title: How the AHR became important in cancer: The role of chronically active AHR in cancer aggression

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Sometimes biological research is an act of faith, a belief that untangling complex biologic interactions on a very basic level in-and-of itself eventually leads to larger and broader implications for human health. Indeed, sometimes focusing on the trees leads to a better view of the forest. This has been the case for the aryl hydrocarbon receptor (AHR). For decades, the AHR was studied for its role in environmental chemical toxicity i.e., as a quirk of nature and a mediator of unintended consequences of human pollution. During that period, it was not certain that the AHR had a “normal” physiological function. However, the ongoing accumulation of data from an ever-expanding variety of studies on cancer, cancer immunity, autoimmunity, organ development, and other areas bears witness to a staggering array of AHR-controlled normal and pathological activities. The objective of this review is to discuss how the AHR has gone from a likely contributor to genotoxic environmental carcinogen-induced cancer to a master regulator of malignant cell progression and cancer aggression. Particular focus was placed on the association between AHR activity and poor outcomes, feedback loops that control chronic AHR activity in cancer, and the role of chronically active AHR in driving cancer cell invasion, migration, cancer stem cell characteristics, and survival.

overall_design: The AHR knock-out (KO) in breast cancer cell lines (MDA-MB231 and SUM149) was generated by CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) gene editing. Each cell line includes Cas9 control and AHR KO with 3 biological replicates. RNA extraction and hybridization on Affymetrix microarrays were processed. The expression profiles between different groups were analyzed and compared.

first: Stefano

last: Monti

first: David

last: Sherr


title: Cardiomyocyte ST-wave depression indel characterisation

status: Public on Dec 11 2023

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Cardiomyocyte ST-wave depression indel characterisation (NuTi Capture-C)

summary: A rare mutation associated with familial ST-wave depression in ECG was predicted to generate a de novo enhancer. This mutation was generated heterozygously in iPSC lines to characterise it's molecular effects by ATAC-seq, Capture-C and RNA-seq

overall_design: NuTi Capture-C was performed on triplicates cardiomyocytes differentiated from IPSC with either WT or heterozygous (Mut) for the ST-wave depression associated indel. Capture was performed on multi-plexed libraries targeting either promoters or enhancers.

middle: J

first: Carin

last: de Villiers


title: CD4 T cell activating neoantigens enhance personalized cancer vaccine efficacy

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

country: USA

institute: University of Maryland, Baltimore

type: Expression profiling by high throughput sequencing

summary: Personalized cancer vaccines aim to activate and expand cytotoxic anti-tumor CD8+ T cells to recognize and kill tumor cells. However, the role of CD4+ T cell activation in the clinical benefit of these vaccines is not well defined. We previously established a personalized neoantigen vaccine (PancVAX) for the pancreatic cancer cell line Panc02, which activates tumor-specific CD8+ T cells but required combinatorial checkpoint modulators to achieve therapeutic efficacy. To determine the effects of neoantigen-specific CD4+ T cell activation, we generated a new vaccine (PancVAX2) targeting both MHCI- and MHCII-specific neoantigens. Tumor-bearing mice vaccinated with PancVAX2 had significantly improved control of tumor growth and long-term survival benefit without concurrent administration of checkpoint inhibitors. PancVAX2 significantly enhanced priming and recruitment of neoantigen-specific CD8+ T into the tumor with lower PD1 expression after reactivation compared to the CD8+ vaccine alone. Vaccine-induced neoantigen- specific Th1 CD4+ T cells in the tumor were associated with decreased T regulatory cells (Tregs). Consistent with this, PancVAX2 was associated with more pro-immune myeloid-derived suppressor cells and M1-like macrophages in the tumor demonstrating a less immunosuppressive tumor microenvironment. This study demonstrates the biological importance of prioritizing and including CD4 T cell-specific neoantigens for personalized cancer vaccine modalities.

overall_design: Subcutaneous Panc02 tumors were harvested from C57BL/6 mice treated with combinations of PancVAX neoantigen peptide vaccine, Anti-PD-1 antibody, and Anti-CTLA-4 antibody. Single cell suspensions were obtained from dissociated whole tumors and enrichment for immune cells by Percoll density separation and subjected to single-cell RNA-sequencing. Cell suspensions from multiple mice receiving the same treatment were pooled into one sample for library preparation. Samples that underwent immune cell enrichment were also subjected to paired single cell T cell receptor sequencing.

first: Jacob

middle: T

last: Mitchell

first: Neeha

last: Zaidi


title: Single-Cell Transcriptomic Analysis of Dental Pulp and Periodontal Ligament Stem Cells [scRNA-seq]

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

country: China

institute: Sun Yat-sen University

summary: In this study, we investigated the heterogeneity of DPSC and PDLSC cells using scRNA-seq and characterized the molecular features of each cell group. Combining the analyses of trajectory route and scoring, our results demonstrated that DPSCs displayed higher differentiation potentials, while PDLSCs exhibited more matured features. These findings provide a new insight into the complex landscape and functions of oral stem cells, which would enrich our understaning on their roles in embryonic development and regeneration of lost tissues due to dental and periodontal infections.

overall_design: In this study, we performed scRNA-seq of DPSCs and PDLSCs profiles to dissect their heterogeneity at the single cell level and characterized features of different cell populations, including expression profiles of featured genes and differentiation potentials, using state-of-the-art bioinformatics methods.

first: Di

last: Wu

first: Alpdogan

last: Kantarci


title: single cell RNA sequencing of mouse blood during acute pancreatitis and recovery

status: Public on Dec 10 2023

city: Fuzhou

first: Changgan

last: Chen

state: --- Select One ---

address: #29 Xinquan Road, Fuzhou 350001, People’s Republic of China

institute: Fujian Medical University Union Hospital

summary: Acute pancreatitis (AP) is an inflammatory disease with a mild to severe course, local and systemic complications, and a high mortality rate. Macrophage activation correlates with disease severity.Single cell RNA-sequencing was performed to identify inflammatory signals during AP and recovery using the blood from experimental AP model. We demonstrate that myeloid-ANXA1 expression is upregulated in peripheral blood during the initial phase of AP.

overall_design: AP was induced in mice by 7 intraperitoneal injections of cerulein (60 mg/kg).The first injection of cerulein starting at time 0 hours and blood samples were collected at 12 hours, 24 hours, and 168 hours.

first: Yu

last: Pan

first: Jiajing

last: Lin


title: Cardiomyocyte ST-wave depression indel characterisation (ATAC-seq)

overall_design: ATAC-seq was performed on cardiomyocytes differentiated from iPSC carrying the identified indel heterozygously to identify open chromatin sites.


title: Changes in DNA methylation in lung tissue after long-term supplementation with an increased dose of cholecalciferol

city: Kraków

first: Alicja

last: Wierzbicka

address: ul. Sarego 2

country: Poland

institute: National Research Institute of Animal Produstion

type: Methylation profiling by high throughput sequencing

summary: Maintaining an appropriate concentration of vitamin D is essential for the proper functioning of the body regardless of age. Nowadays, there are more and more indications that vitamin D supplementation at higher than standard doses may show protective and therapeutic effects. Our study identifies differences in the body's response to long-term supplementation of cholecalciferol at an increased dose. Two groups of pigs were used in the experiment. The first group received a standard dose of cholecalciferol (grower- 2000 and finisher- 1500 IU/kg feed), and the second group received an increased dose (grower- 3000 and finisher- 2500 IU/kg feed). The animals were slaughtered when they reached breeding maturity. Then the lung tissue was collected from the animals. The material was used for RRBS sequencing. Analysis of the methylation results showed that 2349 sites were altered. However, analysis of the results of enrichment analysis using KEGG database showed no significant effect on any biological pathway.

overall_design: Two groups of pigs were used in the experiment. The first group received a standard dose of cholecalciferol (grower- 2000 and finisher- 1500 IU/kg feed), and the second group received an increased dose (grower- 3000 and finisher- 2500 IU/kg feed). The animals were slaughtered when they reached breeding maturity. Then the lung tissue was collected from the animals. The material was used for RRBS and mRNA sequencing.

first: Ewelina

last: Semik-Gurgul

first: Maria

last: Oczkowicz

first: Tomasz

last: Szmatoła


title: Expression data of skeletal stem cells  from young mouse spines and femurs

city: Stanford

first: Malachia

last: Hoover

address: 265 Campus Drive Room G3105

institute: Stanford University

summary:
The spine is a remarkably specialized skeletal structure, exhibiting distinct anatomical phenotypes across different spinal regions.
With this understanding in mind, we hypothesized that skeletal stem cells (mSSCs) originating from various spinal regions (cervical, thoracic, and lumbar) might display varying genotypic signatures that may dictate their skeletal tissue formation and shape. We also analyzed femur SSCs as an additional control.

overall_design: Microarray gene expression profiling of mSSCs and mBCSPs from healthy newborn (post-natal day 3, P3), spinal regions (cervical, thoracic, and lumbar) and femur. Cervical, throracic and lumbar regions of postnatal day 3 (P3) mouse spines and femurs were dissected and subjected to mechanical and enzymatic (collagenase) digestion. The samples were then stainined with a panel of cell surface markers for FACS isolation of skeletal stem cells and their downstream progenitor, bone, cartilage, and stromal progenitors (BCSPs). Samples were then subjected to RNA extraction and hydridization on Affymetrix microarrays.


title: p21 Regulates Wnt-Notch Balance via DREAM/MMB/Rb-E2F1 and Maintains Intestinal Stem Cell Homeostasis

city: Kunming

first: Juhua

last: Dan

state: Yunnan

address: 727 South of Jingming Road

department: Medical School

institute: Kunming University of Science and Technology

summary: The crosstalk and balance regulation of Wnt-Notch have been known to be essential for cell fate decision and tissue regeneration, while how the balance is maintained and how the Wnt-Notch pathways are connected with the cell cycle regulation are still not clear. In the mouse model with accelerated aging phenotypes due to the loss of cell cycle inhibitor p21 function in Werner syndrome background, we observed the imbalance of Wnt-Notch signaling, along with the fast turnover of intestinal epithelia, which might cause the abnormal mobilization of stem cells, exhaust the stem cell reservoir, and result in the accelerated aging phenotypes. We revealed that the loss of p21 caused the shift of DREAM/Rb complex to MMB/E2F1 complex and the fast turnover of intestinal epithelia. Importantly, we identified the E2F1 as the transcriptional regulator for Notch1, which connected the p21-DREAM/MMB/Rb-E2F1 pathway with Wnt-Notch pathway. The overexpression of p21 rescued the imbalance of Wnt-Notch pathway. Our data identify p21 as an important factor in maintaining sequential mobilization, proliferation, and homeostasis of intestinal stem cells.

overall_design: To understand the molecular pathways altered after p21 deletion, we applied RNA-seq to the liver tissue of 3rd generation of TKO mice (G3 p21TKO, p21-/-mTR-/-Wrn-/-), which already showed progeroid symptoms. The G3 DKO mice (mTR-/-Wrn-/-) were used as control. The RNA-seq data was analyzed by ssGSEA (single sample gene set enrichment analysis) to get the differentially regulated pathways in response to the loss of p21 function.

first: Liangxia

last: Jiang

first: Jie

last: Tian

first: Jun

first: Ronggang

last: Luo

first: Yongjin

last: Zhang

first: Chihao

last: Shao

first: Bing

last: Guo

first: Xiaoming

first: Ying


title: An orthotopic syngeneic mouse model of bortezomib-resistant multiple myeloma

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

summary: RNA was extracted from myeloma cell lines which were made engraftable and resistant to bortezomib and the transcriptome was characterised using RNA sequencing.

overall_design: 5TGM1. wt cells were cultured in increasing doses of bortezomib (Selleck Chemicals, Houston, TX), until they could be cultured in 20nM bortezomib (5TGM1 .BR). The engraftable bortezomib-resistant 5TGM1 (5TGM1.BRE) cells came from C57BL/KaLwRij mice bone marrow which were routinely cultured in 10nM bortezomib. Both Bortezomib resistant cell lines were removed from proteasome inhibitor for at least 72h before use in experiments. RNA was extracted from 1x10^7 cells per sample using the Qiagen RNeasy mini kit and RNA-seq was performed.

first: Manjun

last: Li


title: In Vivo Protein Turnover Rates in Varying Oxygen Tensions Nominate MYBBP1A as a Novel Mediator of the Hyperoxia Response

city: San Francisco

first: Xuewen

last: Chen

state: CA

address: 1650 Owens Street

institute: Gladstone Institutes

summary: Oxygen deprivation and excess are both toxic to mammals. Thus, the body’s ability to adapt to varying oxygen tensions is critical for survival. While the transcriptional response to acute hypoxia has been well-studied, the post-translational effects of hypoxia and hyperoxia have been underexplored. In this study, we systematically investigate protein turnover rates in mouse heart, lung, and brain under different inhaled oxygen tensions. We find that the lung proteome is the most responsive to changes in oxygen tension, likely due to the direct exposure of alveoli to inhaled oxygen. In particular, several extracellular matrix (ECM) proteins such as collagens and laminins, are stabilized in the lung under both hypoxia and hyperoxia, suggesting their post-translational regulation. Furthermore, we validate our previous finding that complex 1 of the electron transport chain (ETC) is destabilized in hyperoxia, explaining the exacerbation of associated disease models by hyperoxia and rescue by hypoxia. Moreover, we nominate MYBBP1A as a novel transcriptional regulator in hyperoxic lung, particularly in the context of rRNA homeostasis. Overall, our study highlights the importance of the effects of oxygen tensions on protein turnover rates and identifies novel tissue-specific mediators of oxygen-dependent responses.

overall_design: The WT C57BL/6J mice were exposed to 21% or 80% oxygen for 5 days. Lung tissues were collected for 3' RNAseq (Quant-seq).

first: Isha

last: Jain


title: Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development [4C-Seq]

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

country: Spain

institute: IBiS, Universidad de Sevilla-CSIC

summary: Retinoic acid (RA) functions as a ligand for the nuclear RA receptors (RARs), which regulate the expression of target genes by binding to RA response elements. RA signaling is required for multiple processes during chordate embryonic development, such as body axis extension, hindbrain antero-posterior patterning and forelimb bud initiation. Although some RA target genes have been identified, little is known about the genome-wide effects of RA signaling during in vivo embryonic development. Here we stimulate the RA pathway during development by treating zebrafish embryos with all-trans-RA (atRA), the most abundant form of RA, and use a combination of RNA-seq, ATAC-seq, ChIP-seq and HiChIP to gain insight into the molecular mechanisms by which RA signaling control target gene expression. We find that RA signaling is involved in anterior/posterior patterning and development of the central nervous system, participating in the transition from pluripotency to differentiation. atRA treatment also induces alterations in chromatin accessibility during early development and promotes chromatin binding of RARaa and the RA targets Hoxb1b, Meis2b and Sox3, which cooperate in central nervous system development. Finally, we show that RA induces a rewiring of chromatin architecture, with alterations in chromatin 3D interactions that are consistent with target gene expression. This is illustrated by the specific induction of anterior HoxB genes by RARs, among other examples. Altogether, our findings identify genome-wide targets of RA signaling during embryonic development and provide a molecular mechanism by which developmental signaling pathways regulate the expression of target genes by altering chromatin topology.

overall_design: 4C-seq in wild-type zebrafish whole embryos, at developmental stage 80% epiboly, with and without treatment with 0.1µM all-trans retinoic acid (atRA)

first: Marta

last: Moreno-Oñate

first: Lourdes

last: Gallardo-Fuentes

first: Pedro

middle: M

last: Martínez-García

first: Silvia

last: Naranjo

first: Sandra

last: Jiménez-Gancedo

middle: L

last: Gómez-Skarmeta

first: Juan

last: Tena


title: Transcriptomic profiling of fibro/adipogenic progenitors treated by Musclin in vitro at early timepoint

status: Public on Dec 09 2023

city: Chengdu

first: Xia

last: Kang

address: Rongdu Avenue, #270

institute: General Hospital of Western Theater Command

summary: The aim of this study is to explore the molecular mechanism on how Musclin regulates the biological process of fibro/adipogenic progenitors.

overall_design: RNA-Seq of fibro/adipogenic progenitors treated by Musclin or vehicle for 24 hours in vitro

first: Jin

last: Qian

first: Hong-ming

last: Miao


title: Transcriptomic profile of CD31 and Griffonia simplicifolia isolectin B4 positive pulmonary artery endothelial cells isolated from a rat model of monocrotaline pulmonary arterial hypertension vs. control

first: Bradley

last: Maron

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham & Women's Hospital

summary: Sprague Dawley rats were treated with monocrotaline 60 mg/kg by intraperitoneal injection or vehicle control on day 0. On day 23, animals were sacrificed and pulmonary artery endothelial cells (PAECs) were isolated for transcriptomic analysis.

overall_design: To isolate rat PAECs, lung tissue was excised, enzymatically digested, and the resulting single cell suspension was subjected to immunomagnetic bead selection for CD31. CD31+ cells were subjected to a second sorting step using Griffonia simplicifolia isolectin B4 (GS-IB4) and a different CD31 antibody via fluorescence activated cell sorting. GS-IB4+/CD31+ intact cells were analyzed with RNA sequencing to identify differentially expressed genes between monocrotaline PAH and control. For details of experimental design, please see Wertheim BM et al., PLoS One, 2019;14(2):e0211909.

last: Wertheim


title: Gene expression profiles of glioblastoma tumorspheres cultured in diverse platforms

city: Seoul

first: Junseong

last: Park

address: 222 Banpo-daero, Seocho-gu

department: Cancer Evolution Research Center

country: South Korea

institute: The Catholic University of Korea

summary: We studied five patients with IDH1 wild-type glioblastoma who were newly diagnosed with no treatment history via surgery, chemotherapy, or radiotherapy. Patient-derived glioblastoma tumorspheres (TSs) were established from fresh tissue specimens, and they were cultured in divserse platforms.

overall_design: Gene expression profiles of five glioblastoma tumorspheres cultured in diverse platforms (collagen, normal ECM, tumor ECM, and mouse xenograft)

first: Seok-Gu


title: Individual Variability in Human Cell Type Transcriptomes and Epigenomes [YM3B]

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Diversity and individual variability are essential to human cognitive function. Identifying the conserved and variable (epi)genomic signatures of the brain’s cellular components is critical for understanding the neurobiological basis of individual variation in brain function.  We applied single nucleus methylome and transcriptome sequence (snmCT-seq) to neurons from the frontal cortex of 11 adult human donors spanning a range of ages from 23 to 74, including males and females (Broadmann Area BA46). We clustered cells into brain cell types based on methylation features. We then examined the transcriptome and epigenome features in each cell type between and within individual donors. Taking advantage of the multimodal measurements in single cells, we also identified the relation between RNA expression and methylation level.These data with multiomics measurement from donors with sex and age diversity aims to approach the dimension of inter-individual variability.

overall_design: We apply snmCT-seq to identify the transcriptomic and epigenomic features of neurons from individual adult human frontal cortex, including 3 aged male donors (age range 70-71), 3 aged female donors (71-74 years old), 3 young male donors  (25 years old) and 2 young female donors  (23-30 years old). For each donor, 2 chunks of brain tissue were collected and processed separately, to assess within-donor variability. Data in this series was from  chunk B of a 25 years old male.

first: Jofan

last: Chien

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Rosa

last: Castanon

last: Nery

first: Bang-An

last: Wang

first: Nick

last: Johnson

first: Julia

last: Osteen

first: M

last: Behrens

first: Eran

middle: A

last: Mukamel


title: Multiple myeloma and health individuals  exosomal miRNAs expression profiling

city: changsha

first: XIN

last: CHEN

state: None Selected

address: Department of Hematology, the Third Xiangya Hospital of Central South University, Changsha, China

type: Non-coding RNA profiling by high throughput sequencing

summary: Multiple myeloma (MM) is a hematopoietic malignancy. Based on its laboratory and clinical presentation, it can be categorized as MGUS, smoldering myeloma, and multiple myeloma. Previous studies have indicated that the expression levels of miRNAs differ across various stages of the disease, and exosomes are involved in modulating the progression and metastasis of cancers through miRNAs. This study aims to analyze the expression levels of miRNAs in the serum exosomes of healthy individuals and those with myeloma bone marrow.

overall_design: BM samples were obtained from 7 MM patients and 3 healthy individuals .The exosomes from bone marrow were isolated by ultracentrifugation. Exosomal miRNA profiling was sequencing on Illumina NextSeq 500.

first: Xin

last: Chen

first: Liwen

first: Qian

last: Cheng

last: Li


title: Genetic changes of Hep3B cells with acquired resistance to sorafenib after STIM1 knockout

city: Chongqing

first: Ran

last: Ren

address: Shazheng Street

institute: Chongqing University

summary: In order to explore the role of STIM1 in the acquired resistance of Hep3B cells to sorafenib, we used CRISPR Cas9 technology to knock out STIM1.

overall_design: Comparative gene expression profile analysis of RNA-seq data from wildtype Hep3B SR cells and STIM1 knockout Hep3B SR cells.

first: Yongsheng


title: Genetic changes of Hep3B cells after acquired resistance to sorafenib

summary: In order to explore the genetic changes of Hep3B cells after resistance to sorafenib, we used a dose-increasing method to obtain drug-resistant cell lines from parental Hep3B cells by intermittent stimulation with sorafenib.

overall_design: Comparative gene expression profile analysis of RNA-seq data from Hep3B parental cells and their sorafenib acquired resistance cells.


title: Telomere shortening in hiPSCs results in neuronal and astrocyte aging

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

summary: Telomerase reverse transcriptase (TERT) plays a crucial role in maintaining telomere length, which are specialised protective caps at the end of chromosomes. The lack of in vitro aging models, particularly for the central nervous system (CNS), has impeded progress in understanding aging and age-associated neurodegenerative diseases. In this study, we aimed to explore the possibility of accelerating aging in vitro using hiPSC (human induced pluripotent stem cell) technology. To achieve this, we utilised CRISPR/Cas9 to generate TERT loss-of-function hiPSCs, resulting in a loss of telomerase function and shortened telomeres. Through directed differentiation, we generated motor neurons and astrocytes to investigate whether telomere shortening could lead to age-associated phenotypes in CNS cell types.

overall_design: RNA-seq analysis of neural progenitor cells, astrocytes and motor neurons speciments obtained either from wild type human induced pluripotent stem cells (hiPSC) or from hi PSCs with TERT loss-of-function generated via the CRISPR/Cas9 technology.

first: Munirah

last: Santosa

first: Jasmine

last: Harley

middle: V

first: Shi-Yan

last: Ng


title: The lysine acetyltransferase KAT6A epigenetically facilitates glucose metabolic programming and CD4+ T-cell responses in autoimmunity

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

summary: Epigenetic programs are pivotal regulators of effector CD4+ T cells and determine the fate of many autoimmune disorders. Here, we show that the acetyltransferase KAT6A acts as a novel regulator of glucose metabolism that is required for the proliferation and effector functions of CD4+ T cells in autoimmunity. Clinical analysis shows that KAT6A in CD4+ T cells is linked to the progression of autoimmune Sjogren’s syndrome (SS) . Conditional knockout of KAT6A inhibits the proliferation and Th1/Th17 effector functions of CD4+ T cells both in vitro and that KAT6A-cKO CD4+T cells are less susceptible to induce adjuvant-immunized experimental autoimmune encephalomyelitis (EAE), autoimmune colitis and experimental SS. Combination of metabolomic, epigenetic and transcriptomic analyses show that KAT6A maintains abundant acetylation of H3K9ac and H3K27ac sites of several glycolytic genes, which in turn disrupts the transcriptional activation of MYC and HIF-1α, and potentiates the metabolic programming of glycolysis through its enzymatic amino acid points. Treatment with KAT6A small-molecule inhibitors in various autoimmune mice models shows high therapeutic value for targeting KAT6A to the treatment of autoimmune disorders. Our study reveals a critical role for KAT6A in autoimmunity via the epigenetic modification of glucose metabolic reprogramming and the effector response of CD4+ T cells.

overall_design: The design of this experiment is to interrogate the role of Lysince acetyltransferase, namely Kat6a, to the H3K9ac and H3K27ac abundance at the chromosome of CD4+T cells. Briefly, CD4+T cells from littermate WT mice and conditional knock-out (Kat6afl/flCD4Cre+) mice were magnetically sorted, and then cultured in a 6-well plate at the concentration of 1*10^7 cells per plate. Cells were stimulated with anti-CD3/CD28 and cultured for 48 hrs. Then, ChIP-seq were performed and the following Raw data were produced.

first: Jiayao

last: Fu


title: Intrinsic epigenetic state of primary osteosarcoma drives metastasis [RNA-seq]

city: Bryan

first: Irtisha

last: Singh

state: Texas

address: 8447 Riverside Pkwy

department: Cell Biology and Genetics

institute: Texas A&M University Health Science Center

summary: Osteosarcoma (OS) is a primary malignant bone tumor commonly affecting children, adolescents, and young adults with a potential to metastasize to distal sites, most commonly lung. Here, we mapped the active chromatin landscapes of OS patients with varying extent of disease. We integrated histone H3 lysine acetylated chromatin (H3K27ac) profiles (n=13), chromatin accessibility profiles (n=11) and gene expression (n=13) of OS tumors from four different diseased states to understand the differences in their active chromatin profiles and its impact on molecular mechanisms driving the malignant phenotypes. Primary tumors that undergo metastasis (primary mets) have a distinct enhancer landscape compared to primary tumors that remain localized (localized) during the course of disease. The difference in chromatin activity shapes the transcriptional profile of OS patients. Some of the genes like PPP1R1B, PREX1 and IGF2BP1 whose role in OS pathogenesis and metastasis remains poorly understood, exhibit increased enhancer activity in primary mets along with higher RNA levels. Genome-wide loss-of-function screens also reveal these genes to be as selective dependencies in bone sarcomas, making them promising candidates for further investigation. Overall, differential chromatin activity in primary mets occurs in proximity of genes regulating actin cytoskeleton organization, cellular adhesion, and migration process suggestive of their role in facilitating OS metastasis. Thus, this data demonstrates that metastatic potential is intrinsically present in primary mets OS much before the occurrence of metastasis and when the cells are presented with favorable conditions to migrate and colonize at a distant site, they under undergo metastasis.

overall_design: Comparison of gene expression of osteosarcoma tumors from four different diseased states (primary met, lung met, localized, and local control) to be integrated with histone H3K27ac profiles and the chromatin accessibility profiles to understand the differences in their active chromatin profiles and its impact on molecular mechanisms driving malignant phenotypes

first: Nino

last: Rainusso

first: Lyazat

last: Kurenbekova

first: Abhinaya

last: Muruganandham

first: Jason

last: Yustein


title: In-vivo nerve stimulation of mice and rats

city: Gainesville

first: Mark

middle: Robert

last: Viggars

state: Alachua

address: University of Florida, M531

department: Physiology & Aging

institute: University of Florida

summary:
Investigating acute exercise response over time in mice and rats
Gene expression profiling of mice and rats (different training status), 1 hour after an acute exercise bout.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Implanted stimulators programmed via bluetooth were used to deliver daily training, or once every 3 days for various lengths of time.

first: Jonathan

middle: C

last: Jarvis


title: Intrinsic properties of MWCNT affect immunotoxicity in THP-1 in vitro model

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: The immunomodulatory effects seen with exposure to multiwalled carbon nanotubes (MWCNTs) are key events in the progression to pathological outcomes. Therefore, the study of MWCNT induced immunotoxicity is crucial in determining risks posed to human health.   MWCNT exposure most commonly occurs via airways, where macrophages are first line responders. Here we exploit an in vitro assay, measuring dose-dependent secretion of a wide panel of cytokines secreted from THP-1 macrophages, as a measure of immunotoxicity following the non-lethal, multi-dose exposure (IC5, IC10 and IC20) to 7 MWCNTs with different intrinsic properties. We find that an underlying tangled structure, and small aspect ratio are key properties predicting MWCNT induced immunotoxicity, mediated predominantly by IL1β cytokine secretion. To assess the mechanism of action giving rise to MWCNT immunotoxicity, a transcriptomics analysis was linked to cytokine secretion in a multilayer model established through correlation across exposure concentrations and time points. This reinforced the finding that tangled MWCNTs have greater immunomodulatory potency, displaying enrichment of immune system, signal transduction and pattern recognition associated pathways. Together our results further elucidate how structure, length and aspect ratio; critical intrinsic properties of MWCNTs, are tied to immunotoxicity.

overall_design:
The gene expression profiles of THP-1 macrophages exposed to three concentrations (IC5, IC10 and IC20) of  multi-walled carbon nanotubes were profiled at 24 hours. Each concentration had three biological replicates, while only two untreated negative controls from the same plate as the exposures were used.
Contributor: Saarimäki

first: V

last: Hautanen

first: J

last: Morikka

first: A

last: Serra

last: Bisenberger

first: T

last: Toimela

first: D


title: Expression profiles of plasma transfer RNA-derived small RNAs in patients with pathological cardiac hypertrophy

city: Suzhou

first: jingyi

last: xu

state: Jiangsu

address: No. 242, Guangji Road, Suzhou City

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

summary: Aim: To clarify the expression profile of transfer RNA-derived small RNAs (tsRNAs) and disclose the putative role in the pathogenesis of pathological cardiac hypertrophy (PCH). Materials & methods: Small RNA sequencing was conducted in four pairs plasma from PCH patients and healthy volunteers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for four pairs plasma from PCH patients and healthy volunteers.

first: Kangyun

last: Sun

first: Yuan

last: Li

first: Jingyi

last: Xu

first: Buyun

last: Qian

first: Feng

last: Wang


title: Transcriptomic analysis of radiation-induced neuroendocrine-like cells in prostate cancer

city: West Lafayette

first: Chang-Deng

last: Hu

state: IN

address: 201 S. University St, Hansen Life Sciences Building, Room 401A

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

summary: The main goal of this study is to identify DEGs in radiation-induced NE-like cells

overall_design: mRNA profilles of LNCaP cells treated with cumutative dose of 40 Gy of FIR and untreated LNCaP cells

first: Jake

last: Owens

first: Elena

last: Beketova

first: Sheng

last: Liu

first: Qi

last: Shen

first: Jogendra

middle: S

last: Pawar

first: Andrew

last: Asberry

first: Jie

last: Yang

first: Xuehong

last: Deng

first: Bennett

middle: D

last: Elzey

first: Timothy

last: Ratliff

first: Liang

last: Cheng

first: Richard

last: Choo

first: Jiaoti

last: Huang

first: Chenglong

first: Jun

last: Wan


title: Aberrant centrosome biogenesis disrupts nephron and collecting duct progenitor growth and fate resulting in fibrocystic kidney disease

status: Public on Dec 08 2023

city: Saint Louis

first: Tao

state: MO

address: MSB Room 880M, Nephrology Division,425 South Euclid Ave, Box 8126, St Louis, MO  63110

institute: Washington University in St. Louis

summary: Mutations that disrupt centrosome biogenesis or function cause congenital kidney developmental defects and fibrocystic pathologies. Yet, how centrosome dysfunction results in the kidney disease phenotypes remains unknown. Here, we examined the consequences of conditional knockout of the ciliopathy gene Cep120, essential for centrosome duplication, in the nephron and collecting duct progenitor niches of the mouse embryonic kidney. Cep120 loss led to reduced abundance of both cap mesenchyme and ureteric bud populations, due to a combination of delayed mitosis, increased apoptosis, and premature differentiation of progenitor cells. These defects resulted in dysplastic kidneys at birth, which rapidly formed cysts, displayed increased interstitial fibrosis, and decline in kidney function. RNA sequencing of embryonic and postnatal kidneys from Cep120-null mice identified changes in pathways essential for development, fibrosis, and cystogenesis. Our study defines the cellular and developmental defects caused by centrosome dysfunction during kidney morphogenesis, and identifies new therapeutic targets for patients with renal centrosomopathies.

overall_design: Refer to individual Series


title: An IL-2 mutein increases IL-10 and CTLA-4-dependent suppression of dendritic cells by regulatory T cells [RNA-seq]

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Interleukin-2 (IL-2) variants with increased CD25 dependence that selectively expand Foxp3+ regulatory T (TR) cells are in clinical trials for treating inflammatory diseases. Using an Fc-fused IL-2 mutein (Fc.IL-2 mutein) we developed that prevents diabetes in non-obese diabetic (NOD) mice, we show that Fc.IL-2 mutein induced an activated TR population with elevated proliferation, a transcriptional program associated with Stat5- and TCR-dependent gene modules, and high IL-10 and CTLA-4 expression. Increased IL-10 signaling limited surface MHC class II upregulation during conventional dendritic cell (cDC) maturation, while increased CTLA-4-dependent transendocytosis led to the transfer of CD80 and CD86 costimulatory ligands from maturing cDCs to TR cells.  In NOD mice, Fc.IL-2 mutein treatment promoted the suppression of cDCs in the inflamed pancreas and pancreatic lymph nodes resulting in T cell anergy. Thus, IL-2 mutein-expanded TR cells have enhanced functional properties and restrict cDC function, offering promise for targeted immunotherapy use in autoimmune disease.

overall_design: Sorted cDC1 and cDC2s from mice were treated with IL2 mutein, Anti-IL2, or PBS as a negative control. Mice were also stimulated with either LPS or PBS as a control. Mice used in experiments were between 8 and 12 weeks of age.

first: Braxton

last: Jamison

first: Matthew

last: Lawrance

first: Chun

first: Hannah

last: DeBerg

first: David

last: Sansom

first: Marc

last: Gavin

first: Lucy

middle: K

last: Walker

first: Daniel

last: Campbell


title: Identification of SR34a direct RNA targets in germinated seeds grown for 44 hours and exposed or not to ABA for 2 hours

city: Oeiras

first: Tom

last: Laloum

address: Rua da Quinta Grande, 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

summary: Individual nucleotide crosslinking and immunoprecipitation (iCLIP2) of SR34a-GFP or control GFP from seeds germinated for 44 hours in continuous light and transferred to a control or ABA-containing medium during 2 hours.

overall_design: To investigate the RNA binding landscape of the Arabidopsis thaliana SR34a protein during early seedling establishment, we performed iCLIP2 experiments in germinated seeds expressing the SR34a-GFP or GFP alone (control) grown 44 hours in continuous light and transferred to a control or ABA-containing medium during 2 hours.

first: Martin

last: Lewinski

first: Tino

last: Köster

first: Dorothee

last: Staiger

first: Paula

last: Duque


title: RNA-seq analysis of paired Non-Hodgkin's lymphoma (NHL) tumor samples at pretreatment and after mosunetuzumab relapse coinciding with the loss of CD20 protein

city: Philadelphia

first: Andrei

last: Thomas-Tikhonenko

state: PA

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

summary: CD20 protein-negative diseases were observed for a subset of patients with B-NHL that relapsed after initial responses to mosunetuzumab. For many of these tumors, whole exome (WES) and RNA-seq failed to detect any MS4A1 genetic variants or loss of CD20 mRNA, which could have explained the apparent loss of CD20 protein. For this study, we obtained formalin-fixed paraffin-embedded (FFPE) tumor samples from a similar cohort of four additional patients relapsing after mosunetuzumab, and performed RNA-seq to look for changes in the splicing pattern of CD20.

overall_design: We performed RNA-seq analysis on FFPE tumor samples from 4 patients with B-NHL that have relapsed to mosunetuzumab. All four patients had paired pretreatment (“pre”) tumor samples that were CD20 positive by IHC and mosunetuzumab relapse (“post”) samples that had lost CD20 protein expression.

first: Zhiwei

last: Ang

first: Katharina

middle: E

last: Hayer


title: Gene expression at single cell level in human umbilical cord blood cells enriched for hematopoietic stem cells and cultured in conditions that maintain HSCs ex vivo.

first: Peter

last: Klein

address: 3400 Civic Center Blvd

institute: University of Pennsylvania School of Medicine

summary: The capacity for self-renewal of human hematopoietic stem cells (HSCs) is lost upon typical culture conditions, which often include high levels of multiple hematopoietic cytokines, serum, and/or support cells. We found that culture of HSCs in CR medium (basal culture medium with inhibitors of GSK-3 (CHIR99021) and mTORC1 (Rapamycin) and no serum or cytokines) maintains self-renewal in human HSCs for at least 7 days without loss of repopulating activity (Huang et al PMID 23142822). Here we performed single cell RNA-seq to determine transcriptomic changes associated with HSC maintenance in CR. We compared a population of freshly isolated human hematopoietic cells enriched for HSCs (CD34+CD38-CD45RA-CD90+) to cells cultured for 2 days in basal medium (vehicle control), CR, and CR and low dose cytokines (CRCY). The data show that, compared to Day 0 uncultured cells, the HSC pool is maintained when CR is included (CR or CRCY medium) but not in the vehicle control. The most highly enriched transcript in the HSC population was the chaperone/UPR sensor GRP78/HSPA5. This population was also highly enriched for immediate early response genes and components of the AP-1 complex (FOS and JUN family transcription factors) which mediate the immediate early response to stress.

overall_design: Human umbilical cord blood CD34+ cells (StemCell Technologies, mixed donor, cat# 70008, lot# 1901310270) were sorted for CD34+CD38-CD45RA-CD90+ cells, which enriches for hematopoietic stem cells (HSCs). Sorted cells were cultured with vehicle (DMSO), 3 µM CHIR99021 + 5 nM Rapamycin (CR), or CR with low dose cytokines (CRCY) for 2 days and were then collected for single cell RNA-seq using the 10XGenomics platform. Freshly thawed CD34+ cells from the same pool of donors (Day 0) were sorted and subjected to single cell analysis in parallel (Day 0 control).

first: Chenchen

last: Li

first: Mai

last: Liu

first: Xiang

last: Yu

first: Dheeraj

last: Bhavanasi

first: Brian

last: Gregory


title: Microglial 25-hydroxycholesterol mediates neuroinflammation and neurodegeneration in a tauopathy mouse model.

city: St. Louis

first: Jason

last: Ulrich

address: 660 S Euclid

department: Neurology

institute: Washington University

summary: Alzheimer’s disease (AD) is characterized by amyloid plaques and neurofibrillary tangles in addition to neuroinflammation and changes in brain lipid metabolism. Recent findings have demonstrated that microglia are key drivers of neurodegeneration in tauopathy mouse models. A subset of microglia referred to as disease-associated microglia (DAM) display gene signatures signifying changes in proinflammatory signaling and lipid metabolism in mouse models of amyloid and tau pathology. Ch25h is a DAM gene encoding cholesterol 25-hydroxylase that produces 25-hydroxycholesterol (25HC), a known modulator of inflammation as well as lipid metabolism. However, whether Ch25h influences tau-mediated neuroinflammation and neurodegeneration is unknown. Here, we show that in the absence of Ch25h and 25HC there is strikingly reduced age-dependent neurodegeneration and neuroinflammation in the hippocampus and entorhinal/piriform cortex of PS19 mice which express the P301S mutant human tau transgene. Transcriptomic analyses of bulk hippocampal tissue and single nuclei revealed that Ch25h deficiency in PS19 mice strongly suppressed proinflammatory cytokine and chemokine signaling in microglia and restored sterol synthesis. Our results suggest a key role for Ch25h/25HC in potentiating proinflammatory signaling to promote tau-mediated neurodegeneration. Ch25h may represent a novel therapeutic target for primary tauopathies, AD, and other neuroinflammatory diseases.

overall_design: nuclei were isolated from hippocampal tissue of 6- and 9-month-old PS19 and PS19/Ch25h KO mice and 9-month-old WT mice

first: Anil

last: Cashikar

first: Danira

last: Toral


title: Amelioration of Tau and ApoE4-linked glial lipid accumulation and neurodegeneration with an LXR agonist

summary: Apolipoprotein E (APOE) is a strong genetic risk factor for late-onset Alzheimer’s disease (AD) with APOE4 increasing and APOE2 decreasing risk relative to APOE3. In the P301S mouse model of tauopathy, ApoE4 increases tau pathology and neurodegeneration when compared to ApoE3 or the absence of ApoE. However, the role of ApoE isoforms in regulating lipid metabolism in the setting of tauopathy is unknown. Here, by using targeted lipidomics coupled with histological analysis, we demonstrate that in P301S tau mice, ApoE4 strongly promotes glial lipid accumulation along with significant perturbations in cholesterol metabolism and lysosomal function. Increasing lipid efflux in glia via administration of the LXR agonist GW3965 reduces lipid droplet accumulation in primary E4 microglia in vitro and GW3965 or Abca1 overexpression strongly attenuates tau pathology, neurodegeneration, and synapse loss in P301S/ApoE4 mice. By immunostaining, bulk and snRNA sequencing, we demonstrate reductions in reactive astrocytes and microglia as well as significant changes in cholesterol biosynthesis and metabolism in glia of tauopathy mice in response to LXR activation. These data suggest that promoting efflux of glial lipids via Abca1 could serve as a therapeutic approach to ameliorate tau and ApoE4-linked neurodegeneration.

overall_design: nuclei were isolated from hippocampal tissue of 9.5 month old APOE4-KI mice or PS19/APOE4-KI mice treated with control or GW3965 diet from 6-9.5.months

first: David

last: Holtzman

first: Alexandra

last: Litvinchuk


title: Intrinsic epigenetic state of primary osteosarcoma drives metastasis [ATAC-seq]

first: Irtisha

last: Singh

overall_design: Comparison of the chromatin accessibility profiles of osteosarcoma tumors from four different diseased states (primary met, lung met, localized, and local control) integrated with gene expression and  histone H3K27ac profiles to understand the differences in their active chromatin profiles and its impact on molecular mechanisms driving malignant phenotypes

first: Nino

last: Rainusso

first: Lyazat

last: Kurenbekova

first: Abhinaya

last: Muruganandham

last: Yustein


title: Intrinsic epigenetic state of primary osteosarcoma drives metastasis [ChIP-seq]

overall_design: Comparison of histone H3K27ac profiles of osteosarcoma tumors from four different diseased states (primary met, lung met, localized, and local control) integrated with gene expression and the chromatin accessibility profiles to understand the differences in their active chromatin profiles and its impact on molecular mechanisms driving malignant phenotypes


title: Expression data from CaOV3 TET-On cell line with MYCN inducible expression.

city: Boston

first: Alex

last: Miranda Rodriguez

state: Massachusetts

address: 55 Fruit St.

department: Massachusetts General Hospital

institute: Harvard Medical School

summary:
High-grade serous ovarian cancer (HGSC) is a challenging disease, especially for patients with immunologically 'cold' tumors devoid of tumor-infiltrating lymphocytes (TIL). HGSC exhibits among the highest levels of MYCN transcriptional signature in human cancer, which is strongly linked to diminished features of anti-tumor immunity.
We used microarrays to identify genes potentially dysregulated by the oncogene N-MYC in HGSC cell lines.

overall_design: CaOV3 TET-On MYCN-GFP and GFP control cells were cultured in the presence or absence of 1 ug/ml of Doxycycline (DOX) and collected for RNA extraction and hybridization on Clariom S microarrays.

first: A

first: Swetansu

last: Pattnaik

first: Phineas

last: Hamilton

first: Brad

last: Nelson


title: Intrinsic epigenetic state of primary osteosarcoma drives metastasis.

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


title: Transcriptomic landscape of the Dorsal Root Ganglia (DRG) and the Sciatic Nerve (SN) in a mouse model of Paclitaxel-Induced Peripheral Neuropathy (PIPN)

city: Stony Brook

first: Adam

last: Master

state: NY

address: 101 Nicolls Rd

department: Department of Cancer Prevention

institute: The State University of New York

summary:
Extensive transcriptomic changes associated with paclitaxel-induced peripheral neuropathy in mice: Differential effects in dorsal root ganglia and the sciatic nerve
Background: Paclitaxel (Ptx)-induced peripheral neuropathy (PIPN), a common side effect of this anti-cancer drug, causes chronic pain reflecting the molecular changes in the dorsal root ganglion (DRG) of the sciatic nerve (SN). While the subcellular localization and spatio-temporal control of mRNA translation are critical to nerve function, little is known about the transcriptional landscapes of DRG and SN in PIPN.  Aim: Transcriptome-wide assessment of Ptx-induced changes in gene expression and mRNA distribution in DRG or SN. Methods: Gene expression microarray analysis of the subcellular transcriptomes of DRG and SN in normal and PIPN mice with Transcriptome Analysis Console followed by analysis with 11 pathway databases. Validation of selected results in cultured cells and animal tissues.  Results: In normal mice, transcripts were differentially distributed in DRG and SN. In PIPN, both the gene expression profile and the distribution of the transcripts between DRG and SN were changed compared to normal controls. Functional analysis of gene clusters confirmed changes in pathways known to be affected by Ptx including including cytoskeleton remodeling, cell cycle regulation, immune response and neuronal transmission, as well as less studied pathways such as fatty acid metabolism, Rho GTPases in Wnt signaling, G-protein signal transduction, mRNA splicing and editing. Although the expression and function of cytoskeleton genes is known to be disturbed by Ptx, we found actins, actinins and non-muscle myosins (actomyosin contractility cluster) to be overexpressed by Ptx and accumulated specifically in the SN. For instance, in PIPN, the normalized ratio of SN/DRG mRNA levels for Myh7, Myh2, Actn2, Acta2 and Actb was 32.4, 24.5, 21.9, 3.6 and 3.3 respectively. We also identified transcripts overexpressed and accumulated in PIPN DRGs, with the highest DRG/SN mRNA ratios found for ion channels (ratios in parentheses) SN10a, Kcnd1, Atp1a3, Kcnip3, SN11a, (10.3-21.2); neurotransmitter regulators Syt1, Gabbr2 (14.4, 13.2); fatty acid regulators: Fabp4, Adipoq (22.9, 4.8), some tubulins: Tubb3, Tubb4a, Tubb4b (9.15, 5.5, 2.0) as well as GPCR regulating proteins: Rasgrp1, Gnal, Olfr1098 (16.7, 7.6, 2.0). Furthermore, the  Wikipathways integrated with the Transcriptome Analysis Console revealed that GPCRs were the most significantly altered class of genes, predominantly downregulated by Ptx compared to Naive samples in the DRG (320 downregulated, 88 upregulated) and in the SN (469 downregulated, 74 upregulated). In contrast, the comparison of control Naive samples in the DRG versus SN showed minimal changes (21 downregulated, 5 upregulated). These changes were statistically significant with a p-value < 0.001 and a fold change of -2 > FC > 2.  Conclusion: Our results show that Ptx not only affects the gene expression but also the subcellular localization of transcripts kept in DRG bodies or over-transported to distal parts of Sciatic Nerve along the longest axon of the body. Cargo trafficking including RNA shuttles among nucleus- cytoplasm-axon terminal of nerves might be one of the most critical processes impaired in PIPN. These results might be used in the future to develop a potential therapeutic strategy focusing on normalization of axon cargo trafficking and PIPN prevention.

overall_design: In this study, we chose to use Clariom S Mouse Microarray technology due to its advantages such as standardization, reproducibility, the ability to profile the expression of known genes with approximately 22 probes per transcript, quick and robust analysis, and well-characterized sensitivity and dynamic range. We compared the transcriptomes of the dorsal root ganglia (DRG) and sciatic nerve (SN) in a mouse model of peripheral neuropathy. The groups in our study included DRG-Naive, DRG-Ptx, SN-Naive, and SN-Ptx, with each group consisting of three arrays. For the analysis of each microarray, RNA was isolated from six tissue samples, which included both right and left DRG or SN samples from three mice, resulting in the pooling of six tissue samples per microarray.

first: Liqun

last: Huang

first: Vasiliki

last: Tsirukis

first: Andrew

last: Loiacono

first: Amin

last: Khawja

first: Cameron

last: Takmil

first: Anna

last: Tsioulias

first: Robert

last: Honkanen

first: Basil

last: Rigas


title: ATF4 suppresses hepatocarcinogenesis by inducing SLC7A11 (xCT) to suppress stress-related ferroptosis

city: Shanghai

first: Feng

last: He

address: 1200 Cailun Road

institute: Shanghai University of Traditional Chinese Medicine

summary: The goal of this study is to provide the liver metabolic changes in the liver specific Atf4 knockout MUP-uPA (MUP-uPA/Atf4Δhep) mice and understand the function of ATF4 in the stressed liver

overall_design: RNAs were extracted from livers of 6 week-old Wild Type (Atf4F/F), Atf4Δhep, MUP-uPA/Atf4F/F, and MUP-uPA/Atf4Δhep for RNA-seq analysis.

first: Junlai

last: Liu

first: Randal

last: Kaufman

first: Benjamin

last: Yaden

first: Michael

last: Karin


title: Gene expression of Grx4 regulated strains in the Ustilago maydis FB2 background

city: Vancouver

first: James

last: Kronstad

state: BC

address: 2185 E Mall

department: Mircobiology and Immunology

country: Canada

institute: University of British Columbia

summary: Gene expression of FB2 wt in minimal medium with 2 percent arabinose or glucose after 24h of growth was compared with the conditional promoter regulated strain Pcrg1:grx4 (#55). Glucose is a repressor of this promoter while arabinose acts as inducer. Grx4 was initially pre-depleted during growth on MM with glucose over night. Afterwards cells were transferred to MM with either glucose or arabinose and cells were collected after 24h. 3 biological repeats were performed for each strain and each condition. Cells were flash frozen and used to isolate total RNA. RNA sequencing was done by Genewiz. DEG’s between wt and mutant for the different conditions were obtained. Iron regulated genes such as the high affinity uptake system and the siderophore system of Ustilago maydis were repressed in the Pcrg1:grx4 (#55) strain when grown in glucose. Expression of these genes were similar for wt and the conditional strain when grown in arabinose. Grx4 was identified as an essential gene in Ustilago maydis which regulates the iron regulon and related genes.

overall_design:
A conditional mutant of the Grx4 gene was constructed in Ustilago maydis and grown in minimal media with either 2% arabinose or 2% glucose. 3 biological replicates were included.
Samples were treated for 24 hours before isolating RNA and analysing differences in gene expression.

first: Sean

last: McCotter


title: USP2 inhibition prevents infection with ACE2- dependent coronaviruses in vitro and is protective against SARS-CoV-2 in mice

first: Fabin

last: Dang

address: 3 Blackfan Circle

institute: Beth Israel Deaconess Medical Center

summary: In this study, we identified USP2 as a physiological deubiquitinase of ACE2 and USP2 inhibition led to ACE2 protein destruction, thereby preventing infections of coronaviruses that reliant on ACE2

overall_design: RNA-seq study of lung samples derived from K18-hACE2 mice infected with SARS-CoV-2 (Wuhan strain) and subjected to the treatment of vehicle control or USP2 inhibitor ML364

first: Lei

last: Bai

first: Ke

last: Lan

first: Wenyi

last: Wei


title: An IL-2 mutein increases IL-10 and CTLA-4-dependent suppression of dendritic cells by regulatory T cells [10x scRNA-seq]

first: Stephanie

last: Osmond

summary: Interleukin-2 (IL-2) variants with increased CD25 dependence that selectively expand Foxp3+ regulatory T (TR) cells are under clinical investigation for treating autoimmune and inflammatory diseases. We previously described an Fc-fused CD25-biased IL-2 mutein (Fc.IL-2 mutein) that promotes TR expansion and prevents the onset of autoimmune diabetes in non-obese diabetic (NOD) mice; however, the effects of this treatment on TR function in vivo are unclear. Here we show that Fc.IL-2 mutein treatment induces an activated Foxp3+ TR population characterized by elevated proliferation, a unique transcriptional program associated with Stat5- and TCR-dependent gene modules, and high levels of the immunosuppressive molecules IL-10 and CTLA-4. Increased IL-10 receptor signaling limits the upregulation of surface MHC class II expression during conventional dendritic cell (cDC) maturation, while increased CTLA-4-dependent transendocytosis leads to the transfer of CD80 and CD86 costimulatory ligands from maturing cDCs to Tregs.  In NOD mice, Fc.IL-2 mutein treatment resulted in TR-mediated regulation of cDCs in the inflamed pancreas and draining lymph nodes accompanied by an increase in anergic T cells. Thus, we demonstrate that IL-2 mutein-expanded TR cells have enhanced functional properties and potently act to restrict cDC function in the target tissue and at the site of autoimmune induction, offering promising prospects for targeted immunotherapy.

overall_design: These data contain 10x Gene Expression and Feature Barcode (CITE-seq) data from mouse spleen sorted CD4+ T-cells samples from twelve samples. Each bam file corresponds to a single Pool of three mice. One mouse in each pool represented each treatment -- one IL-2 Mutein treated animal, one IL-2 WT treated animal, and a PBS control animal.

first: Braxton

last: Jamison

first: Matthew

middle: F

last: Lawrance

first: ChunJing

last: Wang

first: Vivian

middle: H

last: Gersuk

first: Hannah

last: Deberg

first: Marc

last: Gavin

first: Lucy

last: Walker

first: Daniel

last: Campbell


title: Aberrant centrosome biogenesis disrupts nephron and collecting duct progenitor growth and fate resulting in fibrocystic kidney disease [Embryonic]

first: Tao

last: Cheng

overall_design: To identify pathways that are disrupted upon centrosome loss that result in the dysplastic kidney phenotype, we performed transcriptional profiling of centrosome-less embryonic kidneys at the onset of the observed developmental defects. Since the Hoxb7-Cre transgene co-expresses GFP in the ureteric bud lineage, we isolated UB cells from Cep120 KO kidneys and WT control at E13.5 by FACS sorting, followed by bulk RNAseq analysis

first: Moe

last: Mahjoub


title: Aberrant centrosome biogenesis disrupts nephron and collecting duct progenitor growth and fate resulting in fibrocystic kidney disease [P15]

overall_design: to identify the pathways that cause the fibrotic and cystic disease phenotypes upon Cep120 loss, Kidneys were collected from Hoxb7-Cep120 KO and WT mice at P15; also, we compared the signaling pathways that are disrupted in cystic kidneys following Cep120 loss versus ciliary signaling (Pkd1-KO), using bulk RNA-seq analysis of kidneys isolated from Hoxb7-Pkd1 KO mice at P15


city: Basel

first: Ilya

last: Flyamer

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Trisomy is the presence of one extra copy of an entire chromosome or its part in a cell nucleus. In humans, autosomal trisomies are associated with severe developmental abnormalities leading to embryonic lethality, miscarriage or pronounced deviations of various organs and systems at birth. Trisomies are characterized by alterations in gene expression level not exclusively on the trisomic chromosome, but throughout the genome. Here, we applied high-throughput chromo-some conformation capture technique (Hi-C) to study chromatin 3D structure in human donor chorion cells carrying additional chromosome 13 (Patau syndrome), chromosome 16 (the most common trisomy), and in cultured fibroblasts with extra chromosome 18 (Edwards syndrome). The presence of extra chromosomes 13 and 16, but not 18, results in systematic changes of contact frequencies between small and large chromosomes. Analyzing the behavior of individual chro-mosomes, we determined that a limited number of chromosomes change their contact patterns stochastically in trisomic cells, and that it could be linked to LAD and gene content. We also found that genome regions which are more compacted in trisomic cells are significantly enriched in housekeeping genes that potentially suggest the decrease of chromatin accessibility and tran-scription level. These results provide a framework for understanding the mechanisms of pan-genome transcription dysregulation in trisomies in the context of chromatin spatial organi-zation.

overall_design:
high-throughput chromosome conformation capture technique (Hi-C) to study chromatin 3D structure in human donor chorion cells carrying additional chromosome 13 (Patau syndrome), chromosome 16 (the most common trisomy), and in cultured fibroblasts with extra chromosome 18 (Edwards syndrome).
Please note that processed data file generated from both samples (e.g. G and Y, I and II, a and b) is linked to the corresponding G, I, and a  sample records.


title: Wnt/β-catenin pathway and cell adhesion deregulation in CSDE1-related intellectual disability and autism spectrum disorders

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

summary: Based on a transcriptomic and functional approach, we performed ex-vivo studies on fibroblasts originated from a patient with Intellectual Disability and Autism Spectrum Disorders (ID-ASD) carrying a nonsense de novo mutation in CSDE1. The aim is to decipher the CSDE1-dependent biological pathways involved in the pathophysiology of ID-ASD. We identified the Wnt/β-catenin pathway and cell adhesion as two deregulated cellular pathways deregulated in the ID-ASD patient.

overall_design: We performed RNA-seq analysis on fibroblasts from the ID-ASD patient presenting a CSDE1 haploinsufficiency and compared them to three healthy individuals. By analysis of the gene expression , we identified the deregulated pathways in the patient's fibroblasts and confirmed the deregulation by specific cellular assays.

first: Irina

last: Giurgea

first: Elma

last: El Khouri


title: RNA-seq experiment of wild-type (WT) and sr34a-1 mutant germinated seeds grown for 44 hours and exposed or not to ABA for 2 hours.

first: Tom

last: Laloum

summary: Transcriptome profiles of wild-type (WT) and sr34a-1 mutant seeds germinated for 44 hours in continuous light and transferred to a control or ABA-containing medium during 2 hours.

overall_design: To investigate the function of SR34a in regulating gene expression and alternative splicing during Arabidopsis seedling establishment and ABA responses, we compared the transcriptomes of WT Col-0 and sr34a-1 mutant germinated seeds under control and in the presence of ABA

first: Guiomar

last: Martín

first: Paula

last: Duque


title: Effect of levamisole on conditionally immortalized human podocytes (cihPod)

city: Nijmegen

first: Susan

last: Veissi

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboudumc

summary:
We performed bulk RNA sequencing to investigate the molecular mechanism of levamisole in podocytes in vitro. We found that levamisole modulates the expression of various genes involved in actin cytoskeleton signaling in podocytes.
We then performed gene expression profiling analysis using data obtained from bulk RNA-seq of two conditions (cihPod compared to cihPod treated with 1 µM levamisole for 24 hours).

overall_design: We performed bulk RNA sequencing on cihPod (vehicle) and cihPod treated with levamisole 1 µM for 24 hours. The two conditions were compared to each other with 3 replicates per condition.

first: Bart

last: Smeets

first: Ans

last: van Wijk

first: Bert

last: van den Heuvel

first: Michiel

last: Schreuder


title: Direct long-read RNA sequencing of Raji cells

first: Andrei

last: Thomas-Tikhonenko

summary: To identify full-length cap-to-poly(A) mRNA isoforms of CD20 and rule out reverse transcription artifacts which are common in cDNA-seq approaches, long-read Oxford Nanopore direct RNA sequencing was performed on the Raji cell line.

overall_design: From whole Raji cells, total RNA was isolated using the Maxwell® RSC simplyRNA Cells Kit (Promega). 500ng of mRNA was isolated from total RNA using Dyna-beads mRNA DIRECT kit (Invitrogen) and used for direct RNA (SQK-RNA002, ONT) library preparation. Subsequently, each library was loaded into a Spot-ON Flow Cell R9 version (FLO-MIN106D, ONT) and sequenced in a MinION Mk1B device (ONT) for 48 hours. Raw Fast5 files were converted to fastq with guppy (v3.4.5)

first: Zhiwei

last: Ang

first: Katharina

last: Hayer


title: sr34a-1 mutant germinated seeds and exposure to ABA

overall_design: Refer to individual Series


title: Mitochondrial GpC and CpG DNA hypermethylation cause metabolic stress induced mitophagy and cholestophagy [RNA-seq]

city: Wilrijk

first: Claudia

last: Theys

state: Antwerpen (nl)

department: FBD

country: Belgium

institute: Universiteit Antwerpen

summary: Metabolic dysfunction associated steatotic liver disease (MASLD) is characterized by a constant accumulation of lipids in the liver. This lipotoxicity in the liver is associated with dysregulation of the first step in lipid catabolism called beta oxidation in the mitochondrial matrix, eventually leading to mitochondrial dysfunction. To evaluate possible involvement of mitochondrial DNA methylation in this lipid metabolic dysfunction we investigated the functional metabolic effects of mitochondrial overexpression of CpG (MSssI) and GpC (MCviPI) DNA methyltransferases in relation to gene expression and (mito)epigenetic signatures. Overall, the results show that mitochondrial GpC and to a lesser extent CpG methylation increase bile acid metabolic gene expression, inducing cholestasis by mito-nuclear epigenetic reprogramming. Moreover, increased expression of metabolic nuclear receptors in both MSssI and MCviPI cells promote mitochondrial swelling and induce basal overactivation of mitochondrial respiration which favours lipid accumulation and metabolic-stress induced mitophagy and autophagy stress responses. Altogether GpC and CpG mitochondrial induce a metabolic challenging environment that is similar to mitochondrial dysfunction in the progression of MASLD.

overall_design: mRNA profiles of GpC (MCviPI), CpG (MSssI) or GpC mutant (MCviPI_mutant) DNMT overexpressing cell lines, both untreated or after a 24h treatment with 1mM FFA

first: Ligia

last: Mateiu


title: Amelioration of Tau and ApoE4-linked glial lipid accumulation and neurodegeneration with an LXR agonist

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

overall_design: RNAseq was performed on hippocampal tissue of 9.5 month old APOE4-KI mice or PS19/APOE4-KI mice treated with control or GW3965 diet from 6-9.5.months

first: David

last: Holtzman

first: Alexandra

last: Litvinchuk

first: Jason

last: Ulrich


title: Mitochondrial GpC and CpG DNA hypermethylation cause metabolic stress induced mitophagy and cholestophagy

type: Methylation profiling by genome tiling array

overall_design: methylation profiles of GpC (MCviPI) or GpC mutant (MCviPI_mutant) DNMT overexpressing cell lines, both untreated or after a 24h treatment with 1mM FFA

first: Anne

last: Scheepers

first: Joe

last: Ibrahim


title: Antitumor drug-induced cellular senescence in breast cancer cells

city: Kyoto

first: Wei

last: Li

address: 54 Shogoin-kawaharacho

department: Breast surgery

country: Japan

institute: Kyoto university

summary: To explore the mechanisms of transcriptomic profile changes in doxorubicin- and abemaciclib-induced senescent breast cancer cells.

overall_design: RNA-seq was derived from therapy-challenged cells for 96 h at Doxorubicin-100 nM and Abemaciclib-500 nM compared with control cells.

first: Sunao

last: Tanaka

first: Chenfeng

last: He

first: Yurina

last: Maeshima

first: Eiji

last: Suzuki

first: Masakazu

last: Toi

first: Kosuke

last: Kawaguchi


title: Changes in the chromatin accessibility  landscape of mouse embryonic endocardial cells after Notch pathway manipulation

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: Analysis by ATAC-seq of the changes in chromatin accessibility in MEEC due to the activity of Notch ligands.

overall_design: ATAC-seq in MEEC co-cultured 1) with OP9, OP9-Dll4 and OP9-Jag1 cells for 6 hours, 2) with OP9, OP9-Dll4 and OP9-Jag1 cells for 24 hours, 3) with OP9 + DMSO and OP9 + RO4929097 for 6 hours

first: Luis

last: Luna-Zurita

first: José


title: Non-coding RNA analysis in IgM monoclonal gammopathies: an underrecognized role of microRNA and long non-coding RNA differentiating Waldenström macroglobulinemia from IgM-MGUS

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

summary: Waldenström macroglobulinemia (WM), is a rare non-Hodgkin lymphoma preceded by a clinically asymptomatic benign monoclonal gammopathy of undetermined significance (IgM-MGUS). The factors underlying the malignant progression between these two IgM-monoclonal gammopathies remain poorly understood. The non-coding genome is increasingly recognized as an important driver of disease pathogenesis, and there remains a lack of exploration of the influence of non-coding RNAs within the IgM-monoclonal gammopathy disease spectrum. The present study explores the role of microRNA (miRNA) and long non-coded RNA (lncRNA) in IgM-gammopathies and specifically elucidates potentially regulated protein-coding genes and pathways. A comprehensive analysis of miRNA, lncRNA and protein-coding coding genes was conducted on 28 subjects, 17 patients with WM, 6 patients with IgM-MGUS, and 5 normal controls. Differential expression analysis revealed a number of dysregulated miRNA and lncRNA between IgM-gammopathies compared to normal controls and specifically between IgM-MGUS and WM. Pathway analysis was conducted utilizing differentially expressed mRNA with correlated biological expression of targeting miRNA. Here, a number of pathways were implicated influencing a gamut of cellular functions, including cell signaling, metabolism, replication, and immune regulation in both WM compared to IgM-MGUS and IgM-gammopathies compared to controls. This report is additionally one of the first published analyses of lncRNAs in WM, where we demonstrate a number of lncRNA associated with transcription and apoptosis regulation genes in WM compared to IgM-MGUS. This study highlights the role of non-coding RNA in IgM-gammopathies and the potential to recognize novel targets which may halt or slow the malignant progression between these two diseases.

overall_design: The study included samples from 28 subjects, 17 patients with WM, 6 patients with IgM-MGUS, and 5 normal controls. Bone marrow samples were collected and selection for CD19+ and/or CD138+ B cells was performed. mRNA and miRNA analyses were peformed on the isolated cells.

first: Stephen

last: Ansell

first: Jonas

last: Paludo

first: Karan

last: Chohan


title: Comparing malignant monocytosis across the updated WHO and ICC classifications of 2022

status: Public on Dec 07 2023

city: Munich

first: Stephan

last: Hutter

address: Max-Lebsche-Platz 31

country: Germany

institute: MLL Munich Leukemia Laboratory

summary: The World Health Organization Classification of Hematolymphoid Tumors (WHO) and the International Consensus Classification (ICC) of 2022 introduced major changes to the definition of CMML. To assess qualitative and quantitative implications for patient care, we started with 3,311 established CMML cases (according to WHO 2017 criteria) and included also 2,130 oligomonocytosis cases fulfilling the new CMML diagnostic criteria. Applying both classification systems from 2022, 356 and 241 of oligomonocytosis cases were newly classified as myelodysplastic (MD)-CMML (WHO and ICC 2022, respectively), most of which were diagnosed as MDS according to WHO 2017. Importantly, 1.5 times more oligomonocytosis cases were classified as CMML according to WHO 2022 than based on ICC, due to different diagnostic criteria. Genetic analyses of the newly classified CMML cases showed a distinct mutational profile with strong enrichment of MDS-typical alterations, resulting in a transcriptional subgroup separated from established MD- and myeloproliferative (MP)-CMML. Despite a different cytogenetic, molecular, immunophenotypic, and transcriptional landscape, no differences in overall survival were found between newly classified and established MD-CMML cases. To the best of our knowledge, this study represents the most comprehensive analysis of routine CMML cases to date, both in terms of clinical characterization and transcriptomic analysis, placing newly classified CMML cases on a disease continuum between MDS and previously established CMML.

overall_design: Whole transcriptome sequencing was performed in order to investigate differences in transcriptional profiles between established CMML cases and cases newly classified as CMML according to updated 2022 WHO and ICC guidelines

first: Francis

last: Baumgartner

first: Constance

last: Baer

first: Stefanos

last: Bamopoulos

first: Edward

last: Ayoub

first: Marietta

last: Truger

first: Manja

last: Meggendorfer

first: Miriam

last: Lenk

first: Gregor

last: Hoermann

first: Heiko

last: Müller

first: Wencke

last: Walter

first: Martha-Lena

last: Mueller

first: Niroshan

last: Nadarajah

first: Piers

last: Blombery

first: Ulrich

last: Keller

first: Wolfgang

last: Kern

first: Claudia

last: Haferlach

first: Torsten


title: Molecular Clusters and Tumor-Immune Drivers of IgM Monoclonal Gammopathies

first: Surendra

last: Dasari

summary: Purpose: IgM monoclonal gammopathy of undetermined significance (MGUS) and Waldenström macroglobulinemia (WM) represent a disease spectrum with highly varied therapeutic management, ranging from observation to chemoimmunotherapy. The current classification relies solely on clinical features and does not explain the heterogeneity that exists within each of these conditions. Further investigation is warranted to shed light on the biology that may account for the clinical differences.    Experimental design: We used bone marrow (BM) clonal CD19+ and/or CD138+ sorted cells, matched BM supernatant, and peripheral blood serum from 32 patients (7 MGUS, 25 WM) to perform the first multi-omics approach including whole-exome sequencing, RNA sequencing, proteomics, metabolomics, and mass cytometry.    Results: We identified three clusters with distinct pathway activation, immune content, metabolomic, and clinical features. Cluster 1 included only patients with WM and was characterized by transcriptional silencing of genes involved in cell cycle and immune response, enrichment of mitochondrial metabolism, infiltration of senescent T effector memory cells, and aggressive clinical behavior. Genetic/structural alterations of TNFAIP3 were distinct events of this cluster. Cluster 2 comprised both MGUS and WM patients with upregulation of inflammatory response, senescence and glycolysis signatures, increased activated T follicular helper and T regulatory cells, and indolent clinical behavior. Cluster 3 also included both MGUS and WM patients and exhibited intermediate features, including proliferative and inflammatory signaling, as well as glycolysis and mitochondrial metabolism.

first: Stephen

last: Ansell

first: Jonas

last: Paludo

first: Patrizia

last: Mondello


title: Early concentrate starter introduction induces rumen epithelial parakeratosis by blocking keratinocyte differentiation with excessive ruminal butyrate accumulation

city: Nanjing

first: Zhang

last: Kai

institute: Njau

summary: Rumen epithelial parakeratosis, a common disease in ruminants caused by abnormalities in the ruminal stratified squamous epithelial keratinization process, negatively impacts ruminant health and performance. While we still lack a comprehensive perception of the underlying mechanisms and the predisposing factors for this disorder.Here, we investigated rumen epithelial cell heterogeneity, differentiation trajectories, and cornification to clarify the rumen epithelial keratinization process

overall_design: RNA-Seq


title: Changes in gene expression in mouse embryonic endocardial cells after Notch pathway manipulation

first: Jose Luis

last: de la Pompa

summary: Analysis by RNA-seq of the changes in gene expression in MEEC due to the activity of Notch ligands.

overall_design: RNA-seq in MEEC  1) co-cultured with OP9, OP9-Dll4 and OP9-Jag1 cells for 6 and 24 hours, 2) co-cultured with OP9 + DMSO and OP9 + RO4929097 for 6 hours, 3) cultured with DMSO, rDLL4 + DMS, rJAG1 + DMSO, rDLL4 + RO4929097 and rJAG1 + RO4929097

first: Luis

last: Luna-Zurita

first: José


title: Genome-wide analysis of stress-responsive genes and alternative splice variants in Arabidopsis roots under osmotic stresses

city: Busan

first: Yong-Hwan

last: Moon

address: Busandaehak-ro 63Beon-gil 2, Geumjeong-gu

department: Molecular Biology

institute: Pusan National University

summary: The shoots and roots of a plant respond differently to osmotic stress, as they have distinct functions and anatomical structures. Under conditions of high solute concentration, such as in saline soils or drought, water uptake by the roots is reduced, resulting in cellular dehydration. In this study, we performed transcriptional profiling of roots of Arabidopsis under osmotic stress conditions such as high salinity and drought using mRNA-Seq for the assessment of gene expression changes in roots of Arabidopsis. mRNA-Seq analysis showed that many differentially expressed genes showed differential expressions under both salt stress and drought stress conditions in roots and were distinct from aerial parts. We confirmed 68 transcription factor genes which is involved in osmotic stress signal transduction in roots and are connected tightly. Interestingly, well-known ABA-dependent and/or -independent osmotic stress-responsive genes were less increased in roots, indicating that osmotic stress response in roots might be regulated by stress pathways other than well-known pathways. We identified 26 osmotic stress-responsive genes, which have alternative splicing variant isoforms, showed distinct expression in roots under osmotic stress conditions from the mRNA-Seq analysis. Quantitative RT-PCR confirmed that alternative splicing variants, such as ANNAT4, MAGL6, TRM19, and CAD9, have differential expressions in roots under osmotic stress conditions, indicating that alternative splicing is an important regulatory mechanism in osmotic stress response in roots. Taken together, our study suggest that many transcription factor families are involved in osmotic stress response in roots and tightly connected each other. In addition, alternative splicing and function of alternative splicing variant isoforms are also important in osmotic stress response in roots. To understand the alternative splicing mechanism in roots, further study is necessary.

overall_design: Differentially expressed genes between in whole seedlings and in roots under NaCl or mannitol treatment at 10 days after germination under SD conditions (8-h-light and 16-h-dark cycle) were explored in whole genome level.

first: Hye-Yeon

last: Seok

first: Sun-Young

last: Lee


title: Vascular senescence and leak are features of the early breakdown of the blood-brain barrier in Alzheimer’s disease models.

city: Sydney

first: Hani Jieun

last: Kim

state: NSW

address: Camperdown

institute: The University of Sydney

summary: Alzheimer’s disease (AD) is an age-related disease, with loss of integrity of the blood-brain barrier (BBB) being an early feature.  Cellular senescence is one of the reported nine hallmarks of aging. Here we show for the first time the presence of senescent cells in the vasculature in AD patients and mouse models of AD.  Senescent endothelial cells and pericytes are present in APP/PS1 transgenic mice but not in wild-type littermates at the time of amyloid deposition. In vitro, senescent endothelial cells display altered VE-cadherin expression and loss of cell junction formation and increased permeability. Consistent with this, senescent endothelial cells in APP/PS1 mice are present at areas of vascular leak that have decreased claudin-5 and VE-cadherin expression confirming BBB breakdown. Further, single cell sequencing of endothelial cells from APP/PS1 transgenic mice confirms that adhesion molecule pathways are among the most highly altered pathways in these cells. At the pre-plaque stage the vasculature shows significant signs of breakdown, with a general loss of VE-cadherin, leakage within the microcirculation, and obvious pericyte perturbation. Although senescent vascular cells were not directly observed at sites of vascular leak, senescent cells were close to the leak area. Thus, we would suggest in AD there is a progressive induction of senescence in constituents of the neurovascular unit contributing to an increasing loss of vascular integrity. Targeting the vasculature early in AD, either with senolytics or with drugs that improve the integrity of the BBB maybe valid therapeutic strategies.

overall_design: Endothelial cells were isolated from the brain of WT and APP/PS1 mice using the Miltenyi Biotec reagents and protocol for "Isolation and cultivation of endothelial cells from adult mouse brain". The cells were then analysed using scRNA-seq.

first: Paul

last: Coleman

first: Hani

middle: J

first: Lipin

last: Loo


title: Macrophage programming is regulated by a cooperative interaction between fatty acid binding protein 5 and peroxisome proliferator-activated receptor gamma

city: Denver

first: Sarah

last: Sasse

state: CO

address: 1400 Jackson St., K720

department: Medicine

institute: National Jewish Health

summary: The resolution of inflammation is an active process that is tightly regulated to achieve repair and tissue homeostasis. In the absence of resolution, chronic inflammation underlies the pathogenesis of chronic lung disease including Chronic Obstructive Pulmonary Disease (COPD) with recurrent exacerbations. Over the course of inflammation, macrophage programming transitions from inflammatory to pro-resolving, and is in part regulated by the nuclear receptor Peroxisome Proliferator-Activated Receptor γ (PPARγ). In our previous work, we demonstrated an association between Fatty Acid Binding Protein 5 (FABP5) expression and PPARg activity in PBMCs. However, the role of FABP5 in macrophage programming is not yet defined, thus, we further investigated its interaction with PPARγ and its role in macrophage programming. Here, we demonstrate that FABP5 is necessary to initiate PPARγ activation and macrophage pro-resolving programming. We used the RNAscope tool in combination with co-immunofluorescence, immunoprecipitation, PPARγ activity assay, and chromatin immunoprecipitation to show that FABP5 and PPARγ not only interact but also regulate one another. By integrating flow cytometry, ELISA, assay for transposase-accessible chromatin by sequencing (ATAC-seq) and the Seahorse technology, we extend our findings to illustrate that lack of FABP5 expression promotes a glycolytic pro-inflammatory macrophage programming. Taken together, these data provide evidence that FABP5 and PPARγ reciprocally regulate each other’s expression and function, consistent with a positive feedback regulatory loop between the two to promote macrophage pro-resolving programming.

overall_design: The Omni method for the Assay for transposase-accessible chromatin by sequencing (Omni-ATAC-seq) was performed in primary mouse bone marrow-derived macrophages for WT or FABP5-deficient mice. All samples were sequenced in duplicate.

first: Manale

last: El Kharbili

first: Katja

last: Aviszus

first: Xiaoyyun

last: Zhao

first: Karina

last: Serban

first: Susan

last: Majka

first: Anthony

middle: N

last: Gerber

first: Fabienne

last: Gally


title: Modifiers of genetic dominance at the Arabidopsis self-incompatibility locus retain proto-miRNA features and act through non-canonical gene silencing pathways - BSAS data

city: Villeneuve d'Ascq

first: Vincent

last: Castric

address: Batiment SN2, bureau 207

institute: CNRS / Universite de Lille - Sciences et Technologies

summary: Self-incompatibility (SI) in flowering plants is a common mechanism that prevents self-fertilization and promotes outcrossing. In Brassicaceae, the locus controlling SI is highly diverse and dozens of distinct alleles are organized in a complex dominance hierarchy: the gene controlling SI specificity in pollen always shows monoallelic expression in heterozygote individuals, and this is achieved through the action of sRNA precursors that resemble miRNAs, although the mechanism behind this remains elusive. Here, we engineered Arabidopsis thaliana lines expressing components of the Arabidopsis halleri SI system and used a reverse genetics approach to pinpoint the pathways underlying the function of these sRNA precursors. We showed that they trigger a robust decrease in transcript abundance of the recessive pollen SI genes, but not through the canonical transcriptional or post transcriptional gene silencing pathways. Furthermore, we observed that single sRNA precursors are typically processed into hundreds of sRNA molecules, with distinct sizes, abundance levels and ARGONAUTE loading preferences. This heterogeneity closely resembles that of proto-miRNAs, the evolutionary ancestors of miRNAs. Our results suggest that these apparent arbitrary features, which are often associated with lack of effects in gene expression, are crucial in the context of the SI dominance hierarchy since they allow one sRNA precursor of a given allele to repress multiple other (more recessive) alleles. This study not only provides an in-depth characterization of the molecular features underlying complex dominance interactions, but also constitutes a unique example of how specific evolutionary constraints shape the progression of sRNA precursors within the proto-miRNA – miRNA evolutionary continuum.

overall_design: To measure DNA methylation in SCR01 target sites we used the BiSulfite Amplicon Sequencing Technique - BSAS (Masser et al., 2013; Sigman et al., 2021) which relies on PCR enrichment of regions of interest using bisulfite converted DNA as a template. To assess if the presence of S-locus sRNA precursors is associated with DNA methylation changes in the respective SCR01 target regions, we isolated immature buds of SCR01, SCR01*mir1887, SCR01 Ah04mir1887 and SCR01*mir1887 Ah20mirS3 plants.

first: Rita

last: A Batista


title: miRNA profile of young mice and aged mice

city: Sendai

first: Kazusa

last: Miyahara

address: Seiryo-machi 2-1

institute: Tohoku University

summary:
Paternal aging has been reported to be related with offspring`s increased risk of autism spectrum disorders. However, effect of miRNAs in sperm has not been investigated.
We used microarray to investigate whether miRNA profile were changed with aging.

overall_design: Sperm from mice at 3 months old (3M), >12M and  >20M were collected and miRNAs of the sperm were extracted. Then, we conducted microarray analyses on the extracted miRNAs.

first: Misako

last: Tatehena

first: Noriko

last: Osumi


title: The role of Atf4 in the embryonic lens at E16.5

city: Newark

first: Melinda

last: Duncan

state: DE

address: 105 The Green

department: Biological Sciences

institute: University of Delaware

summary: Transcriptome analysis reporting genes that are differentially expressed as a result of knockout of the gene ATF4.

overall_design: Lenses were isolated from wildtype and ATF4 knockout mice at E16.5 by microdissection (5 biological replicates of wildtype, 4 biological replicates ATF4 knockout). Total RNA was isolated, cDNA libraries were constructed using Takara SMARTer Stranded Pico v2, and sequencing was performed using Illumina NovaSeq 6000 (DNA Link USA, Inc). The goal was to understand the role of Atf4 in the embryonic lens at E16.5. Each library was sequenced across 4 flow cell lanes.

first: Jiawen

last: Xiang

last: Pompetti

first: Adam

last: Faranda

first: Yan

last: Wang

first: Samuel

last: Novo

first: David

middle: W

last: Li


title: The Role of Butyrate as a Histone Deacetylase Inhibitor in Protecting Pancreatic Beta Cells from IL-1β-Induced Dysfunction

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Butyrate, a gut microbial metabolite, has beneficial effects on glucose homeostasis and has become an attractive drug target for type 2 diabetes (T2D). Recently, we showed that butyrate protects pancreatic beta cells against cytokine-induced dysfunction. In this study, we explored the underlying mechanisms of butyrate action. Pancreatic islets were exposed to a non-cytotoxic concentration of interleukin 1β (IL-1β) for ten days to mimic the low-grade inflammation in T2D. An isoform-selective histone deacetylase 3 (HDAC3) inhibitor normalized IL-1β-reduced GSIS and insulin content similar to the effect of butyrate. In contrast, FFAR2/3 agonists failed to normalize IL-1β-induced impairment of GSIS and reduced insulin content. Butyrate, irrespective of IL-1β, inhibited HDAC activity and increased histone H3 and H4 acetylation by 3- and 10-fold, respectively. Genome-wide analysis of histone H3K27 acetylation (H3K27ac) revealed that butyrate mainly increased H3K27ac at promoter regions (~68 %), while H3K27ac peaks regulated by IL-1β were more equally distributed at promoters (~33 %), introns (~23 %) and intergenic regions (~23 %). Gene ontology analysis showed that butyrate increased IL-1β-reduced H3K27ac  levels near several genes related to hormone secretion and reduced IL-1β-increased H3K27ac levels  near genes associated with inflammatory responses . Butyrate alone increased H3K27ac near many genes related to MAPK signaling, hormone secretion and differentiation, and decreased H3K27ac at genes involved in cell replication. Together, these results suggest that butyrate prevents IL-1β-induced beta cell dysfunction by inhibition of HDACs resulting in changes in H3K27ac levels at genes relevant for beta cell function and inflammatory responses.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variant H3K27ac in mouse pancreas.

first: Signe

last: Pedersen

first: Mathias

last: Olsen

first: Michala

last: Prause

first: Nils

last: Billestrup


title: Lactational exposure to high fat diet

city: Ann Arbor

first: Dave

last: Bridges

state: MI

address: 1415 Washington Heights

department: Nutritional Sciences

country: USA

institute: University of Michigan

summary: To understand how gonadal adpose tissue is altered via maternal HFD feeding, we fed dams a 60% HFD only during weaning.  These data are from the offspring, both control and HFD fed male mice

overall_design: We provided mouse dams with 60% high fat diet after delivering their pups and continued it until postnatal day 21 at weaning. These are the RNA from the male offspring gonadal white adipose tissue depots on postnatal day 16 from control and high fat diet groups.

first: Brigid

last: Gregg

first: Katie

last: Kim

first: Mita

last: Varghese

first: Haijing

last: Sun

first: Simin

last: Abrishami

last: Bowers

first: Jennifer

middle: L

last: Meijer

first: Kanakadurga

last: Singer


title: Expression profiling of LINC01638 interference in hMSC-hTERT20 cells

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

summary: We identified LINC01638 as a lncRNA that is highly expressed in proliferating MSCs and decreases in expression during osteogenesis. We demonstrate that knockdown of LINC01638 in hMSC-hTERT20 cells by CRISPRi during osteogenic differentiation causes an decrease in alkaline phosphatase (ALP) activity and ALPL gene expression. Altered expression of several extracellular matrix proteins was noted. We identified LINC01638 as a nuclear lncRNA that binds to chromatin and where it regulates gene expression.  These results reveal that LINC01638 may act as a negative regulator of osteoblast differentiation, thereby providing a novel mechanism of regulatory control of osteogenesis.

overall_design: RNA-Seq: Human immortalized MSCs (hMSC-hTERT20) were infected with pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-GFP to induce LINC01638 or LINC01114 knockdown. Cells were then induced to osteogenesis using 280 μM ascorbic acid, 10 mM beta-glycerophosphate, 10nM dexamethasone. RNA from cells were harvested at defined time points (0, 7, 14,21 days) in trizol. RNA was hen processed into individually barcoded libraries and sequenced.

first: Coralee

last: Tye

first: Bodhisattwa

last: Banerjee

first: Jane

last: Lian


title: H. pylori-induced PIEZO1 drives gastric carcinogenesis by activating the YAP1-CTGF axis to stiffen the alpha-SMA+ cancer-associated fibroblast-mediated microenvironment

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

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

overall_design: Refer to individual Series


title: Effect of knocking down PIEZO1 in gastric cancer cells

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. Thus, we try to explore the PIEZO1 function in GC by knocking down assay.

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

first: Wei

last: Kang


title: Endothelial DLL4 is an adipose depot specific fasting sensor regulating fatty acid fluxes

city: Toulouse

first: Anaïs

last: Briot

address: 1 avenue Jean Poulhès

department: UMR1297, I2MC

institute: Inserm

summary: Adaptation of adipose depots to change in fuel availability is critical for metabolic flexibility and cardio-metabolic health. The mechanisms responsible for fat depot-specific lipid sensing and shuttling remain elusive. We investigated the contribution of microvascular endothelial cells in this process. We performed transcriptional analysis of native microvascular endothelial cells isolated from paired biopsies of human gluteofemoral (GF-AT) and abdominal (Abdo-AT) subcutaneous adipose tissues. Gene expression profiles were performed using Agilent Sureprint G3 Human GE v3 microarrays.

overall_design: To highlight general profile differences between endothelial cells from subcutaneous fat depots, we classify and study transcripts differentially expressed taking into account Abdo-AT and GF-AT corrected for individual effects.

first: Alex

last: Aupetit

first: Pauline

last: Decaunes

first: Chloé

last: Belles

first: Elodie

last: Riant

first: Yannick

last: Lippi

first: Claire

last: Naylies

first: Anne

last: Bouloumié