title: The homeobox transcription factor DUXBL controls exit from totipotency

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

summary: In mice, exit from the totipotent 2-cell (2C) embryo stage requires silencing of the 2C-associated transcriptional program. However, the molecular mechanisms involved in this process remain poorly understood. Here, we demonstrate that the 2C-specific transcription factor DUX mediates an essential negative feedback loop by inducing the expression of DUXBL to promote this silencing.We show that DUXBL gains accessibility to DUX-bound regions specifically upon DUX expression.Furthermore, we determine that DUXBL interacts with TRIM24 and TRIM33, members of the tripartite motif superfamily involved in gene silencing and co-localizes with them in nuclear foci upon DUX expression. Importantly, DUXBL overexpression impairs 2C-associated transcription, whereas Duxbl inactivation in ESC increases DUX-dependent induction of the 2C-transcriptional program. Consequently, DUXBL deficiency in embryos results in sustained expression of 2C-associated transcripts, leading to early developmental arrest.Our study identifies DUXBL as an essential regulator of totipotency exit enabling the first divergence of cell fates.

overall_design: Three to twelve week-old C57BL6/J female mice were superovulated by intraperitoneal injection of pregnant mare serum gonadotropin (7.5 IU). 48 h later, human chorionic gonadotropin (hCG, 7.5 IU) was delivered i.p. followed by mating with C57BL6/J males. Next morning, zygotes were isolated from ampulla of the oviducts and brought into culture in EmbryoMax® KSOM Mouse Embryo Media  (Millipore-Sigma, MR-106-D) at 37 °C , 5 % CO2, 5% O2. Mouse embryos were injected at the 1-cell stage (24 h post hCG) with 200 ng/ul of either Duxbl-V5-2A-NLS-mCherry- or NLS-mCherry-encoding mRNAs. Embryos were then cultured either until the late 1-cell stage (28-30 h post hCG), until the early 2-cell stage (32 h post hCG) or until the late 2-cell stage (48 h post hCG) and harvested for RNA-seq.

first: Paula

last: Stein

first: Lenka

last: Radonova

first: Virginia

last: Savy

first: Felipe

last: Lüttmann


title: Effect of stimulating PIEZO1 in gastric cancer cells

status: Public on Dec 08 2023

city: Hong Kong

first: Bonan

last: Chen

address: The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, The People's Republic of China

country: Hong Kong

institute: the Chinese University of Hong Kong

type: Expression profiling by high throughput sequencing

summary: In gastric cancer (GC), PIEZO1 was suggested to promote cell migration by interacting with Trefoil factor family 1 (TFF1) and serve as a therapeutic target against invasion and metastasis. In addition, PIEZO1 demonstrates abundant expression in most GC cell lines and primary samples and highly-expressed PIEZO1 is associated with poor disease-specific survival. As Yoda1 is known to be an agonist of PIEZO1, we try to explore the PIEZO1 function in GC by Yoda1 treatment.

overall_design: The potent target genes of PIEZO1 were identified by deep sequencing, using Illumina NovaSeq 6000.

first: Wei

last: Kang


title: Role of the Muscle-Brain-Gut axis in the regulation of skeletal muscle mass

status: Public on Dec 11 2023

city: Chuo-ku, Kobe City, Hyogo

first: Yu

last: Hirata

address: 7-5-1 Kusunoki-cho

department: Department of Internal Medicine Division of Diabetes and Endocrinology

country: Japan

institute: Kobe University Graduate School of Medicine

summary: We propose that the Muscle-Brain-Gut axis regulates skeletal muscle mass through the defined mechanism.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for colon tissue of immobilized mice.

first: Wataru

last: Ogawa


title: The function and mechanism of aldh9a1b in diabetes

city: Mannheim

first: Xin

last: Qian

state: Baden-Wuerttemberg

address: Ludolf-Krehl-Str. 13-17

department: Vascular Biology&Tumor Angiogenesis

country: Germany

institute: Medical Faculty Mannheim, Heidelberg University

summary: Reactive aldehydes such as 4-HNE, MDA and acrolein are implicated in the pathological development of diabetes as their widespread and universally exposed characteristics. Trans, trans-2,4-decadienal (tt-DDE) come from lipid peroxidation of omega-6 and is most abundant aldehyde in cooking oil fumes, while, its role in diabetes remained unknown. Aldh9a1 is a cytosolic enzyme that catalyze the NAD+-dependent oxidation of a variety of aldehydes and has its homology aldh9a1b in zebrafish. To investigate the function of endogenous and exogenous tt-DDE, aldh9a1b knockout zebrafish are established using CRISPR/Cas9 technology. TT-DDE was confirmed to act as substrate for aldh9a1b and a series of experiments are performed on a histological, metabolomic and transcriptomic level in aldh9a1b-/- zebrafish. Both aldh9a1b-/- larvae and adult fish displayed abnormal retinal vasculature and impaired glucose homeostasis, which are caused by tt-DDE induced downregulated insulin signaling pathway. Furthermore, the abnormal hyaloid vasculature in the fish can be reversed by insulin receptor sensitizer and metformin exhibited strongest effects among them. Altogether, these results identified tt-DDE as the preferred substrate for aldh9a1b, which subsequently causes microvascular damage and impaired glucose metabolism by insulin resistance.

overall_design: A CRISPR based knockout ofaldh9a1b was created in zebrafish. The development of the fish was analyzed, as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina, kidney, liver and skeletal muscle were conducted. RNA sequencing was performed on the larvae of aldh9a1b+/+, aldh9a1b-/- and tt-DDE treating aldh9a1b+/+  by BGI .

first: Ye

last: Meng

first: Jens

last: Kroll


title: Transcriptional regulation in the embryonic endocardium after NOTCH pathway manipulation

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We have manipulated the NOTCH signaling pathway in mouse embryonic endocardial cells by the co-culture with OP9 stromal cells expressing Jag1 and Dll4, the culture over recombinant JAG1 and DLL4, and the use of the γ-secretase inhibitor RO4929097. We have performed RNA-seq and ATAC-seq to define the transcriptional profile and the chromatin accessibility landscape specific for each condition.

overall_design: Refer to individual Series


title: Effect of TIM-3 knockout in the tumoroginesis in the NP53 DMG cell line

status: Public on Dec 07 2023

city: Pamplona

first: Marta

middle: Maria

last: Alonso Roldán

state: Navarra

address: CIMA building , Pio XII 55

department: Dpt of Pediatrics

institute: University Hospital of Navarra

summary: To investigate the function of TIM-3 expression in the regulation of NP53 proliferation and tumorigenesis differentiation, we established DMG cell lines in which each target gene has been knocked out by CRISPR/Cas9.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NP53 cells (Gcontrol) and its TIM-3KO derivatives (G2C9 and G1C7).

middle: M

last: Alonso

first: Iker

last: Ausejo-Mauleon


title: Effect of depletion of BBX14 or GLK on gene expression in seedlings pre-grown for 3 days in the dark and then shifted to 1 day in the light

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

type: Non-coding RNA profiling by high throughput sequencing

summary:
Investigation of the contribution of BBX14 and GLK1/2 on mRNA levels in light-shifted seedlings
We performed gene expression profiling analysis using data obtained from RNA-seq of seedlings grown three days in darkness and then shifted for 1 day to light

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bbx14/Col-0


title: Salivary TIMP1 and predicted mir-141, possible transcripts biomarkers for estrus in the buffalo (Bubalus bubalis)

city: Karnal

first: Suneel

middle: Kumar

last: Onteru

state: HARYANA

address: Lab No 154, Animal Biochemistry Division, NDRI, Karnal

department: Animal Biochemistry

country: India

institute: NDRI

summary: RNA Seq data showed 49 differentially altered mRNAs in estrus and diestrus stages of buffalo cell free saliva, that includes 10 mRNAs commonly present in both estrus and diestrus stages, whereas 12 and 27 mRNAs were found to be exclusively present either at the estrus or the diestrus stage respectively. In addition, four mature miRNAs were predicted to be differentially altered in the estrus as compared to the diestrus phase of buffaloes.

overall_design: Differentially expressed transcripts were identified in estrus as compared to diestrus phase in buffaloes

first: Gangu

middle: N

last: Surla

first: Lal

middle: K

last: Kumar

first: Rajeev

last: Chandel

first: Veerappa

middle: G

last: Vedamurthy

first: Dheer

last: Singh


title: Pinch loss in early mesenchymal progenitors alters bone marrow environment

city: Shen Zhen

first: Guozhi

last: Xiao

state: Guang Dong

address: No. 1088, Xueyuan Road

department: Biology

country: China

institute: Southern University of Science and Technology

summary: To investigate the alteration of bone marrow environment caused by Pinch loss, we performed single-cell RNA-sequencing on bone marrow cells, including hematopoietic cells and non-hematopietic stromal cells. As results indicated, we found both cell type proportion and transcriptomic signatures were dramatically altered by Pinch loss. We identified genes related to ossification, extracellular matrix organization, skeletal system development, and vasculature structure development were significantly differentially expressed between control group and dKO group in many mesenchymal stromal cells. Our results revealed Pinch loss disrupted homeostasis of bone marrow niche, monocytes in bone marrow were actively involved in inflammatory response, and functions of mesenchymal stromal cells was severely disrupted.

overall_design: We collected six samples, and two of them were hematopoietic cells from healthy control, two of them were hematopoietic cells from Pinch loss mice, one of them was non-hematopoietic cells from healthy control, one of them was non-hematopoietic cells from Pinch loss mice. In each sample, cells from three mice were pooled together.

first: Huiling

last: Cao

first: Bo

last: Zhou


title: Dynamic metabolism of endothelial triglycerides protects against atherosclerosis

city: Orange

first: Nabil

middle: E.

last: Boutagy

state: CT

address: 419 Butternut Court

department: Pharmacology

country: USA

institute: Yale

summary: Blood vessels are continually exposed to circulating lipids and elevations of ApoB containing lipoproteins cause atherosclerosis. Lipoprotein metabolism is highly regulated by lipolysis, largely at the level of the capillary endothelium lining metabolically active tissues. How large blood vessels, the site of atherosclerotic vascular disease, regulate the flux of fatty acids (FA) into triglyceride (TG) rich lipid droplets (LD) is not known. Here, we show that deletion of the enzyme, adipose triglyceride lipase (ATGL) in the endothelium, leads to neutral lipid accumulation in vessels and impairs endothelial dependent vascular tone and nitric oxide synthesis to promote endothelial dysfunction. Mechanistically, the loss of ATGL leads to endoplasmic reticulum stress-induced inflammation, thereby promoting EC dysfunction. Consistent with this mechanism, deletion of endothelial ATGL markedly increases lesion size in a model of atherosclerosis. Together, these data demonstrate that the dynamics of FA flux through LD impacts EC homeostasis and consequently large vessel function during normal physiology and in a chronic disease state

overall_design: Comparative gene expression of mouse lung endothelial cells isolated from control (ATGL f/f) and endothelial specific  ATGL knock out mice (ATGL ECKO) under basal condition. Cells are immortalized.

middle: E

first: Ana

last: Gamez-Mendez

first: Joseph

middle: W

last: Fowler

first: Hanming

last: Zhang

first: Bal

last: Chaube

first: Enric

last: Espluges

first: Sungwoon

last: Lee

first: Daiki

last: Horikami

first: Jiasheng

first: Kathryn

last: Citrin

first: Abhishek

first: Brian

last: Coon

first: Yajaira

last: Suarez

first: Carlos

last: Fernandez-Hernando

first: William

middle: C

last: Sessa


title: Sorafenib induces cardiotoxicity through RBM20 mediated alternative splicing of sarcomeric and mitochondrial genes

city: Beijing

first: Songming

last: Liu

address: Xueyuan Road No 38,Haidian District

institute: Peking University

summary: Tyrosine kinase inhibitors (TKIs), as a class of small-molecule drugs that exert anti-tumor effects by inhibiting tyrosine kinase-catalyzed phosphorylation, have been used in the treatment of various cancers. Sorafenib, as a multi-targeted TKI drug, is the first-line treatment for advanced renal cell carcinoma and unresectable hepatocellular carcinoma. However, sorafenib has repeatedly been reported to cause cardiac events in patients without a history of heart diseases during clinical use, indicating that it has cardiotoxicity. Alternative splicing of cardiac contraction-related genes happens during heart development and cardiac diseases, and is critical for heart function. However, whether alternative splicing plays a role in drug-induced cardiotoxicity remains unexplored. RBM20 is an important cardiac-specific splicing factor, mutations of which cause dilated cardiomyopathy or other cardiac dysfunctions. Rbm20 also mediates alternative splicing of genes essential for heart contraction, which is often negatively affected in drug-induced cardiotoxicity. Existing studies do not fully explain the mechanism of sorafenib cardiotoxicity, and none of the relationship between cardiotoxicity of sorafenib and alternative splicing mediated by tissue-specific splicing factors, such as Rbm20, have been reported.  In order to explore whether cardiac-specific alternative splicing plays a role in sorafenib-induced cardiotoxicity, we establish both cell and animal models of cardiotoxicity, and obtain the following results: (1) By constructing a rat animal model administered with sorafenib, we find that sorafenib causes abnormal cardiac function in rats, and the genes that undergo alternative splicing in rat hearts are related to cytoskeleton of actin; (2) Alternatively spliced genes induced by sorafenib in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are enriched in sarcomere, actin filament, calcium transient regulation, mitochondria, all of which are critical for cardiac contraction. These genes are associated with dilated cardiomyopathy, hypertrophic cardiomyopathy and other cardiomyopathy; (3) Sorafenib induces a decrease in the expression of cardiac-specific splicing factor RBM20; (3) Many genes whose splicing are altered by sorafenib overlap with Rbm20 targets, indicating that sorafenib may affect alternative splicing through Rbm20; (4) Sorafenib induces pathogenic alternative splicing of FHOD3, which is a RBM20 target gene and participates in myocardial sarcomere formation. Sorafenib also affects alternative splicing of SLC25A3, which encodes a phosphate transporter on the mitochondrial inner membrane and regulates ATP synthesis; (5) Enhancing the expression of RBM20 rescues the cardiotoxicity of sorafenib by reducing apoptosis and increasing ATP levels, which is mediated by reversing the alternative splicing of FHOD3 and SLC25A3 induced by sorafenib.  This paper uncovers that sorafenib reduces the expression of RBM20 to cause pathogenic alternative splicing of genes related to myocardial sarcomere and energy mechanism, resulting in abnormal myocardial function. Increasing the expression of RBM20 reverses the alternative splicing of FHOD3 and SLC25A3 associated with cardiac sarcomeres and mitochondria respectively, rescuing the cardiotoxicity of sorafenib.

overall_design: 180-200 g SD male rats were gavaged with 50 mg/kg sorafenib or the same volume of deionized water once a day for 14 or 28 days. The heart tissues of the rats in the sorafenib group and the control group were collected at 14 or 28 days. After total RNA isolation from rat hearts using Trizol, 1 μg total RNA was used to remove rRNA using Illumina Ribo-Zero plus rRNA Depletion Kit. After purification, mRNAs and lncRNAs were retained for library construction and sequencing. The library concentration was 3 ng/μL, the sequencing strategy was paired-end 150 bp, and sequencing was performed on the Illumina Novaseq 6000 platform.

first: Shanshan

last: Yue

first: Jingyan

last: Han

first: Huan

last: Wang


title: Effects Botryodiplodia theobromeae inoculation on Dalbergia sissoo

city: Faisalabad

first: Iqrar

middle: Ahmad

last: Rana

state: Punjab

address: Jail road

department: Center for Advanced Studies in Agriculture and Food Security

country: Pakistan

institute: University of agriculture

summary: Here we report the NGS RNA-seq data of the D. sissoo treated with the  Botryodiplodia theobromeae.

overall_design: The experiment was conducted on the one year old plants growing in the tempreture controlled green house. The infection culture was applied on the base of the plant by making a small injury at the base. Then after 20 days the leafs of the plants were isolated.

middle: A

first: Ummul

middle: B

last: Zafar

first: Rana

last: Atif

first: Faisal

middle: S

last: Awan

first: Zeeshan

last: Niaz

first: Shazad

last: Khalid

first: Nighat

last: Chughtai


title: DHODH: A promising target in the treatment of T-Acute Lymphoblastic Leukemia

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

summary:
Children with relapsed or refractory T-cell acute lymphoblastic leukemia (T-ALL) have a poor prognosis with few therapeutic options. Multiple lines of evidence point towards the enzyme dihydroorotate dehydrogenase (DHODH) as a metabolic vulnerability in dysregulated and malignant T‑cells. DHODH catalyzes the fourth step of de novo pyrimidine nucleotide synthesis (e.g., uridine, cytidine). Therefore, inhibiting DHODH via small molecule inhibitors (DHODHi) rapidly leads to the depletion of intracellular pyrimidine pools and forces cells to rely on extracellular salvage. In the absence of sufficient salvage, this intracellular nucleotide starvation results in the inhibition of DNA and RNA synthesis, cell cycle arrest, and ultimately death.
T‑lymphoblasts appear to be specifically and exquisitely sensitive to nucleotide starvation following DHODHi. We have confirmed this sensitivity in vitro as well as in vivo in three murine models of T‑ALL. Additionally, we have identified that certain subsets of T-ALL seem to have an increased reliance on oxidative phosphorylation when treated with DHODHi. Through a series of metabolic assays, we show that leukemia cells, in the setting of nucleotide starvation, have changes in their mitochondrial membrane potential and may be more highly dependent on alternative fuel sources. We hope these changes point to a metabolic vulnerability that may distinguish them from normal T-cells and other normal hematopoietic cells and offer an exploitable therapeutic opportunity. The availability of clinical-grade DHODH inhibitors currently in human clinical trials speaks to the potential for rapidly advancing this work into the clinic.

overall_design: Transcriptional profiling of Jurkat cells harvested at 8 and 24 hours following treatment with 1 uM Brequinar (BRQ) vs. DMSO in triplicate.

first: Amy

last: Sexauer


title: Duxbl-mediated suppression of ZGA drives totipotency to pluripotency transition in mice III

first: Carsten

last: Kuenne

summary: In mammalian embryos, Dux transcription factors (TF) drive a cleavage stage-specific transcriptional burst associated with zygotic genome activation (ZGA) during which hundreds of genes and endogenous retroviral (ERV) elements are transiently expressed. In mice, ZGA begins in late 1-cell (1C) embryos and is shut down within hours at the late 2-cell (2C) to 4-cell (4C) stage. While this transition is accompanied by the loss of totipotency, it is not clear whether shutdown of Dux-induced ZGA is required for this process and how ZGA is terminated. Here, we reveal an essential negative feedback axis by which the Dux family member Duxbl terminates Dux-induced ZGA from the mid 2C stage onward by direct suppression of genomic Dux target loci. Consequently, Duxbl inactivation results in sustained expression of Dux-induced ZGA leading to 4C arrest. Our study reveals the Dux/Duxbl axis that determines the timing of totipotency exit enabling the very first divergence of cell fates.

overall_design: Three week-old C57BL6/J female mice were superovulated by intraperitoneal injection of pregnant mare serum gonadotropin (10 IU). 48 h later, human chorion gonadotropin (HCG) (10 IU) was delivered i.p. followed by mating with C57BL6/J males. Next morning, zygotes were surigically isolated from ampulla of the oviducts and brought into culture in EmbryoMax® Advanced KSOM Embryo Medium (Sigma-Aldrich, MR-101-D) at 37 °C and 5 % CO2. WT embryos were collected for RNA-seq at early 2-cell stage (32 h post HCG) and late 2-cell stage (48 h post HCG). Embryos obtained from crossing heterozygous Duxbl-sgKO mice were harvested for RNA-seq at late 2-cell stage (48 h post HCG).

first: Felipe

last: Luettmann

first: Stefan

last: Günther

first: Johnny

last: Kim


title: Duxbl-mediated suppression of ZGA drives totipotency to pluripotency transition in mice

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


title: SRSF2 plays an unexpected role as reader of m5C on mRNA, linking epitranscriptomics to cancer

city: anderlecht

first: Haili

last: Ma

address: route de lennik 808

country: Belgium

institute: ULB

type: Methylation profiling by high throughput sequencing

summary: A common mRNA modification is 5-methylcytosine (m5C), whose role in gene-transcript processing and cancer remains unclear. Here we identify Serine/arginine-Rich Splicing Factor 2 (SRSF2) as a reader of m5C, and impaired SRSF2 m5C binding as a potential contributor to leukemogenesis. Structurally, we identify residues involved in m5C recognition and in the impact of the prevalent leukemia-associated mutation SRSF2P95H. We show that SRSF2 binding and m5C colocalize within transcripts. Furthermore, knocking down the m5C writer NSUN2 decreases mRNA m5C, reduces SRSF2 binding, and alters RNA splicing. We also show that the SRSF2P95H mutation impairs the ability of the protein to read m5C-marked mRNA, notably reducing its binding to key leukemia-related transcripts in leukemic cells. In leukemia patients, low NSUN2 expression leads to mRNA m5C hypomethylation and, combined with SRSF2P95H, predicts poor outcomes. Altogether, we highlight an unrecognized mechanistic link between epitranscriptomics and a key oncogenesis driver.

overall_design:
SRSF2 PAR-CLIP Seq in HeLa and K562 cells.
Bulk RNA-seq in HeLa and K562 cells (wild-type, NSUN2 knockdown, SRSF2 knockdown, and SRSF2P95H mutant).
RNA m5C MeRIP-seq in wild-type and NSUN2 knockdown HeLa cells.
RNA bisulfite sequencing of peripheral blood mononuclear cell RNA from CMML patients.

first: Hai

middle: L

first: Martin

last: Bizet

first: Christelle

last: Soares Da Costa

first: Frédéric

last: Murisier

first: Eric

middle: J

last: de Bony

first: Meng

first: Akihide

last: Yoshimi

first: Kuan

middle: T

last: Lin

first: Kristin

last: Riching

first: Xing

first: John

middle: I

last: Beckman

first: Shailee

last: Arya

first: Nathalie

last: Droin

first: Emilie

last: Calonne

first: Bouchra

last: Hassabi

first: Qing

middle: Y

last: Zhang

first: Ang

last: Li

first: Pascale

last: Putmans

first: Lionel

last: Malbec

first: Céline

last: Hubert

first: Jie

last: Lan

first: Frédérique

last: Mies

first: Ying

last: Yang

last: Solary

first: Danette

last: Daniels

first: Yogesh

last: Gupta

first: Rachel

last: Deplus

first: Omar

last: Abdel-Wahab

first: Yun

first: François

last: Fuks


title: Expression profiling of expressed RNAs during osteogenic differentiation of human donor mesenchymal stromal cells

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

summary: Transriptome profiling to examine mRNA and lncRNA expression during osteogenic differentiation was completed in MSCs from 5 young, healthy male donors.

first: Coralee

last: Tye

first: Joseph

last: Boyd

first: Jane

last: Lian

first: Gary

last: Stein


title: Duxbl-mediated suppression of ZGA drives totipotency to pluripotency transition in mice I

first: Carsten

last: Kuenne

overall_design: Three week-old C57BL6/J female mice were superovulated by intraperitoneal injection of pregnant mare serum gonadotropin (10 IU). 48 h later, human chorion gonadotropin (HCG) (10 IU) was delivered i.p. followed by mating with C57BL6/J males. Next morning, zygotes were surigically isolated from ampulla of the oviducts and brought into culture in EmbryoMax® Advanced KSOM Embryo Medium (Sigma-Aldrich, MR-101-D) at 37 °C and 5 % CO2. Mouse embryos were injected at 1-cell stage (24 h post HCG) with either Duxbl-V5-2A-NLS-mCherry- or NLS-mCherry-encoding mRNAs. Embryos were then cultured until late 2-cell stage (48 h post HCG) and harvested for RNA-seq.

first: Felipe

last: Luettmann

first: Stefan

last: Günther

first: Johnny

last: Kim


title: Transfer learning of an in vivo-derived senescence signature identifies conserved tissue-specific senescence across species and diverse pathologies [bulk RNA-seq]

city: Baltimore

first: Christopher

last: Cherry

state: MD

address: 1800 Orleans St

institute: Johns Hopkins University

summary: Cellular senescence is a state of permanent growth arrest that plays an important role in wound healing, tissue fibrosis, and tumor suppression. Despite their pathological role and therapeutic interest, senescent cells’ (SnCs) phenotype in vivo remains unclear. Here, we developed an in vivo-derived senescence signature using a foreign body response (FBR) fibrosis model in a SnC reporter mouse. We identified stromal cells as the primary SnC in the FBR and produced a SnC transcriptomic signature. Transfer learning identified SnCs in diverse murine and human data single cell RNAseq (scRNAseq) sets. Further, we found both conserved and tissue-specific SnC and secretory phenotypes. Signaling analysis uncovered crosstalk between SnCs and myeloid cells via an IL34-CSF1R-TGFbR signaling axis, contributing to angiogenic and fibrotic responses. Overall, our study identifies a conserved transcriptional profile of SnCs and transfer learning approach that may be broadly applied to identify and understand senescence in vivo.

overall_design: Bulk RNAseq comparing sorted p16+ and p16- stromal cells from foreign body fibrosis model

first: Jennfier

middle: H

last: Elisseeff


title: Regulation of Endogenous Retroviruses and Cellular Genes by HIV-1 Rev [cytoplasmic RNA]

city: Charlottesville

first: Lou

last: Hammarskjold

state: VA

address: 1340 Jefferson Park Avenue

institute: University of Virginia

summary: A combination of bioinformatics, RNAseq, and cell-based functional assays were used to study the changes in host cell gene expression when HIV-1 Rev, Tat, Tat and Rev or HERV-K Rec was expressed. These results suggest that HIV Rev is capable of modulating gene and mRNA isoform expression, during HIV-1 infection.

overall_design: Investigation into host cell gene expression when HIV-1 Rev is expressed in T-lymphocyte cells.

first: Laurie

middle: R

last: Gray

first: David

last: Rekosh


title: RNA-sequencing of abdominal aortic aneurysm (AAA) and control abdominal aorta tissues

city: Hangzhou

first: Zhenjie

last: Liu

address: No. 88, Jiefang Road

department: Vascular Surgery

institute: Second Affiliated Hospital of Zhejiang University School of Medicine

summary: Abdominal aortic aneurysm (AAA) is a permanent segmental dilatation of the abdominal aorta, contributing to a high mortality once rupture. We performed RNA-sequencing analysis of abdominal aorta tissues from 14 participants, including seven patients with AAA and seven control individuals.

overall_design: Abdominal aortic wall samples from a total of 14 individuals were collected, including 7 patients with AAA and 7 control individuals.

first: Kaijie

last: Zhang

first: Li

last: Yin

first: Jianing

last: Yue


title: Duxbl-mediated suppression of ZGA drives totipotency to pluripotency transition in mice II

city: Bad Nauheim

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

overall_design: ES-E14TG2a cells were transfected with a control plasmid or plasmid encoding Dux or Duxbl. 16 h after plasmid transfection, gene expression was induced by addition of Doxycyline to a final concentration of 100 ng/ml for 18 h. Next, RNA was isolated for RNA-seq.


title: lncRNA and mRNA expression data of periosteum from patients with Legg-Calve-Perthes disease (LCPD) and Control patients (with femoral fracture/coxa valga)

city: Wuhan

first: Xin

last: Tang

address: 1277 jiefang avenue

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary:
Since the first recognition of LCPD as a separate disease entity in 1910, numerous theories about the etiology of the disease have been proposed. However, none have been validated conclusively, and the underlying mechanisms and determinants of LCPD still remain unclear
Many lncRNAs have been regarded as diagnostic biomarkers or therapeutic targets.However, the lncRNA expression profiles and the potential regulatory network in the development of LCPD have not been investigated. In this study, we aimed at profiling differentially expressed lncRNA and mRNA and constructing lncRNA-mRNA interacting networks in LCPD tissues to identify novel potential targets for a better understanding of the pathogenesis of LCPD

overall_design: Periosteum specimens (size: about 1 cm × 0.5 cm) were biopsied from the proximal femur of each patient during surgery and transferred to liquid nitrogen immediately after being washed with saline. Informed consent was obtained from the patient's guardians, and this study was approved by the Ethics Committee of Tongji Medical College. The lncRNA and mRNA expression profiling analysis was performed by Genminix Informatics Ltd., Co. (Shanghai, China) using GeneChip™ Human Transcriptome Assay (HTA) 2.0 (Affymetrix, USA)


title: Coordinated regulation of protein synthesis and mitochondrial respiration by the molecular chaperone TRAP1 in cancer cells

city: Napoli

first: Danilo

last: Swann Matassa

address: Via Sergio Pansini 5

department: Molecular Medicine and Medical Biotechnology

country: Italy

institute: University of Naples “Federico II”

summary: Here we show that TRAP1 directly binds translation elongation factors, both inside and outside mitochondria, and slows down translation. TRAP1 overexpression or silencing affects the synthesis of respiratory complex components. Inside mitochondria, TRAP1 binds the Complex III core component UQCRC2 and regulates Complex III activity. This decreases respiration rate upon basal condition but allows sustained oxidative phosphorylation when glucose is limiting, a condition in which TRAP1-UQCRC2 binding is lost. In humans, TRAP1 is co-expressed with the mitochondrial translational machinery, which synthesize respiratory complex proteins. Altogether, our results show an unprecedented level of complexity in the regulation of cancer cell metabolism, in which mitochondrial and cytosolic protein synthesis are co-regulated with energetic metabolism through the contribution of a common molecular chaperone

overall_design: Evaluation of differentially expressed transcripts in sh TRAP1 over sh GFP, and in hyper TRAP1 over hyper GFP expressing HeLa cells

first: Giovanni

last: Calice

first: Valentina

last: Condelli


title: Dissection of anterior mesendoderm segregation at single cell level in zebrafish

status: Public on Dec 06 2023

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

summary:
Purpose: To investigate Ripply1 binding site in zebrafish embryo
Methods:  HA-ripply-injected embryos were harvested at 6hpf. CUT&Tag were performed on the collected cells using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, TD904) following the protocol.The products were sent for paired-end sequencing at 150 bp read length on a NovaSeq 6000 system.
Results: 72,683 peaks were enriched in HA-ripply1-injected samples. And Ripply1 binding peaks were found to be enriched in the immediate upstream region of the gene body of sox17 and sox32.
Conclusions: Ripply1 may repress sox17 and sox32 expression through direct binding.

overall_design: Zebrafish embryos injected with HA-ripply1 mRNA and were harvested at 6hpf. Anti-HA antibody was then used to extract HA-Ripply1 for CUT&Tag experiment.

last: Cheng

first: Yang

last: Dong


title: Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation [RNA-seq]

city: Warsaw

first: Agata

middle: L.

last: Starosta

address: Pawińskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary: Translational control during the intricate process of sporulation in Bacillus subtilis as a response to nutrient limitation is still underexplored. Here, we employed a comprehensive approach including RNA-seq, ribosome profiling and fluorescence microscopy to dissect the translational landscape of B. subtilis during sporulation. We identified two events of translation silencing and described the spatiotemporal changes in the subcellular location of translational machinery during sporulation. Using a triple knock-out strain (3KO) of zinc-independents paralogs of three zinc-dependent ribosomal proteins L31, L33 and S14, we investigated the potential regulatory role of ribosome during sporulation. The 3KO strain exhibited delayed sporulation, reduced germination efficiency, and dysregulated translation including expression of key metabolic and sporulation-related genes as well as disruptions in translation silencing, particularly in late sporulation.

overall_design: RNA was isolated from sporulating Bacillus subtilis WT and 3KO (delta RpmEB, RpmGC, RpsNB) strains at eight timepoints. Cultures were treated with chloramphenicol, and mRNA and ribosomal footprints were purified. rRNA depletion was performed, and cDNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina. Sequencing was carried out on an Illumina NextSeq500, generating single-end 50bp reads.

first: Olga

last: Iwańska

first: Przemysław

last: Latoch

first: Natalia

last: Kopik

first: Mariia

last: Kovalenko

first: Małgorzata

last: Lichocka

first: Remigiusz

last: Serwa


title: RNA sequencing of skin punch biopsies of lesional and non-lesional skin from hidradenitis suppurativa patients

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

summary: This study investigated the underlying inflammatory pathways and cell types in hidradenitis suppurativa using transcriptomic approaches with RNA sequencing of lesional and non-lesional skin biopsies from hidradenitis suppurativa patients.

overall_design: Three-millimetres punch biopsies were collected from hidradenitis suppurativa lesional skin (edge of an inflammatory nodule) and non-lesional skin (uninvolved skin 10 cm from the active lesion) from 15 patients. The biopsies were obtained from the inguinal or axillary regions. Before the collection of the biopsies, the patients did not receive any systemic or topical treatment for four and two weeks, respectively.


title: Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation [Ribo-seq]


title: RNA-seq reveals differentially expressed lncRNAs and circRNAs and their associated functional network in HTR-8/Svneo cells under hypoxic conditions

city: Ningbo

first: Jiaqing

last: Zhou

state: Zhejiang

address: Haishu

institute: Ningbo First Hospital

summary: Placental hypoxia is hazardous to maternal health as well as fetal growth and development. Preeclampsia and intrauterine growth restriction are common pregnancy problems, and one of the causes is placental hypoxia.Placental hypoxia is linked to a number of pregnancy illnessesv. To investigate their potential function in anoxic circumstances, we mimicked the anoxic environment of HTR-8/Svneo cells and performed lncRNA and circRNA studies on anoxic HTR-8/Svneo cells using high-throughput RNA sequencing. The miRNA target genes were predicted by integrating the aberrant expression of miRNAs in the placenta of preeclampsia and intrauterine growth restriction, and a ceRNA network map was developed to conduct a complete transcriptomic and bioinformatics investigation of circRNAs and lncRNAs. The signaling pathways in which the genes were primarily engaged were predicted using GO and KEGG analyses. To propose a novel explanation for trophoblastic organism failure caused by lncRNAs and circRNAs in an anoxic environment.

first: Yuehua

last: Sheng

first: Xiaojiao

last: Zheng

first: Huiqing

last: Ding


title: Transcriptomics profiling reveals novel FGF23 targets in a Klotho-dependent and independent manner

city: Zurich

first: Ganesh

last: Pathare

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

summary: Bone-derived hormone FGF23 and its co-receptor Klotho form a trimeric complex with FGFRs in target tissues, thus governing physiological FGF23 actions. Prolonged excess FGF23 levels in conditions like chronic kidney disease (CKD) may have cardiotoxic and inflammatory effects without requiring Klotho as a coreceptor. If and how FGF23 functions independently of Klotho is a topic of significant interest. Using in-vitro transcriptomics and further bioinformatics analysis, here we show that transient-low FGF23 treatment (~physiological) in presence of Klotho exhibit canonical signaling. However lack of Klotho led to almost no change in transcriptomics after FGF23 treatment. On the other hand, prolonged-excess FGF23 treatment (~pathological) revealed many novels targets of FGF23, which are also emerging biomarkers of CKD, suggesting FGF23 may activate these molecules in CKD. Remarkably, Klotho acted as a molecular switch by regulating, together with FGF23, the above-mentioned transcripts, thus determining the fate of FGF23 signaling. Overall, our findings provide proof-of-principle evidence for the Klotho dependent and independent FGF23 actions, which may hold great potential for investigating a precise role of FGF23 in health and disease.

overall_design: HEK293 and stable Klotho transfected HEK293-Kl were treated with low (0.5nM) and high FGF23 (10nM) for 1 h and 24h respectively. RNA was isolated and and samples were sequenced commercially at Novogene


title: A dicer-related helicase opposes the age-related pathology from SKN-1 activation in ASI [ChIP-seq]

city: Los Angeles

first: Chris

last: Turner

state: CA

address: 3715 McClintock Ave

institute: University of Southern California

summary: Coordination of cellular responses to stress are essential for health across the lifespan.  The transcription factor SKN-1 is an essential homeostat that mediates survival in stress-inducing environments and cellular dysfunction, but constitutive activation of SKN-1 drives premature aging thus revealing the importance of turning off cytoprotective pathways.  Here we identify how SKN-1 activation in two ciliated ASI neurons in C. elegans results in an increase in organismal transcriptional capacity that drives pleiotropic outcomes in peripheral tissues. An increase in the expression of established SKN-1 stress response and lipid metabolism gene classes of RNA in the ASI neurons, in addition to the increased expression of several classes of non-coding RNA, define a molecular signature of animals with constitutive SKN-1 activation and diminished healthspan. We reveal neddylation as a novel regulator of the SKN-1 homeostat that mediates SKN-1 abundance within intestinal cells. Moreover, RNAi-independent activity of the dicer-related DExD/H-box helicase, drh-1, in the intestine, can oppose the effects of aberrant SKN-1 transcriptional activation and delays age-dependent decline in health. Taken together, our results uncover a cell non-autonomous circuit to maintain organism-level homeostasis in response to excessive SKN-1 transcriptional activity in the sensory nervous system.

overall_design: ChIPseq of wildtype and SKN-1gf GFP to asses the genomic binding profiles of each variant of the SKN-1 transcription factor

first: Nicole

last: Stuhr

first: Carmen

last: Ramos

first: Bennett

last: Van Camp

first: Sean

last: Curran


title: A dicer-related helicase opposes the age-related pathology from SKN-1 activation in ASI neurons [RNA-seq]

overall_design: Differential expression analysis: N2 wildtype and SKN-1gf ASI-neurons and N2 wildtype.


title: Allele-Specific gene editing approach for a dominant form of Epidermolysis Bullosa Simplex

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

institute: University of Padova

overall_design: Refer to individual Series


title: The landscape of the histone-organized chromatin of Bdellovibrionota bacteria

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary: Histone proteins have traditionally been thought to be restricted to eukaryotes and most archaea, with eukaryotic nucleosomal histones deriving from their archaeal ancestors. In contrast, bacteria lack histones as a rule. However, in recent years histone proteins have been identified in a few bacterial clades, in particular the phylum Bdellovibrionota, and these histones have been proposed to exhibit a range of divergent features compared to histones in archaea and eukaryotes. However, no experimental functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription and three-dimensional genome organization in a member of Bdellovibrionota (a Bacteriovorax strain). We find that Bacteriovorax chromatin is characterized by preferential accessibility around promoter regions, similar to what is observed in eukaryotes with compact genomes such as yeast, and also to some archaea. As in eukaryotes, chromatin accessibility positively correlates with gene expression. Mapping active transcription through single-strand DNA (ssDNA) profiling revealed that Bacteriovorax promoters exhibit very strong polymerase pausing, unlike in yeast, but similar to the state of mammalian and fly promoters. Finally, the Bacteriovorax genome exists in a three-dimensional (3D) conformation analogous to that of other bacteria without histones, organized by the parABS system and along the axis defined by replication origin and termination regions. These results provide a foundation for understanding the chromatin biology of the unique Bdellovibrionota bacteria and the deep evolution of chromatin organization across the tree of life.

overall_design: ATAC-seq, KAS-seq and Hi-C in Bacterioforax sp. ICPB 3264

middle: K

first: Benjamin

last: Doughty

first: Anshul

last: Kundaje

first: William

last: Greenleaf


title: Allele-Specific gene editing approach for a dominant form of Epidermolysis Bullosa Simplex II

summary: Epidermolysis Bullosa Simplex (EBS) is the most common form of Epidermolysis Bullosa (EB) and it is mainly inherited in an autosomal dominant manner (prevalence 1/30000 – 1/50000). Several clinical variants have been described based on the mutated gene, the site of blister formation and the anatomical distribution, but the vast majority of the patients display dominant mutations in genes encoding keratin 5 (KRT5) and keratin 14 (KRT14). The lack of functional keratin intermediate filaments causes basal keratinocytes to exhibit a dramatic cytoplasmatic softening and rupture, when subjected to minor mechanical traction, leading to the distinctive EBS patients intraepidermal blisters formation. Whilst viral mediated addition of a corrected copy of the altered gene is the ascertained approach to tackle recessively inherited EB (such as Junctional and Dystrophic EB), a potential successful combined cell and gene therapy for EBS dominant forms requires the editing of the mutated gene. In this case study, we outlined an allele specific CRISPR/Cas9 gene editing approach able to specifically detect and disrupt a de novo monoallelic c.475/495del21 mutation within exon 1 of KRT14. Taking advantage of the tailored CRISPR/Cas9 system to induce a NHEJ mediated frameshift mutations introduction, we attained a remarkable mutant allele knock-out efficiency. Following KRT14 mutant allele specific gene editing, patient derived primary keratinocytes (EBS01) restored a normal intermediate filament network and mechanical stress resilience.

overall_design: NGS amplicon sequences of the on-target and off-target in a gene editing allele-specific approach in human primary keratinocyte derived from EBS01 patients.

first: Maria

last: Latella

first: Camilla

last: Cattaneo

first: Elena

last: Enzo


title: Single-Cell RNA Sequencing Unveils Lrg1's Role in Cerebral Ischemia‒Reperfusion Injury by Modulating Various Cells

city: Nanchang

first: Yanni

last: Lv

address: Yongwai street No. 17

institute: The First Affiliated Hospital of Nanchang University

summary: Leucine-rich alpha-2 glycoprotein 1 (Lrg1) appears to be associated with the progression of cerebral ischemia-reperfusion injury, but its exact mechanism remains unknown. Here, we utilized scRNA-seq to compare the microenvironmental changes in the brains of Lrg1 knockout mice and wild-type mice following MCAO/R, in order to elucidate the role of Lrg1 after MCAO/R.

overall_design: The brains of 11 mice were collected, consisting of brains from wild-type mice following sham surgery, Lrg1 knockout mice following sham surgery, Lrg1 knockout mice following MCAO/R and wild-type mice following MCAO/R.

first: Zhaohui

last: Ruan

first: Guosheng

last: Cao

first: Yisong

last: Qian

first: Longsheng

last: Fu

first: Jinfang

last: Hu

first: Tiantian

last: Xu

first: Yaoqi

last: Wu


title: Analysis of genes differentially expressed between rete testis cells and Sertoli cells of the mouse testis

city: Moscow

first: Valeru

last: Mun

address: st. Vavilova, 26

country: Russia

institute: IDB RAS

summary: The rete testis (RT) is a region of the mammalian testis which plays an important role in testicular physiology. The RT epithelium consists of cells sharing some well-known gene markers with supporting Sertoli cells (SCs). However, little is known about the differences in gene expression between these two cell populations. Here, we used fluorescence-activated cell sorting (FACS) to obtain pure cultures of neonatal RT cells and SCs and identified differentially expressed genes (DEGs) between these cell types using RNA sequencing (RNA-seq).

overall_design: Comparison of mRNA profiles of rete testis cells and Sertoli cells obtained from testes of 5-6 dpp mice using FACS and cultured for 3 days. For each cell type, three samples obtained from independently established cell cultures were used in the analysis.

first: Ekaterina

last: Malolina

first: Adelya

last: Galiakberova

first: Valery

middle: V

first: Marat

last: Sabirov

first: Erdem

last: Dashinimaev

first: Andrey

last: Kulibin


title: Cell-based models of ‘Cytokine Release Syndrome’ endorse CD40L and GM-CSF knockout in CAR T cells as mitigation strategy

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Chimeric antigen receptor (CAR) T cells are engineered lymphocytes able to recognize and eradicate cancer cells. While CAR T cell therapy has shown promising outcomes in patients with hematologic malignancies, it can cause undesirable side-effects such as cytokine release syndrome (CRS). CRS is triggered by CAR T cell-based activation of monocytes, which are stimulated via the CD40L–CD40R axis or via uptake of GM-CSF to secrete pro-inflammatory cytokines. Mouse models have been used to model CRS but they are labor intensive and not amenable to screening approaches. To overcome this challenge, we established two cell-based CRS in vitro models that entail the co-culturing of leukemic B cells with CD19-targeting CAR T cells and primary monocytes from the same donor. Upon antigen encounter, CAR T cells upregulated CD40L and GM-CSF which stimulated the monocytes to release IL-6. To endorse these models, we demonstrated that neutralizing antibodies or genetic disruption of the CD40L and/or CSF2 loci in CAR T cells using CRISPR-Cas technology significantly reduced IL-6 secretion by bystander monocytes without affecting the cytolytic activity of the engineered lymphocytes. Overall, our cell-based models were able to recapitulate CRS in vitro, allowing us to validate mitigation strategies based on antibodies or genome editing.

overall_design: CAR T cells, produced via lentiviral transduction were treated with two RNP complexes (Cas9) targeting close sites within CSF2 and/or CD40L. CAST-Seq was performed on cells treated with either one or both nuclease pairs looking at the targeted loci in each sample to assess the formation of stable translocations between the on-target site potential off-target sites.

first: Ala

last: Dibas

first: Manuel

last: Rhiel

first: Melanie

last: Boerries

first: Jamal

last: Alzubi

first: Toni

last: Cathomen


title: Hepatic Huwe1 loss protects mice from non-alcoholic fatty liver disease through lipid metabolic rewiring

city: Kent

first: Manabu

last: Kurowaka

state: OH

address: 800 E Summit St

department: Biological Sciences

institute: Kent State

summary: Non-alcoholic fatty liver disease (NAFLD) is the most prevalent form of liver disease worldwide and is estimated to affect nearly a third of the population. Huwe1, also known as ARF-BP1, MULE, and HectH9, is a HECT (homology to E6-APC terminus)-domain E3 ubiquitin ligase originally identified as a binding partner of the tumor suppressor ARF, as well as a direct negative regulator of the tumor suppressor p53. To further elucidate the in vivo role of Huwe1, we generated a liver-specific Huwe1 (Huwe1LKO) knockout mouse model. Surprisingly, liver-specific knockout of Huwe1 protected mice from the development of age-induced hepatic steatosis. To elucidate the mechanism underlying this phenotype, bulk RNAseq analysis was performed on liver tissues from 1-year-old Huwe1LKO and Huwe1WTmice.

overall_design: Bulk RNAseq was performed on livers from 1-year-old Huwe1 knockout mice as compared to wildtype mice. 4 livers were sequenced per group.

first: William

middle: W

last: Feng

last: Kurokawa


title: GDNPs reprogram macrophages to regulate arginase-1 release for ameliorating T cell exhaustion in tumor microenvironment

city: Nanjing

first: Meng

last: Cao

state: Jiangsu Province

address: Hongshan road 100#

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine

summary: Lines of evidence indicate that, immune checkpoints (ICs) inhibitors enhance T cell immune response to exert anti-tumor effects. However, T cell exhaustion is still a major obstacle to antitumor immunotherapy in colorectal cancer patients. Our previous studies showed that ginseng-derived nanoparticles (GDNPs) inhibited the growth of various tumors by reprograming tumor-associated macrophages (TAMs) and downregulated the ICs expression on T cells in tumor microenvironment (TME), but the underlying effector mechanisms remained unclear. In this study, we demonstrated that GDNPs reprogramed TAMs via reducing arginase-1 (ARG1) production. Moreover, normalized arginine metabolism ameliorate T cell exhaustion through mTOR-T-bet axis, resulting in reduced ICs expression and enhanced CD8+ T cells expansion. Together, these results provide new insights in understanding the mechanisms involved in reversing T cell exhaustion, which may facilitate the development of new therapeutic strategy for cancer treatment.

overall_design:
Single cell RNA seqencing data of six samples from  six colon cancer bearing C57 mice treated with ginseng-derived nanoparticles. Each samples contain one sample from solid tumor of each tumor bearing mouse.
Mouse tumor tissues were scissored into 5 mm pieces and incubation with 100 μg/mL Liberase and 0.2 mg/mL DNase Ⅰ in PBS for 45 min at 37°C. After digestion, 70 μm nylon net was centrifuged at 300 g for 5 min. Subsequently, the supernatants were discarded, and the cell pellets were suspended in 1 mL PBS. To remove red blood cells, 2 mL of GEXSCOPETM red blood cell lysis buffer (Singleron) was added, and cells were incubated at 25 °C for 10 min. The solution was then centrifuged at 500 × g for 5 min and resuspended in PBS.Single-cell suspensions (1×105 cells/mL) with PBS were loaded into microfluidic devices using the Singleron Matrix®Single Cell Processing System (Singleron). Subsequently, the scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM and pooled for sequencing. At last, pools were sequenced on Illumina HiSeq X with 150 bp paired end reads.

first: Yan

last: Lv


title: ATAC-seq for SK-HEP-1 cell line with or without sirolimus treatment

city: Hangzhou

first: Jiongjie

last: Yu

address: Kaixuan Road

summary: The openness of chromatin affects the expression and regulation of genes. In order to figure out the changes of transcriptional factors after sirolimus treatment in hepatocellular carcinoma, ATAC-seq was performed for human hepatocellular carcinoma cell line SK-HEP-1. Here, we found that a series of transcriptional factors, including E2F1, SP1, M2F1, etc. enhanced binding to DNA after sirolimus treatment.

overall_design:
In order to figure out the changes of transcriptional factors after sirolimus treatment in hepatocellular carcinoma, ATAC-seq was performed for human hepatocellular carcinoma cell line SK-HEP-1.
HCC cell line treated with or without sirolimus


title: Effect of TP53 on gene expressions in human hepatocellular carcinoma cell lines

summary: The incidence of TP53 loss-of-function in hepatocellular carcinoma is very high. In order to clarify the gene expression differences induced by the changes of TP53 gene, we used two human hepatocellular carcinoma cell lines, SK-HEP-1 and Hep 3B with TP53 knockdown or overexpression for RNA sequencing . SK-HEP-1 is a TP53 wild-type hepatocellular carcinoma cell line. Thus, we knockdown TP53 in SK-HEP-1. Hep 3B is a TP53 loss-of-function hepatocellular carcinoma cell line. Thus, we overexpress TP53 in Hep 3B. Results of RNA-seq analysis showed the differences after knocking-down or overexpressing TP53.


title: Reallocation of ribosomes as a disease mechanism of Amyotrophic Lateral Sclerosis

city: Povo (TN)

first: Fabio

last: Lauria

address: Via alla Cascata 56

institute: Institute of Biophysics (Italian National Research Council)

summary: The molecular mechanism underlying Amyotrophic Lateral Sclerosis (ALS) is still largely unclear. The RNA binding protein TDP-43 is a major contributor and hallmark of the disease. Here, we show that in multiple TDP-43 models of ALS the alterations of the physiological crosstalk between free RNA/granules and polysomes lead to the global reorganisation of translational resources. We exploited in cellulo and in vivo models of TDP-43 proteinopathy and a unique tag-free miniaturised polysomal profiling coupled with RNA-Seq and biochemical assays with subcellular (i.e. cell body and axon) and compartment (i.e. RNA granules and polysomes) resolution. Using these models, we identified: i) a widespread axonal- and polysome-specific downregulation of TDP-43 target mRNAs, ii) the rewiring of mRNAs in granule and polysome compartments, iii) decrease in ribosome kinetics, iv) a robust ribosome engagement with residual mRNAs and v) downstream alterations in protein synthesis of TDP-43 non-target mRNAs. Irrespective of the ALS model used, we observed a snowball effect in RNA metabolism with redistribution of translational resources. Based on our results we propose a systems-oriented mechanism of disease pathogenesis, leveraging on the conceptual framework of reallocation of cellular resources.

overall_design: In this study, we performed RNA-Seq of total, polysomal and free/granule-associated RNA from mouse primary cortical neurons control and expressing tRFP, exogenous TDP43-WT or TDP43-A315T to investigate the repertoires of defects caused by TDP-43 proteinopathy at subcellular (cell body vs axon) and compartment (RNA granules and polysomes) levels.

first: Federica

last: Maniscalco

first: Cecilia

last: Perrucci

first: Marta

last: Marchioretto

first: Toma

last: Tebaldi

last: Cella

first: Emma

last: Busarello

first: Lorenzo

last: Lunelli

first: Luisa

last: Donini

first: Maria

last: D'Antoni

first: Daniele

last: Pollini

last: Peroni

first: Alessandra

last: Pisciottani

first: Laura

last: Croci

first: Aurora

last: Badaloni

first: Renato

last: Arnese

first: Alessandro

last: Provenzani

last: Quattrone

first: Gian

middle: G

last: Consalez

first: Velia

last: Siciliano

first: Manuela

last: Basso

first: Gabriella

last: Viero


title: Evaluation of Novel Circulating Extracellular Vesicle-packaged microRNAs in Breast Cancer: a Potential Role for miR-128 and miRNA-27a

city: Caserta

first: Gilda

last: Cobellis

address: Viale Abramo Lincoln

institute: University of Campania "Luigi Vanvitelli"

summary: Purpose: Extracellular vesicle (EV)‑derived microRNAs (miRNAs) are a class of circulating miRNAs located in the plasma that are are now considered the next generation of cancer “theranostic” tools, with a strong clinical relevance. Although the potential role of EV-packaged miRNAs in breast cancer diagnosis has been widely reported, further studies are still demanded to address this challenging issue. The present study examined the expression profiles of EVs and circulating miRNAs with the aim of identifying novel miRNA signatures in breast cancer, and verify their diagnostic accurancy.

overall_design:
Methods: Circulating EVs were isolated from helathy volunteers, and breast cancer patients and characterized by Transmission Electron Microscopy (TEM), Nanoparticle Tracking Analysis (NTA), and protein marker expression. Assessment of EV-miRNAs was performed in a screening and a validation cohort by RNA-seq and qRT-PCR analyses, respectively. Bioinformatic analysis was performed to uncover significantly enriched biological processes, molecular functions and pathways. A comprehensive literature search was conducted to outline the role of the identified miRNAs in breast cancer.
Results: A total of two miRNAs, including miRNA‑128, and miRNA27a, were found to be significantly down-regulated in breast cancer-derived EVs compared to healthy individuals. Metacore GO processes, Molecular Functions and Localizations on target genes of the two deregulated miRNAs indicated roles in regulation of cellular cycle and migration. Moreover, ROC analyses highlighted the ability of miRNA‑128, and miRNA27a in distinguishing breast cancer cases from non-cancer controls. According to other reports, levels of EV-derived miRNAs did not not associate with circulating plasma levels, indicating how the EV-incorporated and whole plasma miRNA profiles could be clearly different. These results were subsequently compared with evidence from studies included in the final systematic review.
Conclusion: Our findings unraveled a potential role for serum EV-derived miRNA‑128, and miRNA27a in breast cancer, adding these two miRNAs to the list of multiple biomarkers that could be exploited in the clinic to diagnose breast cancer.
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*This submission consists of healthy controls only

first: CINZIA

last: GIORDANO


title: The mRNA expression in the sarcomas of Li-Fraumeni syndrome mouse harboring a deleterious p53 mutation

city: Shanghai

first: Jia

middle: bing

last: Li

address: 197, Ruijin Er Street

institute: Shanghaijiaotong university

summary: Determining the mRNA expression profiles in the sarcomas of W/+ mice before and after ATO treatment by RNA-seq.

overall_design: Compare the differences in transcriptome profiles between the sarcomas samples before and after ATO treatment.

first: Jiabing

first: Lu

last: Min


title: Effect of HAPLN1-PTR1 on STAT1 knockout RPMI8226 multiple myeloma cells

city: Madison

first: Hae Yeun

last: Chang

state: WI

address: 1111 Highland ave., WIMR II

institute: UW-Madison

summary: To identify the HAPLN1-induced genes regulated by STAT1 in multiple myeloma, we treated RPMI8226 multiple myeloma cells (WT or STAT1 KO) with recominant HAPLN1-PTR1. 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 RPMI8226 multiple myeloma cells (WT or STAT1 KO) treated with 100 nM MBP (control) or MBP-PTR1 (experimental group) for 6 h.

first: Hae

first: Shigeki

last: Miyamoto


title: DNA methylation profiles in human iPSC-derived neurosphere exposed to environmental chemicals

city: Miyazaki

first: Yoshikazu

last: Arai

department: Faculty of Agriculture

institute: University of Miyazaki

summary: Various chemicals, including pesticides, heavy metals, and metabolites of tobacco, have been detected in fetal environment. Fetuses are exposed to these chemicals at relatively low concentrations; however, their risk of developing neurological and behavioral disorders increases after birth. We aimed to evaluate the effects of five chemicals (diethylphosphate, cotinine, octachlorodipropyl ether, mercury, and selenium) detected in the serum of pregnant mothers on DNA methylation status during neural development using human neural stem cells.

overall_design: Bisulfite converted DNA were hybridised to the Illumina Infunium MethylationEPIC

first: Koichiro

last: Nishino


title: Effect of Bacteroides vulgatus on colitis and depressive-like behavior in a murine model of inflammatory bowel disease: involvement of the gut-brain axis

city: Changsha

first: Xing

last: Wu

address: 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China

department: Department of Gastroenterology

institute: The Third Xiangya Hospital of Central South University

summary: IBD is characterized by chronic recurrences of intestinal inflammation and intestinal immune disturbances.Bacteroides vulgatus can alleviate DSS-induced colitis in mice, but the mechanism is unknown. The aim of this study was to examine the changes in gene expression in the intestinal tissue of mice with colitis following treatment with Bacteroides vulgatus by RNA sequencing.

overall_design: To clarify the role of B. vulgatus in colitis, we treated dextran sulfate sodium salt (DSS)-induced mice with B. vulgatus. The body weight, disease activity index (DAI), Colon length and colon tissue H&E staining was used to evaluate the severity of colitis. In mice, we compared the severity of colitis between DSS and DSS+BV groups and randomly selected three mice from each group for RNA sequencing analysis.

first: Jiahao

last: Xu

first: Xiaoyan

last: Wang


title: RNA-sequencing analysis on induced brown adipocytes derived from the SVFs of U-IRX3ov and control mice.

first: Zhiyin

last: Zhang

state: Huangpu

address: Xu Jia Hui Road.

department: Department of Endocrinology and Metabolism, Ruijin Hospital

institute: Shanghai Jiao Tong University

summary: Purpose: Over expression of hIRX3 increase thermogenesis in vitro and in vivo. To further elucidate the effects of hIRX3 overexpression on thermogenesis, and to explore the possible downstream target molecular and interferring pathway, we use induced brown adipocytes derived from the SVFs of U-IRX3ov and control mice for RNA sequencing analysis.

overall_design: RNA-sequencing analysis on induced brown adipocytes derived from the stromal vascular fractions (SVFs) of U-IRX3ov and control mice. SVFs were isolated from the BAT of five-week-old U-IRX3ov and control mice and then induced for 8 days. Total RNA was extracted from cultured cells or frozen adipose tissue using the Eastep Super Total RNA Extraction Kit (Promega (Beijing) Biotech Co., China).


title: Effects of strigolactone analogue dGR24 on the transcriptome of Bacillus subtillis

city: Perth

first: Muhammad

last: Kamran

state: WA

address: 35 Stirling Hwy, Crawley WA

department: School of Molecular sciences

country: Australia

institute: The University of Western Australia

summary: Objective: to compare and contrast the effects of exogenous application of strigolatone analogue rac-dGR24, on gene expression in bacillus subtilis. The experiment compared the effects on three genotypes: wild type and two mutant lines, a ∆rsbQ and RsbQS96A.

overall_design: Two treatments (mock, 10 µM rac-dGR24) were applied to three genotypes (WT, ∆rsbQ, RsbQS96A) in triplicate at an optical density (OD 600) ranging from 1.0 to 1.1. Cultures were harvested at OD ranging from 1.4 to 1.5 and transferred to liquid nitrogen prior to extraction of total RNA.

first: Mark

last: Waters


title: IL-15-DEPENDENT IMMUNE CROSS-TALK BETWEEN NK CELLS AND DENDRITIC CELLS IN HIV-1 ELITE CONTROLLERS [CUT&RUN]

city: Cambridge

first: Ce

last: Gao

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

summary: As the principal effector cell population of the innate immune system, NK cells may make critical contributions to natural, immune-mediated control of HIV-1 replication. Using genome-wide assessments of activating and inhibitory epigenetic chromatin features, we here demonstrate that cytotoxic NK (cNK) cells from elite controllers (ECs) frequently display elevated activating histone modifications at the IL-2/IL-15 receptor β chain and the BCL-2 gene loci. These epigenetic changes translated into increased responsiveness of cNK cells to paracrine IL-15 secretion, which coincided with higher levels of IL-15 transcription by myeloid dendritic cells in ECs. The distinct immune crosstalk between these two innate immune cell populations resulted in improved IL-15-dependent cNK cell survival, paired with a metabolic profile biased towards IL-15-mediated glycolytic activities. Together, these results suggest that cNK cells from ECs display an epigenetically-programmed IL-15 response signature, and support the emerging role of innate immune pathways in natural, drug-free control of HIV-1.

overall_design: We performed CUT&RUNseq on NK cells from PBMCs of five HIV-1 Elite controllers, five people living with HIV-1 on antiretroviral treatment and five HIV-1 negative individuals to prolife histone modifications in the genomic regions.

first: Ciputra

middle: A

last: Hartana

first: Yelizaveta

last: Rassadkina

first: Mathias

last: Lichterfeld

first: Xu

last: Yu


title: IL-15-DEPENDENT IMMUNE CROSS-TALK BETWEEN NK CELLS AND DENDRITIC CELLS IN HIV-1 ELITE CONTROLLERS [RNA-seq]

overall_design: The current study comprehensively examined NK cells from three different groups: HIV-1 elite controllers, people living with HIV-1 on antiretroviral treatment and healthy donors.


title: Re-evaluating the melanoma TIL compartment and its unexpected spectrum of exhausted and functional T cells

city: Cleveland

last: Cameron

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: Significant heterogeneity exists within the tumor infiltrating CD8 T cell population, and exhausted T cells harbor a subpopulation that may be replicating and retain signatures of activation, with potential functional consequences in tumor progression. Dysfunctional immunity in the tumor microenvironment is associated with poor cancer outcomes, making exploration of these exhausted but activated (Tex/act) subpopulations critical to the improvement of therapeutic approaches. To investigate mechanisms associated with Tex/act cells, we sorted and performed transcriptional profiling of CD8+ tumor infiltrating lymphocytes (TIL) coexpressing the exhaustion markers PD-1 and TIM-3, from large volume melanoma tumors. We additionally performed immunologic phenotyping and functional validation, including at the single cell level, to identify potential mechanisms that underlie their dysfunctional phenotype. We identified novel dysregulated pathways in CD8+PD-1+TIM-3+ cells that have not been well studied in TIL; these include bile acid and peroxisome pathway-related metabolism, and mammalian target of rapamycin (mTOR) signaling pathways, which are highly correlated with immune checkpoint receptor expression. Through bioinformatic integration of immunophenotypic data and network analysis, we propose unexpected targets for therapies to rescue the immune response to tumors in melanoma.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for peripheral CD8 T-cells and CD8+ tumor infiltrating lymphocytes (TIL) coexpressing the exhaustion markers PD-1 and TIM-3, from large volume melanoma tumors.

first: C

first: B

last: Richardson

first: J

middle: B

last: Golden

first: Y

middle: P

last: Phoon

last: Tamilselvan

first: L

last: Pfannensttiel

first: S

last: Thapaliya

first: G

last: Roversi

first: X

last: Zagore

first: M

last: Gastman


title: Transcriptome of isolated mouse peritoneal endothelial cells

city: Guangzhou

first: Si

last: Zekun

state: Guangdong

address: Guangdong,China

department: Division of Nephrology

institute: Nanfang Hospital, South Medical University

summary: To characterize the metabolic profile of peritoneal endothelial cells (ECs) in response to peritoneal dialysis (PD), we performed RNA sequencing of peritoneal ECs isolated from mice treated with PD fluid for 6 weeks (n = 3) and from mice treated with saline for 6 weeks (n = 3). We demonstrated that peritoneal ECs had a hyperglycolytic metabolism in response to PD fluid treatment, which is associated with the development of microvascular alterations and peritoneal dysfunction.

overall_design: We isolated peritoneal ECs from mice treated with PD fluid for 6 weeks (n = 3) and from sham mice treated with saline for 6 weeks (n = 3). We then performed RNA sequencing of peritoneal ECs.

first: Wei

last: Cao

first: Zekun

last: Si

first: Wenyan

last: Su

first: Zuoyu

last: Hu


title: Transcriptional changes by RBN-2397 treatment and FRA1 knockdown in NCI-H1975 cells

city: Zurich

first: Michael

last: Hottiger

address: Winterthurerstrasse 190

department: DMMD

institute: University of Zurich

summary: PARP7 inhibitors reduce tumor growth in a cell-autonomous manner and by enhancing immune recognition through restoring nucleic acid (NA)-sensing-dependent innate immune signaling. However, the molecular targets of PARP7-mediated ADP-ribosylation, regulating cell survival and innate immune signaling, remained elusive. Here, we identified PARP7 as a nuclear and cysteine-specific mono-ART that ADP-ribosylates proteins critical for regulating gene expression, such as the AP-1 transcription factor FRA1. Upon PARP7 inhibition the loss of FRA1 ADP-ribosylation increased FRA1 degradation in a PSMC3 and proteasomal-dependent manner. To further investigate how FRA1 promotes cell survival, we investigated transcriptional changes after RBN-2397 treatment and FRA1 knockdown in the PARP7 inhibitor sensitive cell line NCI-H1975 by RNA sequencing.

overall_design: RNA sequencing of NCI-H1975 cells after RBN-2397 treatment (6h) or FRA1 knockdown (48h)

first: Patrick

last: Manetsch

middle: O


title: Granulosa cell-derived serum TNF-α mediates inflammation and apoptosis in renal tubular cells through NF-κB signaling and indicates PCOS-related kidney injury.

first: Huiyun

last: Ye

address: 1838 North Guangzhou Ave

institute: Southern Medical University

summary: Serum TNF-α plays a key role in mediating inflammation and apoptosis in renal tubular cells and indicates PCOS-related kidney injury.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for kidney in PCOS mice.


title: Vpr attenuates antiviral immune responses and is critical for full pathogenicity of SIVmac239 in rhesus macaques

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: The accessory viral protein R (Vpr) is encoded by all primate lentiviruses. Vpr counteracts DNA repair pathways, modulates viral immune sensing, and induces cell-cycle arrest in cell culture. However, its impact in vivo is controversial. Here, we show that deletion of vpr is associated with delayed viral replication kinetics, rapid innate immune activation, development and maintenance of strong B cell responses, and generation of higher avidity p27 Gag antibodies in rhesus macaques. All wild-type SIVmac239 infected animals maintained high viral loads and five of six developed fatal immunodeficiency during ~80 weeks of follow-up. Lack of Vpr was associated with better preservation of CD4+ T cells, lower viral loads and an attenuated clinical course of infection in most animals. Our results demonstrate that Vpr contributes to efficient viral immune evasion and the full pathogenic potential of SIVmac in vivo. Inhibition of Vpr may improve humoral immune control of viral replication.

overall_design: Six rhesus macaques were infected with a mutant SIVmac239 construct containing a large deletion of 101 nucleotides eliminating the vpr gene (Δvpr), and six rhesus macaques were infected with wild type (wt) SIVmac239, and 10 rhesus macaques were uninfected. Blood samples (PBMC) were collected in two sets of experiments, A and B. Set A consists of  wt (n=3) and Δvpr (n=3) infected animals at 2 and 24 weeks post-infection. For Set A, PBMC samples were also collected from uninfected control animals (n=10). Set B consists of blood samples from wt (n=3) and Δvpr (n=3) infected animals at both pre- (4 and 8 weeks) and post-infection (2 and 24 weeks) time-points.

first: Alexandre

last: Laliberté

first: Caterina

last: Bozzo

first: Christiane

last: Stahl-Hennig

first: Victoria

last: Hunzinger

first: Simone

last: Joas

first: Ulrike

last: Sauermann

first: Berit

last: Roshani

first: Antonina

last: Klippert

first: Maria

last: Daskalaki

first: Kerstin

last: Mätz-Rensing

first: Nicole

last: Stolte-Leeb

first: Dietmar

last: Fuchs

first: Prachi

middle: M

last: Gupta

first: Guido

last: Silvestri

first: Sydney

last: Nelson

first: Laura

last: Parodi

first: Luis

last: Giavedoni

first: Steven

last: Bosinger

first: Konstantin

last: Sparrer

first: Frank

last: Kirchhoff


title: Mature oligodendrocyte (OL) translatome changes at various times after moderate contusive spinal cord injury at the thoracic T9 level

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: OL translatome was determined in female RiboTag:Plp1-CreERT2 mice (C57Bl6 background) at 2, 10, and, 42 days after moderate contusive T9 SCI. Ribotag expression was induced by daily tamoxifen injections (1 mg i.p. over 8 days). Three weeks after completion of the induction protocol moderate contusive SCI was performed at T9 level (IH imactor, 50 kdyn). Uninjured mice (naive) were used as controls. At the time of surgery, animal age was 10-12 weeks. After euthanasia, RNA was isolated from a 5 mm spinal cord segment spanning the injury epicenter. OL tranlsatome was immunopurified using anti-HA antibody and protein A/G coupled magnetic beads following the Ribotag protocol. Total spinal cord RNA and OL translatome RNA samples were analyzed by RNASeq. Each biological sample was prepared by pooling material from two mice (3 biological samples representing 6 animals were used for each timepoint).

overall_design: Analyzing effects of spinal cord injury on mRNA levels in total spinal cord transcriptome and OL translatome

first: Michael

last: Forston

first: George

last: Wei

first: Michal

last: Hetman

first: Scott

last: Whittemore

first: Julia

last: Chariker

middle: C


title: Division-Independent Differentiation of Muscle Stem Cells During a Growth Stimulus

city: Lexington

first: Ahmed

last: Ismaeel

address: 900 S Limestone St

department: Physiology

institute: University of Kentucky

summary: Adult muscle stem cell (MuSC) behavior has been predominantly studied in the context of regeneration, a condition under which MuSCs exit quiescence and replicate upon activation before differentiating and fusing into myocytes. We use single-cell RNA-seq (scRNA-seq) to identify transcriptionally diverse subpopulations of MuSCs after 5 days of a growth stimulus.

overall_design: MuSCs from plantaris muscles of doxyxycline treated Pax7rtTA; TRE-H2B-GFP mice, subjected to either sham surgery or 5-days of a growth stimulus, were isolated by Fluorescence-activated cell sorting (FACS) according to the prescence of GFP signal and analyzed using scRNA-seq.

first: A

first: Y

last: Wen

first: C

last: Peterson

first: John

middle: J

last: McCarthy


title: Marker-based CRISPR screening reveals a direct MED12-p63 interaction that activates basal identity in pancreatic ductal adenocarcinoma

city: Cold Spring Harbor

first: Diogo

last: Maia e Silva

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: We report a novel p63-MED12 transcriptional complex that is selectively required for basal pancreatic cancer and squamous cell carcinoma survival. This transcription factor-imposed genetic vulnerability on a general coactivator will inform future p63-blocking therapeutic strategies.

overall_design: RNA-seq and ChIP-seq of p63 and MED12 manipulation in basal and classical human pancreatic cancer cell lines. FACS-based and negative selection CRISPR screens (genome-wide, Mediator exon tiling) to nominate lineage regulators of basal pancreatic cancer.

last: Maia-Silva

first: Christopher

last: Vakoc


title: Differentiation of CFTR knockout hPSCs into salivary gland epithelial progenitors models the development of cystic fibrosis patients

city: Beijing

first: Shuang

last: Yan

address: zizhuyuanstreet

institute: Peking University

summary: The differentiation of pluripotent stem cells has been broadly used in studying the disease mechanism and development process. We previously described a method for differentiating human pluripotent stem cells (hPSCs) into salivary gland epithelial progenitors (SGEPs). Here, to investigate whether the hPSCs-derived SGEPs are capable of modeling the characteristics of cystic fibrosis (CF), a disease impact SG function caused by mutation of cystic fibrosis transmembrane conductance regulator (CFTR) gene, the CFTR knockout hPSCs were differentiated into CF-SGEPs using the same protocol. Firstly, we successfully generated CFTR knockout hPSCs with reduced CFTR protein expression using the CRISPR-Cas9 system. After 16-day of differentiation, the protein expression of CFTR was also decreased in SGEPs generated from CFTR knockout hPSCs. RNA-sequencing shows that multiple genes modulating SG development, function and were down-regulated and positive regulators of inflammation were up-regulated in CF-SGEPs, which was correlated with salivary phenotype in CF patients. These results demonstrated that suppression of CFTR disrupted the differentiation of hPSCs-derived SGEPs, which modeled the SG development of patients with CF. In summary, this study not only provided the proof that the hPSCs-derived SGEPs could serve as manipulatable and easily accessible models to study the SG developmental diseases, but also provided new avenues for the study of the CF mechanism.

overall_design: Analysis of global transcriptomes of salivary gland epithelial progenitors derived from CFTR knockout human embryonic stem cell (H1) and the wild type human embryonic stem cell (H1). There are six replicates. Control groups are the wild type human embryonic stem cell (H1) derived salivary gland epithelial progenitors

first: Siqi

last: Zhang

first: Shicheng


title: The transcriptional factor Clr-5 is involved in cellulose degradation through regulation of amino acid metabolism in Neurospora crassa

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

summary: Filamentous fungi are one of the primary degraders of plant biomass because of their ability to produce enzymes that break down complex polysaccharides. The production of cellulolytic enzymes in fungi is dependent on transcription factors. In this article, we identified a N. crassa Zn2Cys6 transcription factor Clr5 that regulates the expression of cellulase on cellulose. N. crassa Δclr5 exhibited a significant decrease in secreted proteins (~46%), endo-glucanase (~55%), xylanase (~33%), β-glucosidase (~38%), and exocellulase (~40%) compared with the WT, while transcriptomic analysis revealed that clr5 was essential in cellulase expression. We also determined that clr5 is crucial in amino acid- Leucine and Histidine metabolism. When using Leucine or Histidine as solo nitrogen source, Δclr5 strain cannot grow as normally as WT, and the expression of most CAZyme genes were reduced obviously, which indicated nitrogen metabolism played an important role in cellulose degradation. Moreover, the function of Clr5 is conservative in M. thermophila, the other fungi with a capacity for biomass degradation.

overall_design: mRNA profiles of Neurospora crassa exposed to Avicel.


title: Adipose stem cells from people with obesity show impaired mitochondrial and lysosomal functions

city: shanghai

first: bo

last: wang

address: 130 Meilong Rd.

institute: East China University of Science and Technology

summary:
Adipose stem cells (ASCs) have been widely used in preclinical and clinical trials for the treatment of various diseases. However, ASCs from people with obesity (O-ASCs) are not thoroughly investigated. In this study we aimed to evaluate the changes of the biological activity and the function of mitochondria and lysosomes in O-ASCs.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data forAdipose stem cells from people with lean and obesity.

first: Bo

last: Wang

first: Ge


title: Allele-Specific gene editing approach for a dominant form of Epidermolysis Bullosa Simplex I

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

institute: University of Padova

summary: Epidermolysis Bullosa Simplex (EBS) is the most common form of Epidermolysis Bullosa (EB) and it is mainly inherited in an autosomal dominant manner (prevalence 1/30000 – 1/50000). Several clinical variants have been described based on the mutated gene, the site of blister formation and the anatomical distribution, but the vast majority of the patients display dominant mutations in genes encoding keratin 5 (KRT5) and keratin 14 (KRT14). The lack of functional keratin intermediate filaments causes basal keratinocytes to exhibit a dramatic cytoplasmatic softening and rupture, when subjected to minor mechanical traction, leading to the distinctive EBS patients intraepidermal blisters formation. Whilst viral mediated addition of a corrected copy of the altered gene is the ascertained approach to tackle recessively inherited EB (such as Junctional and Dystrophic EB), a potential successful combined cell and gene therapy for EBS dominant forms requires the editing of the mutated gene. In this case study, we outlined an allele specific CRISPR/Cas9 gene editing approach able to specifically detect and disrupt a de novo monoallelic c.475/495del21 mutation within exon 1 of KRT14. Taking advantage of the tailored CRISPR/Cas9 system to induce a NHEJ mediated frameshift mutations introduction, we attained a remarkable mutant allele knock-out efficiency. Following KRT14 mutant allele specific gene editing, patient derived primary keratinocytes (EBS01) restored a normal intermediate filament network and mechanical stress resilience.

overall_design: Single cell-RNA seq of in vitro cultivated human primary keratinocytes derived from patient affected by Epidermolysis Bullosa Symplex, untreated or treated with KRT14-specific editing strategy

first: Maria

last: Latella

first: Camilla

last: Cattaneo

first: Elena

last: Enzo


title: The IL6Myc mouse is an immunocompetent model for the development of aggressive multiple myeloma (MM) [tumor RNA-seq]

city: Milwaukee

first: Michael

last: Pisano

state: Wisconsin

address: 8701 W Watertown Plank Rd MFRC 6033

department: Medicine

institute: Medical College of Wisconsin

summary: Multiple Myeloma (MM) is a neoplasm of plasma cells originating in the bone marrow and is the second most common blood cancer in the United States. One challenge in understanding the pathogenesis of Multiple Myeloma (MM) and improving treatment is a lack of immunocompetent mouse models. We previously developed the IL6Myc mouse that generates plasmacytomas at 100% frequency that phenotypically resemble aggressive MM. Using comprehensive genomic analysis, we found that the RNA expression patterns between tumors were somewhat heterogenous, but nonetheless resembled MMSET (multiple myeloma SET domain), an aggressive form of human myeloma with poor prognosis. Cell lines derived from the mouse tumors expressed cell-surface markers typical of MM, but also expressed BAFF-R, which is infrequently found in human MM. The cell lines also had heterogeneous responses to chemotherapeutic drugs typically used to treat human MM. Interestingly IL6Myc tumors accumulated variants in genes like those seen in human MM, as well as recurrent Ig translocations, a common characteristic of human MM. These data indicate that the IL6Myc model is a useful model for aggressive MM that can be used to develop treatment and understand how early myc expression influences disease etiology.

overall_design: RNA extracted from 7 MLN and Splenic tumors from IL6Myc transgenic mice. Samples for which the numbers are the same indicate that they are tumors from the same mouse. Controls for this study were LPS activated B cells and quiescent B cells from WT Balb/c mice. Prior to RNA isolation all tissue samples were sorted for B cells using negative selection magnetic bead separation.

first: Miles

last: Pufall


title: The IL6Myc mouse is an immunocompetent model for the development of aggressive multiple myeloma (MM) [WES]

overall_design: WES of 45 MLN tumor samples from independent IL6Myc transgenic mice and of 5 kidney samples from WT Balb/c mice (controls)

first: Ramakrishna

last: Sompallae


title: The IL6Myc mouse is an immunocompetent model for the development of aggressive multiple myeloma (MM) [cell line RNA-seq]

overall_design: RNA extracted from cell lines derived from IL6Myc mice named IL6Myc-1, IL6Myc-2, IL6Myc-3, IL6Myc-4, and IL6Myc-5. Three technical replicates were collected from each cell line.


title: The IL6Myc mouse is an immunocompetent model for the development of aggressive multiple myeloma (MM)

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

overall_design: Refer to individual Series


title: RNA-seq profiling of ITPKC overexpression in normal human lung fibroblasts

city: Rochester

first: Jack

middle: Henry

last: Wellmerling

state: Minnesota

address: 200 1st St SW

institute: Mayo Clinic

summary: Idiopathic pulmonary fibrosis (IPF) is characterized by pathogenic accumulation of scar tissue in the lung. Many of the processes implicated in fibrosis also occur following pneuomonectomy, but fibrotic changes are absent. We aimed to characterize differences between the responses to pneumonectomy and bleomycin, a fibrosis-inducing drug. We identified Itpkc as a gene uniquely up-regulated following pneumonectomy and identified it to have anti-fibrotic effects in cell culture. We then used RNA-sequencing on normal human lung fibroblasts overexpressing ITPKC or control to gain a deeper understanding of its role.

overall_design: Normal human lung fibroblasts overexpressing recombinant human ITPKC (n=3) or control (n=2)

first: J

first: D

last: Tschumperlin

first: Q

last: Tan


title: Osteosarcoma cells-derived secretome induce pre-metastatic changes in the lung microenvironment that support lung metastasis formation

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary: To investigate the molecular and cellular alterations occurring in the lung tissue during the pre-metastatic niche formation in osteosarcoma, we used two different approaches in which mice were implanted subcutaneously with the 143B OS cells for a primary tumour (PT) formation or treated with the 143B cell-derived secretome (SCR) to mimic the release of secreted factors by a locally primary tumour.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of the lung tissue collected from control, SCR-treated or PT-bearing mice.

first: Sara

middle: F

last: Almeida

first: Gabriela

last: Ribeiro

first: Liliana

last: Santos

first: Nuno

last: Lima

first: Monica

last: Abreu

first: Rui

last: Caetano

first: Mónica

last: Zuzarte

first: Artur

last: Paiva

first: Tania

last: Martins-Marques

first: Henrique

last: Girao

first: Ana

middle: S

first: Catarina

last: Miranda

first: Luís

last: Pereira de Almeida

first: Amilcar

last: Falcao

first: Antero

last: Abrunhosa

first: Celia

last: Gomes


title: Digital Spatial Profiling reveals tumor microenvironment of Hodgkin-like adult T-cell leukemia/lymphoma.

city: Krume

first: Koichi

last: Ohshima

state: Fukuoka

address: Asahimachi 67

department: Pathology

institute: Kurume University

summary: Hodgkin-like adult T-cell leukemia/lymphoma (ATLL) is a rare subtype of ATLL harboring human T cell lymphotropic virus type-1-infected Hodgkin-Reed-Sternberg (HRS)-like cells and small to medium CD4+ T cells, which histologically mimics classic Hodgkin lymphoma (CHL). CD30+ tumor cells or HRS cells are surrounded by CD4+ non-neoplastic T cells in a rosette-like manner in CHL. Interaction between HRS cells and surrounding CD4+ T cells is important for tumor microenvironment (TME) in CHL. Tumor microenvironment of Hodgkin-like ATLL remains unclear. Here, Digital Spatial Profiling was performed on Hodgkin-like ATLL to elucidate the interaction between HRS-like cells and CD4+ T cells in Hodgkin-like ATLL. We identified CD4+ T cells expressing co-stimulatory molecules, CD28 and inducible T cell co-stimulator (ICOS), in CD4+ T cells surrounding the HRS-like cells than in those apart from HRS-like cells. Immunohistochemistry was performed in 11 cases of Hodgkin-like ATLL, which detected distinct CD4+ T cells expressing CD28 in a rosette-like manner around HRS-like cells. HRS-like cells widely expressed CD80 and CD86, which suggested CD28-CD80/CD86 interaction was important in pathogenesis of Hodgkin-like ATLL. ICOS and immune checkpoint molecules, including T cell immunoreceptor with immunoglobulin and ITIM domain (TIGIT) and programmed death-1 (PD-1) were also variably expressed in CD4+ T cells surrounding HRS-like cells. Our findings provide new insights into the tumor microenvironment of Hodgkin-like ATLL and implicate a new therapeutic strategy targeting these molecules.

overall_design: Total 12 areas of interest from 4 Hodgkin-like ATLL were sequenced using GeoMx Digital Spatial Profiler (Nanostring Technologies), with the Human Whole Transcriptome Altas (18,000+ genes)

first: M

last: Takeuchi

first: H

last: Miyoshi

first: K


title: Identification of differentially expressed circRNAs in prostate cancer of different clinical stages by RNA sequencing

city: Nanchang

first: Xing

last: Wang

state: Jiangxi

address: No. 1 Minde Road

institute: The Second Affiliated Hospital of Nanchang University

summary:
Nine samples of prostate cancer and three samples of benign prostatic hyperplasia were selected (circRNA expression profiles were analyzed by circRNA-seq.
A total of 13047 circRNAs were identified in these tumor tissues, which were widely distributed in all chromosomes. Analysis of variance showed that prostate cancer was significantly dysregulated in 605 cases compared to BPH tissue (log2 (fold change) > 1, p < 0.05). Our study undoubtedly provide a new insight in investigating the initiation of prostate cancer.

overall_design: Identification of dysregulated circRNA between prostate cancer prostate tissue and benign prostatic hyperplasia tissue using circRNA-seq

first: Chiyu

last: Zhang

first: Ruizhen

last: Huang

first: Honglin

last: Hu


title: Thyroid hormone receptor agonist promotes hair growth in mice

first: Peiqiu

last: Zhu

address: Xishiku Street 8

department: Dermatology

institute: Peking University First Hospital

summary: We report the application of RNA-sequencing technology for topical application of the thyroid hormone receptor agonist (TDM10842) in murine skin tissue. Twenty-nine 8-week-old C3H mice were obtained, and randomly divided into 3 groups, after depilation, with topical use of TDM, Vehicle and Blank respectively. We found 857, 782, and 276 differentially expressed genes were identified from the skin tissue between 3 groups. Weighted correlation network analysis (WGCNA) was used to find clusters of highly correlated genes from the 3 groups. From which, we found one gene, Pclaf, as a differentially expressed gene compared with the other two groups. We scored their pathway activities. We found that signaling pathway of E2F TARGETS, G2M CHECKPOINT, MYC TARGET V1, HEDGEHOG SIGNALING, MYC TARGET V2, WNT BETA CATENIN SIGNALING, EPITHELIAL MESENCHYMAL TRANSITION, MITOTIC SPINDLE, UNFOLDED PROTEIN RESPONSE and DNA REPAIR were up regulated in the TDM group compared with the other 2 control groups.

overall_design: RNA-seq in mice skin tissue after topical application of the thyroid hormone receptor agonist.

first: Weiwei

last: Deng

first: Jin

last: Yu

first: Shuxia

last: Yang


title: KARR-seq reveals principles of high-order ribonucleoprotein structure assembly

city: Farmington

first: Youzhi

last: Cheng

state: Connecticut

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

summary: We designed KARR-seq, which reveals RNA-RNA interactions transcriptome-wide. The frequency of KARR-seq chimeras accurately reveals the physical distances between RNAs in vivo. Using KARR-seq, we systematically analyzed celullar effect on RNA-RNA interactions.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus
Vesicular stomatitis virus
Respiratory syncytial virus

overall_design: KARR-seq were performed in difference cell lines under normal or treatment conditions. Treatments include knocking down selective RBPs, adding tranlation inhibitors, adding arsenite stress, etc. KARR-seq for in vitro refolded RNA and intact nuclei were also perfromed.

first: Tong

last: Wu

first: Anthony

middle: Y


title: The transcriptome signature of the mouse brain after bulbectomy suggests a new model of Alzheimer’s disease with elements of major depression.

status: Public on Dec 05 2023

city: Moscow

first: Alexander

middle: Petrovich

last: Rezvykh

address: Obninsk, Zvyozdnaya st. 15 - 130

institute: EIMB

summary: In general, analysis of the functional significance of genes in the brain of OBX mice indicates that the balance of the GABA/glutamatergic systems is disturbed with hyperactivation of the latter, which leads to the development of excitotoxicity and induction of apoptosis on the background of severe mitochondrial dysfunction and astrogliosis. The synthesis of neurotrophic factors decreases, which leads to disruption of the cytoskeleton of neurons, an increase in the level of intracellular calcium, and activation of tau protein phosphorylation. The acetylcholinergic system is deficient on the background of hyperactivation of acetylcholinesterase. Importantly,  the activity of the dopaminergic, endorphin, and opiate systems decreases, and hormonal dysfunction develops. Genes associated with the regulation of circadian rhythms, cell migration, and impaired innate immunity are activated. All this occurs on the background of down-regulation of genes of ribosomal proteins. It is clear that OBX mice are a model of complex neuropathology with elements of Alzheimer's disease and major depression. This model with a certain degree of probability can be attributed to subtype B2 in humans.

overall_design: Single-end RNA-seq of dissected brain tissues from Sham-operated and bulbectomic mice

first: L

last: Chuvakova

first: A