesenchymal transition (EMT) and T cell-mediated inflammation in hypertensive and diabetic nephropathy

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

summary: We comparatively evaluated transcriptomes from renal biopsies obtained from patients with T2DN or HN, main causes of CKD, and control renal tissues (n=6 per group). RNA was extracted from formalin-fixed and paraffin-embedded kidney samples and processed for RNA sequencing. Principal component analysis effectively separated diseased and control tissues. Gene and protein expression profiles revealed that EMT-related markers were upregulated in both diseases. Moreover, activation of CD4 and CD lymphocytes, as well as upregulation of the complement system were also observed in both T2DN and HN. These data, suggesting partially common pathogenetic mechanisms, were largely confirmed by IHC analysis.

overall_design:
Formalin-fixed and paraffin-embedded kidney biopsies from adult patients were selected from the Norwegian Kidney Biopsy Registry. Specimens from patients with HN, T2DN and normal-appearing control renal biopsies (Ctrl) (n=6 for each group) were assessed. Total RNA was extracted from 10 μm whole kidney sections and processed for RNA sequencing, while immunohistochemistry (IHC) was performed on 3-μm tissue sections.
*** Submitter declares that the raw data is being deposited in the European Genome-phenome Archive (EGA) due to patient privacy concerns.***

first: Ole

last: Nordbo

first: Lea

last: Landolt

first: Piotr

last: Mydel

first: Oystein

last: Eikrem

first: Andreas

last: Scherer

first: Sabine

last: Leh

first: Jessica

last: Furriol Palmer

first: Terje

last: Apeland

first: Hans-Peter

last: Marti


title: CD24-dependent expression of microRNAs in ovarian cancer cells

city: Seoul

first: Baek Gil

last: Kim

address: 50-1 Yonsei-Ro

institute: Yonsei University

summary: To understand whether CD24, a potential marker for ovarian cancer stem cells,-dependent microRNA expression affects ovarian cancer stemness, microRNA expression was compared between CD24-negative and CD24-positive ovarian cancer cells.

overall_design:
CD24-negative and CD24-positive cells were sorted from Caov-3 and an ovarian cancer patient tissue by flow cytometry cell sorter. The microarray was performed in triplicates with separately prepared samples.

*** Submitter declares that the raw files cannot be submitted because the company that provided the microarray service is no longer operational ***

first: Baek

first: Ji

middle: E

last: Kwon

first: Nam

middle: H

last: Cho


title: Establishment of a 3D hyperuricemia model based on cultured human liver organoids

city: Guangzhou

first: Maojin

last: Yao

address: No.195, West Dongfeng Road, Yuexiu District

department: Guangzhou Institute of Respiratory Health

institute: Guangzhou Medical University

summary: Hyperuricemia (HUA) is a metabolic disease caused by abnormal purine metabolism, the prevalence of which has increased worldwide. Here, a 3D organoid culture system for mimicking HUA in vitro was established using cultured human liver organoids. Liver organoids can be generated from single hepatocytes and passaged for several months, retaining key morphological features, functional purine metabolism and global gene expression profile. Furthermore, organoids can be differentiated into hepatocytes with high expression of maturation markers including HNF4α, E-cadherin, and ALB. Importantly, organoids can produce high level of uric acid after xanthine induction which is the substrate of xanthine oxidase. Furthermore, the preclinical application potential of this organoid model was verified by measuring the anti-hyperuricemic effect of the widely used allopurinol, as well as the reported bioactive substance puerarin. The results demonstrate that this novel organoid model could be used for high-throughput screening of both chemical and food-derived compounds with antihyperuricemic bioactivity.

overall_design: Primary Hepatocytes were isolated from paracarcinomatous liver tissues by two-step collagenase digestion, and suspended the cells in Matrigel. The mRNA profile of human liver organoids after 5 days of differentiation and amplification. Total RNA was extracted from 3 liver-organoids from different passages in expansion medium (EM) and differentiation medium (DM) (P4, P6, P8) using TRIzol reagent. RNA quality and quantity using was analyzed by NanoDrop spectrophotometer (BioRad, USA) and a Bioanalyzer 2100 system (Agilent, USA). Transcriptional sequencing library was constructed by TruSeq™ RNA Sample Preparation Kit (Illumina, USA). The libraries were then sequenced on an Illumina Hiseq platform. Sequencing data analysis was performed using the DESeq2 package (CIT) in the R software environment. HEM represents organoids cultured in EM, and HDM represents organoids cultured in DM.

first: Jiaoyan

last: Ren

first: Chuanli

last: Hou

first: Yang


title: Comparison of E14.5 embryonic kidney transcriptomes (Grb2 ureteric-specific knockout vs wild-type)

city: Chicago

first: Rizaldy

middle: Paz

last: Scott

state: IL

address: 303 E. Superior St.

department: Medicine (Division of Nephrology & Hypertension)

institute: Northwestern University Feinberg School of Medicine

summary:
Grb2 is a small SH2-SH3 adaptor molecule that interacts with activated tyrosine kinase receptors (RTKs), providing a crucial link towards downstream activation of pro-proliferative and pro-survival ERK and Akt signaling pathways. Ret and FGFR2, two RTKs that interact with Grb2, play important roles in ureteric branching and the proper establishment of the renal collecting duct system, but it is unclear whether Grb2 is required in this process. In this study, we selectively ablated a conditional floxed allele of the Grb2 gene within the ureteric epithelial lineage in mice and demonstrate that Grb2 signaling is essentially required for proper collecting duct development. Ureteric Grb2 deficiency results in perinatal lethality and severe renal hypodysplasia closely reminiscent of the rudimentary kidney phenotypes observed in Ret-null mutant mice.  Grb2 loss attenuates ERK and Akt activation in the ureteric epithelia resulting in pronounced impairment of ureteric branching. Gene expression analysis reveals that Grb2 deficiency results in defective induction of genes implicated in both ureteric branching and reciprocal mesenchymal metanephric induction. Our findings therefore strongly indicate that Grb2 is a physiologically-relevant major RTK signaling relay partner that promotes renal branching morphogenesis and the proper development of the collecting duct system and the urogenital tract.
Microarray was used to profile and compare the transcriptomes of developing kidneys of E14.5 Grb2 conditional knockout (ureteric-bud specific) and wild-type embryos

overall_design: E14.5 kidneys were dissected and processed for total RNA extraction. A total of 4 pairs of control wild-type and 4 pairs of Grb2 knockout mutant kidneys were analyzed. All samples came from the same litter


title: Long reads Nanopore-seq of pulled down RNA using probes against mbl-exon2

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

department: Biology department

institute: Brandeis University

summary: To analyzed the different mbl issoforms we pulled down RNA using probes against mbl-exon2 and performed long read sequencing

overall_design: 2 samples of Canton S flies head RNA were pulled down using probes against mbl-exon2. Nanopore PCR-cDNA Sequencing Kit sequencing was performed following manufacturer instructions.


title: Type-I interferome in human peripheral blood mononuclear cells (PBMC)

city: Aurora

first: Kejun

last: Guo

state: Colorado

department: Division of Infectious Diseases

institute: University of Colorado Anschutz Medical Campus

summary:
Rationale: Humans encode 12 different IFNa proteins. All of them, except IFNa1 (only binds with IFNAR1), bind with IFNAR1 and IFNAR2 to activate their downstream functions. Currently in the field, it is still a debate whether there are qualitative difference between different IFNa subtypes or the differences are merely quantitative. The current study was set out to elucidate the question.
Methods: Commercially purchased PBMCs from 7 donors were mock treated or with ISRE activity normalized IFNa1, IFNa2, IFNa4, IFNa5, IFNa8, IFNa14, or IFNb. RNAs were extracted from cells after 18 hrs of incubation. RNASeq libraries were generated using Lexogen Quant Seq 3’ mRNA-Seq library (FWD) Prep Kit. RNASeq were performed on Illumina NovaSEQ6000.
Results: An average of 12.6 million gene counts were identified for each donor/treatment. A total of 50,133 genes were mapped, and among them 333 genes were differentially expressed due to type I interferon treatments. Each of IFNa subtypes or IFNb has their specifically regulated genes in PBMCs.
Conclusion: These are the further evidences that there are qualitative differences between type I interferons.

overall_design: Transcriptomic profiles of PBMCs treated with different Type I interferons.

first: Brad

last: Barrett

first: Emily

last: Cooper

first: Mario

last: Santiago


title: 3' RNA-seq of brains from control and circMbl KD flies

summary: To determine functions of circMbl in brain in vivo we generated genetically encoded shRNA directed against individual circRNA-specific back-spliced junctions. We analyzed gene expression by 3' RNA-seq from control (actin-Gal4) and flies expressing the shRNA under the control of a constitutive driver (actin-Gal4; circRNA KD).

overall_design: Brains from eight miss match (8MM) sh control flies and circMbl KD flies were disected. 5 control samples and 2 KD fly samples were sequenced and procesed


title: Engineering class-B vitamin biosynthesis in Saccharomyces cerevisiae

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

summary: Saccharomyces cerevisiae is bradytroph for class B vitamins, it means that yeast cells exhibit slower growth in the absence of an external source of these metabolites. Alleviating these nutritional requirements for optimal growth performance would represent a valuable phenotypic characteristic for industrial strains since this would result in cheaper processes that would also be less susceptible to contaminations. In the present study, suboptimal growth of S. cerevisiae in absence of either pantothenic acid, para-aminobenzoic acid (pABA), pyridoxine, inositol and biotin were corrected by single or double gene overexpression of native FMS1, ABZ1/ABZ2, SNZ1/SNO1, INO1 and the Cyberlindnera fabianii BIO1, respectively. Several strategies were attempted to improve growth of S. cerevisiae CEN.PK113-7D in absence of thiamine, revealing that overexpression of THI4 and THI4/THI5 was able to improve growth up to 83% of the maximum specific growth rate of the reference CEN.PK113-7D in medium including all vitamins. Although the initial aim of this study was to combine all identified mutations in a single strain, the engineered strain IMX2210 only harboured genes to correct biotin, pABA, pantothenate and inositol bradotrophies. Firstly, this strain was fast-growing at a maximum specific growth rate of 0.28 ± 0.01 h-1 in medium devoid of all vitamins. Secondly, this strain exhibited physiological variables in aerobic glucose limited chemostat cultures at a dilution rate of 0.1 h-1 in absence of vitamins similar to that of the reference strain CEN.PK113-7D grown in the same conditions but in a fully supplemented complete medium. These physiological similarities were further emphasized by the limited differences observed in comparative transcriptome analysis from the chemostat culture grown cells that were essentially affecting genes of the class B vitamins biosynthetic pathways. This work paves the way towards construction of the first fast growing vitamin-independent S. cerevisiae strain.

overall_design: The goals of this study were to investigate whether strategies can be found to eliminate single vitamin requirements and if the found solutions could be combined yielding a vitamin-independent S. cerevisiae strain. Next, the engineered strain was characterized for growth performance in batch and chemostat cultures and compared to a parental strain requiring vitamin supplementation for optimal growth. Finally, transcriptome data of the engineered strain grown in absence of vitamins was analyzed and compared to its isogenic reference grown in presence of vitamins.

first: Anna

middle: K

last: Wronska

first: Thomas

last: Perli

first: Marcel

last: van den Broek


title: Methionine availability influences essential H3K36me3 dynamics during cell differentiation [ChIP-seq]

status: Public on Nov 30 2023

city: Durham

first: Yudong

last: Sun

state: NC

address: 308 Research Drive

institute: Duke University

summary: Histone modifications are integral to epigenetics through their influence on gene expression and cellular status. While it's established that metabolism, including methionine metabolism, can impact histone methylation, the direct influence of methionine availability on crucial histone marks that determine the epigenomic process remains poorly understood. In this study, we demonstrate that methionine, through its metabolic product, S-adenosylmethionine (SAM), dynamically regulates H3K36me3, a cancer-associated histone modification known to influence cellular status, and myogenic differentiation of mouse myoblast cells. We further demonstrate that the methionine-dependent effects on differentiation are mediated in part through the histone methyltransferase SETD2, which senses methionine levels. Additionally, methionine restriction leads to preferential decreases in H3K36me3 abundance and genome accessibility of genes involved in myogenic differentiation. Importantly, the effects of methionine restriction on differentiation and chromatin accessibility can be phenocopied by the deletion of Setd2. Collectively, this study demonstrates that methionine metabolism through its ability to be sensed by chromatin modifying enzymes can have a direct role in influencing cell fate determination.

overall_design: H3K36me3 ChIP-Seq in C2C12 cells at D0, D1, and D5 under control or methionine restriction conditions for WT and Setd2 KO lines

first: Jason

middle: W

last: Locasale


title: Targeting of the YAP/SMAD molecular circuit inhibits a TGFb1-induced myofibroblast phenotype

city: Groningen

first: Bram

last: Piersma

state: Groningen

address: Hanzeplein 1

department: Pathology and Medical Biology

institute: University Medical Center Groningen

summary: The goal of this study was to elucidate the genomic occupancy of YAP in repsonse to transforming growth factor beta (TGFb) 1 in primary human dermal fibroblasts, through ChIP sequencing.

overall_design: Genome binding/occupancy profiling of YAP in response to TGFb1, by high throughput sequencing. Two independent replicates of both unstimulated and TGFb1 stimulated cells were analyzed.

first: Rutger

last: Gjaltema

first: Miriam

last: Boersema

first: Ruud

last: Bank


title: Single-cell Landscape Analysis Reveals HSA21 Induced Regulatory Network in Mammalian Down Syndrome

city: Hangzhou

first: Yao

last: Chen

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medicine

institute: Zhejiang University

summary: Down syndrome (DS), characterized by various malfunctions, is the most common genetic chromosomal disorder. As DS population size keeps growing and most of them live beyond their puberty, their early‐onset health problems come into view. However, the molecular alterations have not been thoroughly surveyed before. Here we provide the first description of DS in single-cell resolution, including human and mouse, covering seven different organs. With 71934 mouse cells and 93207 human cells employed, we systematically revealed DS cells, across different cell types and different organs suffering from serious cellular stresses. We observed senescence stresses including ribosomal protein gene accumulation, mitochondrial dysfunction, apoptosis, and sterile inflammation in fetus DS cells. We further raised an HSA21 gene-induced regulatory network driving genome-wide expression alteration. Hence, this study provides valuable information to understand the pathological processes under DS condition.

overall_design: scRNA-seq analysis of aneuploidy (trisomy 21) and diploid fetuses.

first: Yanyu

last: Xiao

first: Renying

last: Wang


title: Methionine availability influences essential H3K36me3 dynamics during cell differentiation

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

overall_design: Refer to individual Series


title: Effect of deletion of Impdh2 on gene expression in the  forlimbs from E12.5 embryos and osteoclasts (OCs)

first: cheng

last: xu

address: Sanjiaohu Road

institute: Jianghan University

summary: Many factors are essential for skeletal development and homeostaisis. Here we report that inosine monophosphate dehydrogenase type II (Impdh2) is a key positive regulator for limb development and bone resorption. Deletion of Impdh2 in limb mesenchymal progenitors  impaired the differentiation of mesenchymal cells into chondrocyte. Meanwhile, deletion of Impdh2 in osteoclast precursors results in mice an osteopetrotic phenotype via suppressing osteoclast differentiation. Our results reveal a previously unrecognized role of Impdh2 on skeletal development and homeostasis.

overall_design: To investigate the physiological significance and function of Impdh2 in the regulation of limb development and osteoclastogenesis, we respectively generated limb mesenchymal progenitors and myeloid lineage cells, i.e., osteoclast precursors specific Impdh2 knockout mice (Prx-cKO and  LysM-cKO mice). We then performed gene expression profiling analysis using data obtained from RNA-seq from forelimbs of  Impdh2 WT and Prx-cKO mice embryos at E12.5, and osteoclasts of Impdh2 WT and LysM-cKO mice.

first: Xu

last: Cheng

first: Hu

last: Zhangfeng


title: Bulk RNAseq of post-mortem brain tissue of Aicardi-Goutières Syndrome patients and non-diseased controls

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary: Post mortem brain tissue of three Patients suffering from Aicardi-Goutières Syndrome from different brain regions was used to isolate RNA and perform RNAseq analysis compared to age matched control patients with no underlying brain pathology.

overall_design: Disease vs control with two AGS patients and two to three control samples for each group and brain region were analysed.

first: Marco

last: Prinz


title: Superior Expansion of Zone 2 Hepatocytes in Pregnancy

first: Mingshan

last: Zhou

address: No. 600 Dunyu Road Sandun Town

institute: Westlake University

summary: We found that the hepatocyte proliferation wave initiated from zone 1/2 to zone 2/3 during early-to-late pregnancy, resulting in the generation of most new hepatocytes in zone 2. By single-cell RNA sequencing, we identified that Ccnd1 was highly enriched in zone 2.

overall_design: Mouse primary hepatocytes were isolated from 8-week-old mice by two-step collagenase perfusion, and analyzed using scRNAseq.

first: Lingjuan

last: He

first: Shun


title: Analysis of m6A methylome in ABRO1 Knockout heart

city: Qingdao

first: Kun

address: 308 Ningxia Road

institute: Qingdao University

summary: To find the m6A methylation targets of ABRO1,  we performed m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) in  ABRO1 Knockout or Wild type (WT) mice heart. The analysis of the distribution of m6A peak density in mRNA transcripts showed that m6A peaks are mainly found in coding sequences (CDS) and a considerable amount of m6A peaks enriched around start codon and stop codon regions in mRNA transcripts from ABRO1 KO and WT hearts. Among the total RNA transcripts with m6A sites, more than half (59.4%) of mRNA transcripts contain ≤ 2 m6A peaks, 27.4% mRNA transcripts comprise 3 to 5 m6A peaks and more than 5 m6A peaks exist in 13.2% of mRNA transcripts. MeRIP-seq analysis results from ABRO1 deleted hearts showed that a total of 3444 m6A peaks were upregulated and 4631 m6A were downregulated compared to WT hearts.

overall_design:
Total RNAs were extracted from ABRO1 Knockout or Wild type (WT) mice heart. MeRIP was performed to enrich m6A methylated mRNAs using anti-N6-methyadenosine (m6A) antibody. We used commercial kit (KAPA Stranded mRNA-seq Kit) for RNA-seq library preparation of both m6A enriched RNAs and input mRNAs. Then, high throughput RNA sequencing was performed to identify differences in the gene expression profile.
Please note that each processed data was generated from both input and IP samples, and is linked to the corresponding IP sample records.

first: Tao

first: Kao-Wen

last: Yan

first: Yun-Hong

first: Fang

last: Liu


title: Spatial transcriptomics reveal signatures of histopathological changes in muscular sarcoidosis

status: Public on Nov 29 2023

city: Bremerhaven

first: Cyril

last: Degletagne

address: Am Handelshafen

department: Functional Ecology

institute: Alfred Wegener Institute

summary:
Sarcoidosis is a multisystemic disease characterized by non-caseating granuloma infiltrating various organs. The form with symptomatic muscular involvement is called muscular sarcoidosis. The impact of immune cells composing the granuloma on the skeletal muscle is misunderstood. Here, we investigated the granuloma-skeletal muscle interactions through spatial transcriptomics. Five major transcriptomic clusters corresponding to perigranuloma, granuloma, and three successive muscle tissue areas (proximal, intermediate and distal) around the granuloma were identified. Analyses revealed upregulated pathways in the granuloma corresponding to the activation of T-lymphocytes and monocytes/macrophages cytokines and upregulation of extracellular matrix signatures and induction of the TGF-β signaling in the perigranuloma. Comparison between proximal and distal muscles to the granuloma revealed an inverse correlation between distance to the granuloma and upregulation of cellular response to interferon-γ/α, TNF-α, IL-1,4,6, fibroblast proliferation, epithelial to mesenchymal cell transition and downregulation of muscle gene expression.
These data shed light on the intercommunications between granulomas and the muscle tissue and provides pathophysiological mechanisms by showing that granuloma immune-cells have a direct impact on proximal muscle tissue by promoting its progressive replacement by fibrosis via the expression of pro-inflammatory and pro-fibrosing signatures. These data could possibly explain the evolution towards a state of disability for some patients.

overall_design: We perform Visium v1 on two FFPE slides from patients identified for granulomatous myositis associated with multisystemic sarcoidosis.

first: Hippolyte

last: Lequain

last: Dégletagne

first: Nathalie

last: Streichenberger

first: Julie

last: Valantin

first: Thomas

last: Simonet

first: Laurent

last: Schaeffer

first: Pascal

last: Sève

last: Leblanc


title: Improving Thymus Implantation for Congenital Athymia with Interleukin-7

first: Shane

middle: Mitchell

last: O'Neil

address: 701 W Main St

department: Neuroscience

summary: Patients receiving thymus implantation develop a functional but incomplete T cell compartment. Our objective was to develop a mouse model to study clinical thymus implantation in congenital athymia and to optimize implantation procedures to maximize T cell education and expansion of naïve T cells. Treating implanted mice with recombinant interleukin (IL-7) promoted homeostatic expansion that improved T cell development, expanded the T cell receptor repertoire, and normalized the naïve T cell compartment.

overall_design: After culturing, slices of thymus were transplanted intrarenally, under the kidney capsule, into 4-week old male Foxn1nu mice. After 12 weeks, cells were collected and pooled from spleens, lymph nodes, and blood. After RBC lysis using ACK Lysing Buffer, T cells were isolated using a MojoSort Mouse T Cell Isolation Kit. RNA samples were collected from T cells using NucleoSpin RNA purification kit. Before implant, osmotic pumps were primed in 0.9% NaCl saline at 37°C for 2 days. On the day of thymus implantation, the pump was filled with 10 mg IL-7 in 180 μL PBS (or vehicle) and implanted in mouse subcutaneously after thymus implantation. Naive treatment group received no surgical procedures or treatment.

first: Hyunjung

last: Min

first: Laura

last: Valente

first: Li

last: Xu

first: Lauren

middle: R

last: Begg

first: Joanne

last: Kurtzberg

first: Anthony

middle: J

last: Filiano


title: Transcriptome sequencing of gingival tissues from impacted third molars patients reveals the alterations of gene expression

city: Zunyi

first: chen

last: bin

address: Xuefu West street num 6

institute: Zunyi Medical University

summary: This first transcriptome analysis of gingival tissues from patients with surgical removal of impacted third molars provides new insights into postoperative genetic changes. The results may establish a basis for future research on minimizing the incidence of complications after flap-treated third molars.

overall_design: The gingival tissues of three patients with flap surgical removal of impacted third molars and two healthy volunteers were collected for gene expression testing by RNA sequencing (RNA-seq) technology and quantitative real-time PCR (qRT-PCR) validation was performed.

first: Bin

last: Chen

first: Guohui

last: Bai

first: Yuan

last: Tian

first: Miao

last: Wang


title: Contrasting effects of whole-body and hepatocyte-specific deletion of the RNA polymerase III repressor Maf1 in the mouse [RNA-Seq]

status: Public on Nov 28 2023

city: Lausanne

first: Gilles

last: Willemin

state: VD

address: Génopode

department: Center For Integrative Genomics

country: Switzerland

institute: Université de Lausanne

summary: MAF1 is a nutrient-sensitive, TORC1-regulated repressor of RNA polymerase III (Pol III). MAF1 downregulation leads to increased lipogenesis in Drosophila melanogaster, Caenorhabditis elegans, and mice. However, Maf1−/− mice are lean as increased lipogenesis is counterbalanced by futile pre-tRNA synthesis and degradation, resulting in increased energy expenditure. We compared Chow-fed Maf1−/− mice with Chow- or High Fat (HF)-fed Maf1hep−/− mice that lack MAF1 specifically in hepatocytes. Unlike Maf1−/− mice, Maf1hep−/− mice become heavier and fattier than control mice with old age and much earlier under a HF diet. Liver ChIPseq, RNAseq and proteomics analyses indicate increased Pol III occupancy at Pol III genes, very few differences in mRNA accumulation, and protein accumulation changes consistent with increased lipogenesis. Futile pretRNA synthesis and degradation in the liver, as likely occurs in Maf1hep−/− mice, thus seems insufficient to counteract increased lipogenesis. Indeed, RNAseq and metabolite profiling indicate that liver phenotypes of Maf1−/− mice are strongly influenced by systemic inter-organ communication. Among common changes in the three phenotypically distinct cohorts, Angiogenin downregulation is likely linked to increased Pol III occupancy of tRNA genes in the Angiogenin promoter.

overall_design: Three mouse cohorts, with KO and CTRL samples : Maf1-/- on CHOW diet (5 KO, 7 CTRL), Maf1Hep-/- on CHOW diet (4 KO, 4 CTRL) and Maf1Hep-/- on High Fat diet (4 KO 5 CTRL).

first: François

last: Mange

first: Viviane

last: Praz

first: Séverine

last: Lorrain

last: Cousin

first: Catherine

last: Roger

first: Ian

middle: M

last: Willis

first: Nouria

last: Hernandez


title: Methionine availability influences essential H3K36me3 dynamics during cell differentiation [ATAC-seq]

first: Yudong

last: Sun

overall_design: ATAC-Seq in C2C12 cells at D0, D1, and D5 under control or methionine restriction conditions for WT and Setd2 KO lines

first: Jason

last: Locasale


title: Vascular smooth muscle cell senescence instigates thoracic aortic aneurysm

first: Li

address: 111 T.W. Alexander Dr

institute: NIH

summary: In this study, we identified various cell clusters in human normal/sporadic TAA ascending aorta samples by single-cell RNA sequencing (scRNA-seq), and discovered the senescent vascular smooth muscle cells (VSMCs) significantly increased in TAA samples. Then we explored the molecular basis of TAA progression, and recognized the key regulators and pathways involved in the TAA progression regulation.

overall_design: Single cell RNA-Seq of human normal/sporadic thoracic aortic aneurysm (TAA) ascending aorta samples

first: Fang

last: Yao

first: Yinan


title: Higher colonic proliferation and tumor prevalence amongst azoxymethane treated A/J mice receiving fecal microbiota transplants from old mice compared to recipients of young mice [16S rRNA-Seq]

city: Boston

first: Samuel

last: Beck

address: 609 Albany st.

department: Dermatology

institute: Boston University School of Medicine

summary: Gut microbial dysbiosis can play a causal role of in colorectal cancer. Gut microbiota chnages with age and becomes moer pro-inflammatory. We sought to determine whether microbiota from Old donors promotes more tumor formation in recipients than meterial from young donors.

overall_design: We conducted fecal material transplants (FMT) from young (~6 wk) and old (~72 wk) donor mice into young (8 wk) recipient mice that were pre-treated with antibiotics. After initiating tumorigenesis with azoxymethane, recipients were maintained for 19 weeks during which time they received monthly FMT boosters.

first: Nicholas

middle: A

last: Crossland

first: Wei

middle: Y

last: Tan

first: Ming

last: Lo

first: Joel

middle: B

last: Mason

first: Chao

last: Zhang

first: Jimmy

last: Crott


title: Higher colonic proliferation and tumor prevalence amongst azoxymethane treated A/J mice receiving fecal microbiota transplants from old mice compared to recipients of young mice [RNA-Seq]


title: OSKM-induced epithelial cells of mouse intestine [scRNA-seq]

status: Public on Nov 26 2023

city: Pohang

first: Somi

last: Kim

address: 47, Jigok-ro

department: Life Sciences

institute: POSTECH

summary: Tissue regeneration after injury is thought to involve the dedifferentiation of somatic cells, which is often understood as evidence for natural adaptative reprogramming in vivo. In the intestinal epithelium, acute tissue damage triggers the rapid emergence of injury-responsive cells with fetal-like characteristics, a sign of dedifferentiation. However, there is no direct evidence that tissue regeneration involves a shared molecular mechanism with direct cellular reprogramming. It is also not known whether dedifferentiation shares a single (de)differentiation pathway or consists of multiple parallel routes between adult and fetal states. Here, we induced dedifferentiation of intestinal epithelial cells by forced partial reprogramming in vivo using the “Yamanaka factors” (Oct4, Sox2, Klf4 and c-Myc: OSKM). The induced dedifferentiation showed shared molecular features of intestinal regeneration, with rapid transition from homeostatic intestinal cell types to injury-responsive-like cells sharing a common gene signature of revival stem cells and atrophy-induced villus epithelial cells. When applied to intestinal organoids, induced dedifferentiation allowed the organoids to adopt fetal characteristics ex vivo, suggesting a direct effect on the intestinal epithelium. In vivo, induced dedifferentiation promoted regeneration from acute tissue injury caused by ionizing radiation (IR) via the formation of injury-responsive-like cells. Taken together, in the intestinal epithelium, in vivo reprogramming shares the same molecular pathway as damage-induced tissue regeneration and facilitates the repair process.

overall_design: We used Doxycline-inducible OSKM-overexpressing mice to induce OSKM in vivo. Dox was administrated to a mouse to induce OSKM.

first: Jumee

first: Bon-Kyoung

last: Koo

first: Jong

first: Hyuk-Jin

last: Cha


title: Life-cycle multiomics of rice shoots reveals growth stage-specific effects of drought stress and time-lag drought responses

city: Tsukuba

first: FUMIYUKI

last: SOMA

state: Ibaraki

address: 2-1-2 Kan-non-dai

department: Institute of Crop Science

country: Japan

institute: National Agriculture and Food Research Organization

summary: In order to revael the relationship between gene expression and plant phenotype under drought, we conducted transcriptome analysis under six drought and control conditions.

first: Fumiyuki

last: Soma

first: Yuka

last: Kitomi

first: Taiji

last: Kawakatsu

first: Yusaku

last: Uga


title: Partial in vivo reprogramming enables injury-free intestinal regeneration via autonomous Ptgs1 induction [RNAseq_Fetal]

summary: Tissue regeneration after injury involves the dedifferentiation of somatic cells, a natural adaptive reprogramming that leads to the emergence of injury-responsive cells with fetal-like characteristics. However, there is no direct evidence that adaptive reprogramming involves a shared molecular mechanism with direct cellular reprogramming. Here, we induced dedifferentiation of intestinal epithelial cells using OSKM (Oct4, Sox2, Klf4, and c-Myc) in vivo. The OSKM-induced forced dedifferentiation showed similar molecular features of intestinal regeneration, including a transition from homeostatic cell types to injury-responsive-like cell types. These injury-responsive-like cells, sharing gene signatures of revival stem cells and atrophy-induced villus epithelial cells, actively assisted tissue regeneration following damage. In contrast to normal intestinal regeneration involving Ptgs2 induction, the OSKM promotes autonomous production of prostaglandin E2 via epithelial Ptgs1 expression. These results indicate prostaglandin synthesis is a common mechanism for intestinal regeneration, but involves a different enzyme when partial reprogramming is applied to the intestinal epithelium.

overall_design: We used intestinal organoids from adult and fetal mice.

first: Seung-Yeon

last: Lee

first: Hwa-Ryeon


title: Fibroblasts-derived from Pluripotent Cells Harboring a Single Allele Knockout in Two Pluripotency Genes Exhibit DNA Methylation Abnormalities and Reprogramming Defects [RNA-seq]

status: Public on Nov 27 2023

city: Jerusalem

first: Yosef

last: Buganim

address: Hadassah Medical School

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University

summary: Transcription profile analysis at day 6 of reprogramming to iPSCs revealed dissimilarities between NGFP2 N+/- and the double heterozygous mutant lines : NGFP2 N+/-;S+/-, NGFP2 N+/-;E+/-, NGFP2 N+/-;U+/-

overall_design: Secondary MEFs with OSKM factors from the different iPSCs backgrounds mentionned above were exposed to dox for 6 days and submitted to RNA-seq and compared to control ESC and control MEFs.

first: Rachel

last: Lasry

first: Noam

last: Maoz

first: Ahmed

last: Radwan


title: Targeted ASO-mediated Atp1a2 knockdown in astrocytes reduces SOD1 aggregation and accelerates disease onset in mutant SOD1 mice

city: St. Louis

first: Abhirami Kannan

last: Iyer

state: MISSOURI

address: 425 South euclid ave, BJC Institute of Health, Room 9202

department: Psychiatry

institute: Washington University in St. Louis

summary: Astrocyte-specific ion pump α2-Na+/K+-ATPase plays a critical role in the pathogenesis of amyotrophic lateral sclerosis (ALS). Here, we test the effect of Atp1a2 mRNA-specific antisense oligonucleotides (ASOs) to induce α2-Na+/K+-ATPase knockdown in the widely used ALS animal model, SOD1*G93A mice. Two ASOs led to efficient Atp1a2 knockdown and significantly reduced SOD1 aggregation in vivo. Although Atp1a2 ASO-treated mice displayed no off-target or systemic toxicity, the ASO-treated mice exhibited an accelerated disease onset and shorter lifespan than control mice. Transcriptomics studies reveal downregulation of genes involved in oxidative response, metabolic pathways, trans-synaptic signaling, and upregulation of genes involved in glutamate receptor signaling and complement activation, suggesting a potential role for these molecular pathways in de-coupling SOD1 aggregation from survival in Atp1a2 ASO-treated mice. Together, these results reveal a role for α2-Na+/K+-ATPase in SOD1 aggregation and highlight the critical effect of temporal modulation of genetically validated therapeutic targets in neurodegenerative diseases.

overall_design: RNA-sequencing was performed on total RNA extracted from SOD1*G93A primary mouse astrocytes nucleofected with either control ASO or Atp1a2 ASO and harvested 96 hours later. Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovoSeq. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2. All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions. KEGG and WikiPathways (species: Mus musculus, year queried: 2019) were used to derive functional annotations of the differentially expressed genes into pathways.

first: Abhirami

first: Kathleen

last: Schoch

first: Anna

last: Oldenborg

first: Hao

last: Chen

first: Sarah

last: Smith

first: Timothy

last: Miller

first: Celeste

last: Karch

first: Azad

last: Bonni

first: Anthony

last: Verbeck

first: Grant

last: Galasso


title: Tendon injury

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University


title: Contrasting effects of whole-body and hepatocyte-specific deletion of the RNA polymerase III repressor Maf1 in the mouse

first: Gilles

last: Willemin


title: Spatiotemporal signaling underlies progressive vascular rarefaction in myocardial infarction

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

institute: University of British Columbia

summary: Therapeutic angiogenesis represents a promising avenue to revascularize the ischemic heart. Its limited success is partly due to our poor understanding of the cardiac stroma, specifically mural cells, and their response to ischemic injury. Here, we combine single-cell and positional transcriptomics to assess the behaviour of mural cells within the healing heart. In response to myocardial infarction, mural cells adopt an altered state closely associated with the infarct and retain a distinct lineage from fibroblasts. This response is concurrent with vascular rarefaction and reduced coverage by mural cells. Positional transcriptomics reveal that the infarcted heart is governed by regional-dependent and temporally regulated programs. While the remote zone acts as an important source of pro-angiogenic signals, the infarct zone is accentuated by chronic activation of anti-angiogenic, pro-fibrotic, and inflammatory cues. Together, our work unveils the spatiotemporal programs underlying cardiac repair and establishes an association between vascular deterioration and mural cell dysfunction.

overall_design: Characterization of cardiac mural cells and their role in heart repair post myocardial infarction (MI)

first: Lin

last: Tung

first: Elena

last: Groppa

first: Hesham

last: Soliman

first: Tara

last: Stach


title: Contrasting effects of whole-body and hepatocyte-specific deletion of the RNA polymerase III repressor Maf1 in the mouse [ChIP-Seq]

overall_design: Three mouse cohorts, with KO and CTRL samples : Maf1-/- on CHOW diet (3 KO, 2 CTRL), Maf1Hep-/- on CHOW diet (3 KO, 2 CTRL) and Maf1Hep-/- on High Fat diet (2 KO 3 CTRL). Each ChIP seq sample has its corresponding Input.

first: François

last: Mange

first: Viviane

last: Praz

first: Séverine

last: Lorrain

first: Pascal

last: Cousin

first: Catherine

last: Roger

first: Ian

last: Willis

first: Nouria

last: Hernandez


title: Transcriptional landscape of the developing human adipose tissue

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: University of Ulm

summary:
We collected adipose tissue specimens during elective surgery (inguinal hernia, cryptorchism). Samples were proceesed for extraction of total RNA, using phenol:chlorophorm extraction. Next generation RNA sequencing were performed.

Published article: https://www.mdpi.com/1422-0067/24/23/16706

overall_design: Samples are labeled as patient groups (UCP1 high, UCP1 low). The UCP1 high samples strongly expressed uncoupling protein 1 (UCP1) and were lacking the interferon regulatory factor 7 (IRF7) protein, while the UCP1 low samples were lacking UCP1 and had high IRF7 levels. We have shown previously that high IRF7 level is associated with obesity. Our aim was to identigy differentially expressed genes (DEGs), to understand molecular mechanisms and cellular processes that are affected by IRF7. Project number: F22FTSEUHT0137_HOMrgmzR


title: CRISPR gene editing, cardiac disease modelling and transcriptomics interpretation of a novel GATA4 patient genetic variant

status: Public on Nov 23 2023

city: Nedlands

first: Kathryn

middle: Olivia

last: Farley

address: 15 Hospital Avenue

department: Precision Health

country: Australia

institute: Telethon Kids Institute

summary: Over 400 million people worldwide live with a rare disease. Whole exome and whole genome sequencing often identifies potential disease causative genetic variants that are novel, which must be classified as variants of uncertain significance (VUS). Functional laboratory assays must be performed to prove disease causation, creating major delays in patient diagnostics. Here we investigate a GATA4 (p.Arg283Cys) VUS in a with congenital heart disease.  The variant was CRISPR gene edited into inducible pluripotent stem cells, followed by cardio-myocyte differentiation. Genetic variant and healthy cells were similar at the level of cardiomy-ocyte cell marker expression of troponin T (cTNNT), and GATA4 protein expression. Strik-ingly, transcriptomics profiling identified differences in differentiation consistent with the pa-tient’s disease characteristics, and elucidated changes in calcium signaling and adrenergic sig-naling in cardiomyocytes. Altered action potential changes in GATA4,p.Arg283Cys (GA-TA4_HDR) cardiomyocytes were indicative of cardiac abnormalities.   Our work provides strong molecular evidence for classifying the GATA4 p.Arg283Cys variant as pathogenic. Furthermore, we demonstrate the combined utility of iPSCs, CRISPR gene edit-ing and differentiation into cardiomyocytes in assessing variants associated with cardiac pheno-types.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for GATA4_WT and SNV KOLF-2 iPSCs and their derived cardiomyocytes.

GATA4 CRISPR gene editing in KOLF-2C.  Genomic DNA representation of GATA4 in clones with introduced GATA4 c.847C>T mutation.

first: Vanessa

last: Fear

last: Forbes

first: Nicole

middle: C

last: Shaw

middle: O

first: Jessica

last: Mantegna

first: Jasmin

last: Htun

first: Genevieve

last: Syn

first: Livia

last: Hool

first: Helena

last: Viola

first: Henrietta

last: Szappanos

first: Michelle

last: Ward

first: Gareth

last: Baynam

first: Timo

last: Lassmann