title: Single-cell and bulk RNA sequencing of mouse atherosclerosis disease stage course [scRNASeq_WAT_Mono]

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

summary: Atherosclerotic coronary artery disease (CAD) development encompasses changes in immune cell activation across different tissues, including white adipose tissue (WAT). However, the specific disease-associated transcriptional changes occurring within each of the tissue cell types remain incompletely characterized. Here, we provide a scRNA-seq dataset allowing the characterization of disease-associated cell states within the major WAT cell types. For the myeloid cells, we further analyzed sub-populations and characterized their protein-coding and miRNA gene markers. By comparing to naive monocytes isolated from blood, we further used the tissue profiles to interrogate how the tissue infiltration changes the monocyte and dendritic cell transcriptome profiles.

overall_design: A disease stage course of atherosclerosis in mouse was established by varying genotype (wild type and proatherogenic) and diet (0, 1 or 3 months of high-fat diet), followed by scRNA-Seq (all cell types) and bulk RNA-Seq of the thoracic aorta.

first: Ana

last: Hernandez de Sande

first: Maria

last: Bouvy-Liivrand

first: Tanja

last: Turunen

first: Tiit

last: Örd

first: Tapio

last: Lönnberg

first: Senthil

last: Palani

first: Heidi

last: Liljenbäck

first: Jenni

last: Virta

first: Anne

last: Roivainen

first: Minna

middle: U

last: Kaikkonen


title: KDM3B inhibitors disrupt PAX3-FOXO1 oncogenic activity in fusion positive rhabdomyosarcoma.

status: Public on Dec 31 2023

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

country: USA

institute: NCI, NIH

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Fusion-positive alveolar rhabdomyosarcoma (FP-RMS) is an aggressive pediatric sarcoma driven primarily by the PAX3-FOXO1 fusion oncogene, for which therapies targeting PAX3-FOXO1 are lacking. We screened 62,643 compounds using an engineered cell line that monitors PAX3-FOXO1 transcriptional activity identifying a hitherto uncharacterized compound, PFI-63. RNA-seq, ATAC-seq, and docking analyses implicated histone lysine demethylases (KDMs) as its targets. Enzymatic assays confirmed the inhibition of multiple KDMs with highest selectivity for KDM3B. Structural similarity search of PFI-63 identified PFI-90 with improved solubility and potency. Biophysical binding of PFI-90 to KDM3B was demonstrated using NMR and SPR. PFI-90 suppressed the growth of FP-RMS in vitro and in vivo through downregulating PAX3-FOXO1 activity, and combined knockdown of KDM3B and KDM1A phenocopied PFI-90 effects. Thus, we report novel KDM inhibitors with highest specificity for KDM3B. Its potent suppression of PAX3-FOXO1 activity can be exploited as a new therapeutic approach for FP-RMS and other transcriptionally driven cancers.

overall_design: RNA-seq, ChIP-seq, ATAC-seq, Hi-C, scRNA-seq.  No replicates.  Drug treatment versus control analysis.

first: Yong

middle: Y

last: Kim

first: Xinyu

last: Wen

first: Hsien-Chao

last: Chou


title: Sepsis Induces Heterogeneous Transcription of Coagulation- and Inflammation-Associated Genes in Renal Microvasculature

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

summary:
# Background
Acute kidney injury (AKI) in sepsis patients increases patient mortality. Endothelial cells are important players in the pathophysiology of sepsis-associated AKI (SA-AKI), yet knowledge regarding their spatiotemporal involvement in coagulation disbalance and leukocyte recruitment is lacking. This study investigated the identity and kinetics of responses of different microvascular compartments in kidney cortex in response to SA-AKI.
# Methods
Laser microdissected arterioles, glomeruli, peritubular capillaries, and postcapillary venules from kidneys of mice subjected to cecal ligation and puncture (CLP) were analyzed using RNA sequencing. Differential expression and pathway enrichment analyses identified genes involved in coagulation and inflammation. A selection of these genes was evaluated by RT-qPCR in microvascular compartments of renal biopsies from patients with SA-AKI. The role of two identified genes in lipopolysaccharide-induced endothelial coagulation and inflammatory activation were determined in vitro in HUVEC using siRNA-based gene silencing.
# Results
CLP-sepsis in mice induced altered expression of approximately 400 genes in the renal microvasculature, with microvascular compartments exhibiting unique spatiotemporal responses. In mice, changes in gene expression related to coagulation and inflammation were most extensive in glomeruli at early and intermediate time points, with high induction of Plat, Serpine1, Thbd, Icam1, Stat3, and Ifitm3. In human SA-AKI, PROCR and STAT3 were induced in postcapillary venules, while SERPINE1 expression was diminished. IFITM3 was increased in arterioles and glomeruli. In vitro studies revealed that STAT3 and IFITM3 partly control endothelial coagulation and inflammatory activation.
# Conclusion
Renal microvascular compartments in mice and humans exhibited heterogeneous changes in coagulation- and inflammation-related gene expression in response to SA-AKI. Additional research should aim at understanding the functional consequences of the here described heterogeneous microvascular responses to establish the usefulness of identified genes as therapeutic targets in SA-AKI.

overall_design: mRNA analysis in microvascular compartments from mouse kidney cortex (arterioles, glomeruli, peritubular capillaries, post-capillary venules) to reveal altered gene expression in response to sepsis-induced acute kidney injury

first: Matthijs

last: Luxen

first: Peter

middle: J

last: Zwiers

first: Rianne

middle: M

last: Jongman

first: Jill

last: Moser

first: Marianne

last: Pultar

first: Susanna

last: Skalicky

first: Matthias

last: Hackl

first: Matijs

last: van Meurs

first: Grietje

last: Molema


title: Targeting of Focal Adhesion Kinase enhances the immunogenic cell death of PEGylated liposome doxorubicin to optimize therapeutic responses of immune checkpoint blockade

city: Shanghai

first: Baoyuan

last: Zhang

state: Please Select

address: No.197,Rui Jin Er Road,Shanghai 200025 China

country: China

institute: Ruijin hospital

summary: Focal adhesion kinase (FAK) is frequently amplified and acts as an immune modulator across cancer types. However, evidence illustrates that targeting FAK is most effective in combination therapy rather than in monotherapy. Here, we demonstrated that the FAK inhibitor, IN10018, and pegylated liposome doxorubicin (PLD) exerted effective antitumor activity preclinically and clinically (clinical trial ID: CTR20200913). The clinical study is a phase Ib trial which includes dose confirmation and expansion sections. The primary endpoint is objective response rate (ORR). Secondary endpoints include disease control rate (DCR), duration of response (DoR), progression-free survival (PFS), overall survival (OS), and safety. As of the data cutoff date (30 November 2022), a total of 61 platinum-resistant ovarian cancer (PROC) patients were enrolled and no IN10018-related grade 4 or 5 adverse effects (AEs) were reported. The ORR was 46.3% (95% confidence interval (CI): 32.6%, 60.4%) and the DCR was 83.3% (95% CI: 70.7%, 92.1%). The median PFS was 7.26 months (95% CI: 5.16 - 8.02 months), and the median duration of response (DoR) was 6.93 months (95% CI: 4.17 - 9.13 months). The primary and secondary endpoints were met. The median OS was not reached, and still maturing. Notably, the regimen exhibited response latency and long-lasting effects in the clinical trial, outcomes frequently observed in immunotherapy. Our preclinical study revealed that the 2-drug combination can maximize the immunogenic cell death (ICD) of cancer cells, boosting the maturation of dendritic cells (DCs) and stimulating CD8 T cells to strengthen the antitumor effects. At present, immune checkpoint blockade (ICB) is widely considered to exert long-term treatment benefits by activating antitumor immunity. However, many cancer patients show poor clinical responses to ICB due in part to the lack of immunogenic niche. Our work confirmed that IN10018 in combination with PLD can prime the tumor microenvironment, supplementing it with sufficient tumor-infiltrating lymphocytes (TILs) to activate antitumor immunity. Correspondingly, animal studies validated that the antitumor effects of ICB can be significantly enhanced by this doublet regimen. The preclinical results warrant further clinical exploration for the triplet regimen with IN10018, PLD, and ICB.

overall_design: Transcriptome profiling was performed to determine the mechanism of the observed clinical antitumor effects. In brief, the SK-OV-3 cells were treated with DMSO, 300 nM doxorubicin, 3 μM IN10018, and a combination of IN10018 and doxorubicin for 24 hours. The total mRNA was extracted for the RNA sequencing.

first: Dongmei

last: Ji

first: Lingying

last: Wu

first: Ruibao

last: Ren


title: Kinetic RNA  profiles in mouse ApcDeltaHep hepatocytes  at day 6, 15 and 21 after activation vs wt hepatocytes

city: Paris

first: Angelique

last: Gougelet

address: 15 rue de l'école de médecine

country: France

institute: INSERM U1138

summary: We analyzed the expression of RNAs  in hepatocytes isolated from  Apclox/lox livers, after injection of adenovirus Ad5-Cre-GFP and hepatocyte sorting on the basis of GFP signal at day 6, 15 and 21 post-injection. Our aims was to study the transcriptional impact of the beta-catenin during the early steps of liver tumorigenesis.

overall_design: RNA profiles from GFP+ hepatocytes versus GFP- hepatocytes isolated from  ApcdeltaHep livers  versus

first: Julie

last: Sanceau

first: Angélique


title: Cardiac p62/Sqstm1 maintains Nrf2 protein levels and protects from oxidative stress

city: salt lake city

first: Sihem

last: Boudina

state: Utah

department: Nutrition and Integrative Physiology

institute: University of Utah

summary: Squestosome 1 (SQSTM1), also known as p62, is a multi-functional adaptor protein known for its pleotropic roles in autophagy, proteostasis, inflammation and cancer. Recently, p62 has emerged as an important modulator of protein quality control and aging. However, its role in the heart is not well understood.   Our understanding of the role of p62 in the heart has been limited to the indirect assessment of its function in the setting of autophagy inhibition or proteotoxic stress. However, whether p62 is required to maintain cardiac function at rest or in response to stress has not been explored. Here we investigated the functional consequence of cardiac p62 deletion in the absence of other contributing phenotypic and systemic factors observed in the whole-body p62 deleted mice. Lack of cardiomyocytes p62 precipitated cardiac aging in mice and was associated with reduced contractile function and a progressive development of cardiac hypertrophy and fibrosis. Transcriptomic analysis of p62-deleted heart revealed a selective impairment in Nrf2 transcription, which was confirmed in the hearts of p62cKO mice. We further showed that absence of p62 in adult mice resulted in excessive oxidative stress and cell death when mice were rendered hypoxic. To gain mechanistic insights, we employed loss and gain of p62 function in H9c2 cardiomyoblasts and showed a sustained reduction in Nrf2 protein expression, nuclear translocation and transcriptional activity in p62-deficient cells. Mechanistically, p62-deficient cells exhibited an increase in proteasome-mediated Nrf2 degradation. In contrast, gain of p62 function led to Nrf2 stabilization and transcriptional activity.

overall_design: Whole heart tissue from 2 and 15 months old wildtype and cardiac-specific p62 KO mice (Myh6-Cre-Sqstm1fl/fl) were used to isolate RNA and then sequenced.


title: Gene expression in sarcoma cell lines

city: Goyang

first: HYE JIN

last: YOU

email: hjyou@ncc.re.kr, hyejin.you@gmail.com

state: Gyeonggi

address: 323 Ilsan-ro, Ilsandong-gu

department: Cancer Biology

country: South Korea

institute: National Cancer Center

summary: As a high-grade soft-tissue sarcoma (STS), undifferentiated pleomorphic sarcoma (UPS) is highly recurrent and malignant.  UPS is categorized as “tumor of uncertain differentiation” and few options for treatment resulting from lack of targetable genetic alterations.  There are also few cell lines representative subtype for UPS, leading to poor experimental evidence.  Here, we have established and characterized new cell lines derived from recurrent two UPS tissues.  Cells were obtained UPS tissues by mincing followed by extracting or dissociating using enzymes and cultured by regular culture environment.  Cells were maintained and immortal for months without artificial treatment and some cell clones were tumorigenic in immunodeficient mouse model.  Interestingly, some cells formed tumor in vivo when injected after aggregation in non-adherent culture system for 24 h.  The tissues from in vivo study and tissues from patients were compared if it is representative for UPS by immunohistochemistry.  Pathways related to cell cycle as DNA replication were common between cell clones while cell clones, tumorigenic in regardless of aggregation for injection, were increased expression of pathways related to cell-cell adhesion, as well as cell-cell signaling, implying a role of mesenchymal to epithelial transition for tumorigenicity in vivo.  This study showed that new UPS cell lines might be a good resource for UPS study to get new insights leading to better therapeutic strategy against UPS.

overall_design: mRNA expression profiling analysis of RNA-seq data for the sarcoma cell lines

first: Hye

last: You

first: Eun-Young

last: Lee


title: Methylome analyses by Infinium MethylationEPIC assay from umbilical cord and placenta samples of mothers with or without obesity before pregnancy and mothers with and without gestational obesity

city: Salt

first: Abel

last: López-Bermejo

state: Girona

address: Dr. Castany s/n

department: Pediatrics

country: Spain

institute: IDIBGI

summary: Maternal obesity before and during pregnancy may have an effect on the offspring outcomes. Epigenetic modifications, such as DNA methylation, might mediate this association by causing changes in gene expression. The study tried to find epigenetic marks in umbilical cord and placenta samples related to unfavourable outcomes in the offspring that could be used as biomarkers.

overall_design: Bisulphite converted DNA from the 12 placental samples and 12 umbilical cord samples of mothers with or without obesity before pregnancy and mothers with and without gestational obesity were hybridised to the Infinium Human DNA Methylation EPIC 850K.

first: Berta

last: Mas-Parés

first: Ariadna

last: Gómez-Vilarrubla

first: Judit

last: Bassols


title: chromatin openin profiles in mouse ApcDeltaHep or wt hepatocytes

summary: We analyzed  chromatin opening in hepatocytes isolated from  ApcDeletaHep livers or wt by ATAC-seq. We thus explore how an aberrant activation of beta-catenin signaling modifies chromatin structure in hepatocytes

overall_design: ATAC-seq profiles from hepatocytes isolated from  ApcdeltaHep livers or wt livers


title: Modeling neurodevelopmental disorder-associated human AGO1 mutations in C. elegans Argonaute alg-1. [smallRNA-Seq]

status: Public on Dec 30 2023

city: Worcester

first: Ye

last: Duan

state: MA

address: 373 Plantation Street, Biotech Two, Suite 306

institute: Umass Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNA) associate with Argonaute proteins and negatively regulate gene expression by base pairing with complementary sequences in the 3’ UTRs of target genes. De novo coding variants in the human Argonaute gene AGO1 were reported to cause neurodevelopmental disorder (NDD) with intellectual disability (ID). Most of the altered amino acids are conserved between the miRNA associated Argonautes in H. sapiens and C. elegans, suggesting that the human AGO1 mutations could disrupt evolutionarily conserved functions in miRNA biogenesis or target repression. We genetically modeled four human AGO1 mutations in C. elegans by introducing identical mutations into the C. elegans AGO1 homolog, ALG-1. These alg-1 NDD mutations caused phenotypes in C. elegans indicative of disrupted miRNA processing, miRISC formation, and/or target repression. We show that the alg-1 NDD mutations are antimorphic as they cause developmental and molecular phenotypes stronger than those exhibited by the alg-1 null mutants, likely by sequestrating functional miRNA silencing complex (miRISC) components into non-functional complexes that fail to confer robust gene repression. The alg-1 NDD mutations cause allele-specific disruptions in mature miRNA profiles, both in overall abundances and ALG-1 NDD association, accompanied by perturbation of downstream gene expression, including altered translational efficiency and/or mRNA abundance. The perturbed genes include those with human orthologs whose dysfunction is associated with NDD. These cross-clade genetic studies illuminate fundamental Argonaute functions and provide insights into the conservation of miRNA-mediated post-transcriptional regulatory mechanisms.

overall_design: To profile the miRNA expression and miRNA association with ALG-1, we performed miRNA sequencing of total small RNA and sRNA co-IP with ALG-1 of the four alg-1 NDD mutants, the alg-1 null mutants, and WT C. elegans

first: Ganesh

last: Prabhakar Panzade

first: Li

last: Li

first: Amélie

last: Piton

first: Victor

last: Ambros

first: Anna

last: Zinovyeva


title: changes of global gene expression for early neonatal keratinocyte

city: seoul

first: Jimin

last: Cha

address: 50-1, Yonsei-ro

institute: Yonsei university

summary: To understand transcriptomic difference during early neonatal keratinocyte

overall_design: We obtained mouse keratinocyte in postnatal day 1,7 and 14. keratinocytes were processed for bulk RNA sequencing.

first: Ji-Hwan

last: Ryu

first: Tae-Gyun

last: Kim


title: Peroxisomal β-oxidation enzyme, DECR2, regulates lipid metabolism and promotes treatment resistance in advanced prostate cancer

city: Adelaide

first: Chui Yan

last: Mah

address: North Terrace

country: Australia

institute: University of Adelaide

summary: Peroxisomes are central metabolic organelles that have key roles in fatty acid homeostasis, including β-oxidation, and emerging evidence has linked aberrant peroxisome metabolism to cancer development and progression. While targeting mitochondrial β-oxidation in prostate cancer (PCa) has gained significant attention in recent years, the contribution of peroxisomal β-oxidation (perFAO) to PCa tumorigenesis is comparatively unexplored. Herein, we explored the therapeutic efficacy of targeting perFAO in PCa cells and clinical prostate tumours, and subsequently identified peroxisomal 2,4-dienoyl CoA reductase 2 (DECR2), as a key therapeutic target. DECR2 is markedly upregulated in clinical PCa, most notably in metastatic castrate-resistant PCa. Depletion of DECR2 significantly suppressed proliferation, migration, and 3D growth of a range of CRPC and enzalutamide-resistant PCa cell lines, and inhibited LNCaP tumour growth and proliferation in vivo. Using transcriptomic and lipidomic analyses, we determined that DECR2 influences cell cycle progression and lipid metabolism to enable tumour cell proliferation. We further demonstrated a novel role for perFAO in driving resistance to standard-of-care androgen receptor pathway inhibition, using genetic and pharmacological approaches to alter DECR2/perFAO in treatment-resistant PCa cells. Our findings highlight a need to focus on peroxisomes to suppress tumour cell proliferation and reveal new therapeutic targets for advanced, treatment-resistant PCa.

overall_design: RNA-seq following DECR2 knockdown in V16D and MR49F cells

first: Chui

first: Lisa

last: Butler


title: Modeling neurodevelopmental disorder-associated human AGO1 mutations in C. elegans Argonaute alg-1.

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

overall_design: Refer to individual Series


title: Modeling neurodevelopmental disorder-associated human AGO1 mutations in C. elegans Argonaute alg-1. [ribosome profiling]

overall_design: To profile the translatome and transcriptome of the alg-1 NDD mutants, we performed ribosome profiling (Ribo-seq) and RNAseq of the four alg-1 NDD mutants, the alg-1 null mutants, and WT C. elegans


title: Epitranscriptome profiling of m6A in colon cancer cell lines

city: Chennai

first: Samson

last: Mani

state: Tamilnadu

address: 38, Sardar Patel Road

department: Molecular Oncology

country: India

institute: Cancer Institute (WIA)

type: Methylation profiling by high throughput sequencing

summary: N6-methyl adenosine (m6A) is one of the most important RNA modifications involved in several biological and pathological processes, including cancer. Dysregulation of m6A has been linked with tumor initiation, progression, and metastasis of several cancer types, including colon cancer. A transcriptome of colon cancer describes the dysregulated coding and non-coding RNAs but does not reveal the mechanisms like m6A modifications that determine the post-transcriptional and pre-translational regulations. Epi-transcriptome profiling of m6A in colon cancer cell lines was performed using Methylated RNA Immunoprecipitation (MeRIP) sequencing.  Overall, the study illustrates the distribution of m6A across the transcriptome of various colon cancer cell lines.

overall_design: N6-methyladenosine RNA immunopreciptiation of colon cancer cell lines

first: Deepa

last: Ramasamy

first: Arunagiri Kuha Deva Magendhra

last: Rao


title: Effect of VEGF-C treatment on sorted meningeal lymphatic endothelial cells

status: Public on Dec 29 2023

first: Ruchith

last: Singhabahu

address: 47 bd de l'Hôpital

institute: Institut du Cerveau

summary: Transcriptional profiling of mouse dural lymphatic endothelial cells (LECs) in comparing AAV-Controls with AAV-VEGFC treaded mice. Objective was to determine the effect of the VEGFC treatment on global gene expression of LECs.

overall_design: Total RNA was obtained from sorted dural Lymphatic endothelial cells of 10 to 12 pooled meningeal samples for each condition (AAV-CTRL vs AAV-VEGFC pre-treated mice). The experiment was repeated 3 times for each condition.

first: Marie-Renée

last: El Kamouh

first: Justine

last: Guégan


title: Change of transcriptome characterisitcs by microbiota in atopic dermatitis like skin inflammation

summary: To understand immunological difference between germ-free (GF) mice as compared with specific-pathogen free (SPF) mice.

overall_design: We obtained mouse ear skin treated with Ethanol and MC903 (material that induced skin inflammation). Skin tissues were processed for bulk RNA sequencing.

last: KIm


title: Transcriptomic analysis of salt stress responsive genes related pigment metabolism in photoheterotrophic Arabidopsis calli

city: ISTANBUL

first: Haluk

last: Çelik

state: Vezneciler

address: İstanbul Üniversitesi Fen Fakültesi Moleküler Biyoloji ve Genetik Bölümü

country: Turkey

institute: Istanbul University

summary: In order to investigate the salt stress induced chlorophyll biosynthesis-related genes in photoheterotrophic cultures, we performed RNA-Seq analysis on A. thaliana calli exposed to 100 mM NaCl on MS medium containing 0.5 mg/L 2,4-D 30 days. Four different conditions of samples were sequenced on Illumina HiSeq Platform in total and generated about 4.49 Gb per sample. The average genome and gene mapping rates were 93.52% and 90.78%, respectively. According to expression profile analysis, some DEGs demonstrated altered related to chlorophyll pigment metabolism. According to analysis, green callus color of photoheterotrophic calli were mainly connected with the induction of LHCB4.3 light harvesting complex photosystem II (Gene ID:818599), AT1G49975 photosystem I reaction center subunit N (Gene ID: 841421), PAM68 PAM68-like protein (DUF3464) (Gene ID: 2745715) and AT3G63540 thylakoid lumenal protein (Mog1/PsbP/DUF1795-like photosystem II reaction center PsbP family protein)(Gene ID: 7922413) genes. Furthermore, 8 DEGs were randomly selected to validate the transcriptome profiles via qPCR. These results will provide a foundation for further studies aimed at giving photosynthetic properties to in vitro plant cultures.

overall_design: Morphological observation and total RNA-Seq analysis of pigment formation under NaCl treatment in Arabidopsis thaliana (Col-0)

first: Burcu

last: Arıkan

first: Özgür

last: Çakır

first: Cüneyt

last: Uçarlı

first: Neslihan

middle: T

last: Kara


title: Single-cell transcriptome characteristics of postnatal ILC from mice skin

first: Jimin

last: Cha

summary: To identify dynamics of postnatal skin ILC populations

overall_design: We obtained ILC from postnatal day 1 and 14 mice skin. Skin ILC was processed for single cell RNA sequencing.


title: Endothelial cells drive organ fibrosis and dysfunction by inducing the transcription factor SOX9 (CUTNTAG)

city: Mannheim

first: Joerg

last: Heineke

state: Baden Wuttemberg

address: Ludolf-Krehl-Str. 7-11

department: – Department of Cardiovascular Research (HKF)

country: Germany

institute: Medizinische Fakultät Mannheim

summary: Fibrosis is a hallmark of chronic disease. Although fibroblasts are known to be involved, it is unclear to what extent endothelial cells might contribute. We detected increased expression of the transcription factor Sox9 in endothelial cells of fibrotic mouse organs in models of systolic heart failure by pressure overload, diastolic heart failure by high-fat diet and L-Name administration, pulmonary fibrosis after bleomycin treatment, and liver fibrosis as consequence of CDAA diet. We also observed endothelial SOX9 upregulation in human heart tissue in patients with heart failure. To test whether this SOX9 induction was sufficient to cause disease, we generated mice with endothelial cell-specific overexpression of Sox9, which indeed triggered extensive fibrosis in multiple organs and promoted signs of heart failure. Endothelial Sox9 deletion, in turn, prevented fibrosis and organ dysfunction in pre-clinical surgical and pharmacological mouse models of heart failure as well as of lung, and liver injury. Bulk and single cell RNA sequencing of endothelial cells across multiple vascular beds revealed that SOX9 induced extracellular matrix, growth factor, and inflammatory genes leading to matrix deposition by endothelial cells. Moreover, in part through triggering an increased expression of the secreted growth factor Ccn2 as direct SOX9 target, endothelial cells activated neighboring fibroblasts to migrate and deposit matrix in response to SOX9. Endothelial Sox9 deletion reversed these changes, suggesting a role for endothelial SOX9 as fibrosis-promoting transcription factor across organs in response to disease stimuli.  Therefore, endothelial cells could be a promising target to counteract fibrotic heart, liver and lung disease

overall_design: Cariac CD146 positive EC from WT and Sox9-overexpressing mice were used to performed Cut&Tag protocol

first: Felix

middle: A

last: Trogisch

first: Julio

last: Cordero

first: Adel

last: Elsherbiny

first: Merve

last: Keles


title: Endothelial cells drive organ fibrosis and dysfunction by inducing the transcription factor SOX9 (ATAC-Seq)

overall_design: ATAC-seq was performed in cardiac EC from Ctr and Sox9_OE induced mice after 1 month of tamoxifen treatment.


title: Modeling neurodevelopmental disorder-associated human AGO1 mutations in C. elegans Argonaute alg-1. [RNA-Seq]

first: Ye

last: Duan

first: Ganesh

last: Prabhakar Panzade

first: Li

last: Li

first: Amélie

last: Piton

first: Victor

last: Ambros

first: Anna

last: Zinovyeva


title: Single-cell RNA-sequencing data and functional analysis revealed that ACC1, a rate limiting enzyme of fatty acid biosynthesis, is responsible for survival of thymic iNKT cells.

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

country: Japan

institute: KAZUSA DNA Research Institute

summary: Invariant Natural Killer T (iNKT) cells are a unique subset of T lymphocytes with a memory like phenotype which express invariant T cell receptor (TCR) chain comprised of a Vα14-Jα18 rearrangement in mice. In the present study, we characterize the transcriptomes of thymic iNKT cells at the single cell level to reveal the underlying metabolic adaptation that exists over the course of iNKT cell development.

overall_design: Thymic CD1d tetramer+ iNKT cells were collected with Magnetic cell sorting (MACS). Then, CD3+CD1d tetramer+ iNKT cells were collected with cell sorter for scRNA-seq library preparation.

first: Keisuke

last: Miyako

first: Takeru

last: Endo

first: Satoru

last: Yokoyama

first: Hikari

middle: K

last: Asou

first: Kazuko

last: Yamada

first: Osamu

last: Ohara

first: Toshinori

last: Nakayama

first: Motoko

last: Kimura

first: Yusuke


title: Mouse methylation microarray data related to TIME-Seq benchmarking

status: Public on Dec 28 2023

city: Boston

first: Patrick

last: Griffin

address: 77 Avenue Louis Pasteur

department: Harvard Medical School, Dept. of Genetics

institute: Patrick Griffin

summary: These data are published in a series with the TIME-Seq sequencing data. TIME-Seq is a method for efficient methylation sequencing, primarily used for epigenetic clock analysis.

overall_design: Illumina methylation BeadChip microarray applied to DNA extracted from blood from humans and mice. After processing of data, analysis included age prediction using epigenetic clocks.

first: David

last: Sinclair


title: Methylation microarray data related to TIME-Seq benchmarking


title: Loss of B cell Tolerance is TCR Dependent [amplicon-seq]

first: Elliot

last: Akama-Garren

address: 200 Longwood Ave

institute: Harvard Medical School

summary: We tested orphan TCR autoreactivity using the peptide MHC-TCR chimeric receptor (MCR) co-culture system.  In this system, cognate antigen recognition leads to TCR specific NFAT activation in MCR reporter cells expressing a mouse I-Ab MHC class II extracellular domain covalently linked to candidate peptides and an intracellular TCR signaling domain.  We used mixed autoimmune bone marrow chimera spleens and kidneys as sources of cDNA to generate a transcriptome-wide library of natural autoantigen peptides .  We cloned this cDNA-derived peptide (CDP) autoantigen library into the MCR retroviral backbone and transduced NFAT reporter cells to make a murine autoantigen MCR reporter library (MCR-Lib). We then used this library to screen orphan TCRs identified by scTCR-seq for autoreactivity.

overall_design: Amplicon NGS was performed on PCR-amplified peptide sequences from MCR-Libraries following screening with orphan TCRs

middle: H

first: Michael

middle: C

last: Carroll


title: Low testosterone and intermittent hypoxia act in synergy to determine hepatic expression of flavin-containing monooxygenases in mice.

city: Quebec

first: Vincent

last: Joseph

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Université Laval / IUCPQ

summary: Intermittent hypoxia induces oxidative stress and alters hepatic metabolism, likely underlying the association of sleep apnea with non-alcoholic fatty liver disease. In male patients with sleep apnea, metabolic or liver diseases, the levels of testosterone are reduced, and in patients with metabolic diseases, low levels of testosterone are associated with oxidative stress. To assess potential interactions between testosterone and IH on hepatic oxidative stress we used sham-operated or orchiectomized (ORX) mice exposed to normoxia (Nx) or IH (6% O2, 12 cycles/h, 12h/day) for 2 weeks. The activity of prooxidant (NADPH oxidase – NOX), antioxidant enzymes (superoxide dismutase, catalase, and glutathione peroxidase – SOD, Cat, GPx), lipid peroxidation (MDA concentration) and the total concentration of glutathione (GSH) were measured in liver. IH induced a prooxidant profile of enzyme activity (lower SOD activity and higher NOX/SOD and NOX/Cat activity ratio) without altering hepatic MDA and GSH content. Using RNA sequencing followed by a pathway enrichment analysis we identified putative hepatic genes underlying the interactions between IH and testosterone. ORX and IH altered the expression of genes involved in oxidoreductase activities, cytochromes dependent pathways, and glutathione metabolism. Among the genes upregulated in ORX-IH mice, the flavin-containing monooxygenases (FMO) are particularly relevant since these are potent hepatic antioxidant that could help prevent overt oxidative stress in ORX-IH mice.

overall_design: Male mice subjected to orchiectomy or sham-surgery were exposed to normoxia or intermittent hypoxia for 2 weeks. Liver samples were used to assess profiles of mRNA expression with RNA sequencing.

first: Gauthier

last: Ganouna-Cohen

first: François

last: Marcouiller

first: Charles

last: Joly Beauparlant

first: Arnaud

last: Droit

first: Elise

last: Belaidi

first: Aida

last: Bairam


title: Effect of d-alanine

city: Suita

first: Tomonori

state: Osaka

address: Yamadaoka 2-2

institute: Osaka University

summary: To investigate the effect of d-ala in mice

overall_design:
We performed gene expression profiling analysis using data obtained from RNA-seq
Comparative gene expression profiling analysis of RNA-seq data for mice treated with d-ala.

first: Shinsuke

last: Sakai


title: Gene expression profile at single cell level of tumor infiltrated Treg from the WT and the jmjd1c TregcKO mice

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

summary: Tumor infiltrated treg cells are considered to be crucial in the cancer immunotherapy. We used single cell RNA sequencing (scRNA-seq) to analyze the differences between WT and jmjd1cTreg cko mice and clarify the important function of jmjd1c.

overall_design: Tumor infiltrated treg of the WT and jmjd1c tregcKO mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of fluorence signal and analyzed using scRNAseq.

first: Xiaoming

last: Wang

first: Xuehui

last: Long

first: Yuliang


title: Effect of d-alanine on circadian rhythm

summary: To investigate the effect of  d-ala on circadian rhythm.

overall_design:
We analyzed RNA-seq of 4 kidneys from different mice treated with d-alanine. This experiment was performed twice. The final analysis was 8 kidneys per time point of 6.
Comparative gene expression profiling analysis of RNA-seq data


title: Cell type specific regulation of m6A modified RNAs in the aging brain

city: Philadelphia

first: Alexandra

last: Perlegos

state: PA

address: 231 Lynch Laboratories

department: Biology

institute: University of Pennsylvania

summary: The aging brain is highly vulnerable to cellular stress, and neurons often employ numerous mechanisms to combat neurotoxic proteins and promote healthy brain aging. The RNA modification m6A has been shown to be a critical regulator of RNA stability and translation in cells during stress. m6A is highly enriched in the Drosophila brain and is critical for the acute heat stress response. Here we examine m6A response to chronic stresses of aging and degenerative disease. In the brain, m6A levels dynamically increased with age and disease, marking critical signaling pathway transcripts that become downregulated in age and disease.  Unexpectedly, there is opposing regulation of m6A transcript translation in neural vs glial cells, which conferred different outcomes on animal healthspan with Mettl3 knockdown to reduce m6A. Moreover, these data reveal that knockdown of Mettl3 in glial tauopathy is beneficial, leading to increased animal survival. These findings provide mechanistic insight into regulation of m6A modified transcripts with age and disease that varies based on cell type.

overall_design:
head m6A-IP, total brain RNA-seq, FACS sorted Repo GFP+/- or Elav GFP+, and TRAP IP from Repo or Elav cells expressing UAS-RPL3-FLAG tag  used to investigate the role of the m6A RNA modification in age and with AB expression and Mettl3 knockdown.
For experiment 21 and 08, m6A-IPseq libraries were made using SMARTer Stranded Total RNA-Seq Kit V3 without rRNA depletion (takarabio, 634486) for IPed and input RNA. Experiment 07 brain RNA-seq libraries were prepared using the Tru-seq stranded mRNA library prep. Experiment 25, 27, and 29 FACS sorting and TRAP-seq libraries were made using SMART-Seq V4 + NexteraXT Library Preparation. All libraries were sequenced using illumina Illumina NovaSeq 6000 with 40M paired end reads (2x150bp).

first: Nancy

last: Bonini


title: PEGylated nanoparticles interact with macrophages independently of immune response factors and trigger a non-phagocytic, low-inflammatory response

status: Public on Dec 27 2023

city: Knoxville

first: Paul

last: Dalhaimer

state: Tennessee

address: 1512 Middle Drive, Room 420

department: Chemical and Biomolecular Engineering

institute: University of Tennessee

summary:
Poly-ethylene-glycol (PEG)-based nanoparticles (NPs) - including cylindrical micelles (CNPs), spherical micelles (SNPs), and PEGylated liposomes (PLs) - are hypothesized to be cleared in vivo by opsonization followed by liver macrophage phagocytosis. This hypothesis has been used to explain the rapid and significant localization of NPs to the liver after administration into the mammalian vasculature. Here, we show that the opsonization-phagocytosis nexus is not the major factor driving PEG-NP – macrophage interactions. First, mouse and human blood proteins had insignificant affinity for PEG-NPs. Second, PEG-NPs bound macrophages in the absence of serum proteins. Third, lipoproteins blocked PEG-NP binding to macrophages. Because of these findings, we tested the postulate that PEG-NPs bind (apo)lipoprotein receptors. Indeed, PEG-NPs triggered an in vitro macrophage transcription program that was similar to that triggered by lipoproteins and different from that triggered by lipopolysaccharide (LPS) and group A Streptococcus. Unlike LPS and pathogens, PLs did not increase transcripts involved in phagocytosis or inflammation. High-density lipoprotein (HDL) and SNPs triggered remarkably similar mouse bone-marrow-derived macrophage transcription programs. Unlike opsonized pathogens, CNPs, SNPs, and PLs lowered macrophage autophagosome levels and either reduced or did not increase the secretion of key macrophage pro-inflammatory cytokines and chemokines. Thus, the sequential opsonization and phagocytosis process is likely a minor aspect of PEG-NP – macrophage interactions. Instead, PEG-NP interactions with (apo)lipoprotein and scavenger receptors appear to be a strong driving force for PEG-NP – macrophage binding, entry, and downstream effects. We hypothesize that the high presence of these receptors on liver macrophages and on liver sinusoidal endothelial cells is the reason PEG-NPs localize rapidly and strongly to the liver.
To investigate the response of macrophages to nanoparticles, we incubated PEGylated liposomes (PLs), spherical nanoparticles (SNPs), high-density lipoproteins (HDL), low-density lipoproteins (LDL), Group A Streptococcus pathogens (JRS4), and lipopolysaccharide (LPS) with RAW264.7 and primary bone-marrow derived mouse macrophages

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone-marrow-derived macrophages (BMDMs) that were incubated with hHDL and SNPs

first: Monireh

last: Asoudeh

first: Nicole

last: Nguyen

first: Mitch

last: Raith

first: Desiree

middle: S

last: Denman

first: Uche

last: Anozie

first: Mahshid

last: Mokhtarnejad

first: Bamin

last: Khomami

first: Kaitlyn

last: Skotty

first: Sami

last: Isaac

first: Taylor

last: Gebhart

first: Lauren

last: Vaigneur

first: Aga

last: Gelgie

first: Oudessa

last: Kerro Dego

first: Trevor

last: Freeman

first: Jon

last: Beever


title: Non-invasive modulation of meningeal lymphatics ameliorates ageing and Alzheimer’s disease-associated pathology and cognition in miceted pathology and cognition in mice

city: Haikou

first: Feifan

last: Zhou

address: No 58, Renmin Avenue, Haikou, Hainan province

institute: School of Biomedical Engineering, Hainan University

summary: Meningeal lymphatic vessels (mLVs) have been shown to be involved in amyloid beta (Aβ) clearance, which is considered as a potential therapeutic target for Alzheimer’s disease (AD). In this study, based on the superficial spatial distribution of mLVs, a near-infrared light is employed to modulate lymphatic drainage, significantly improving cognition of both aged and AD (5xFAD and APP/PS1) mice, and alleviating AD-associated pathology by reducing Aβ deposition, neuroinflammation and neuronal damage. Furthermore, transmission electron microscopy imaging and RNA sequencing data indicate amelioration of mitochondrial metabolism and cellular junction of meningeal lymphatic endothelial cells (mLECs) by light modulation. These studies collectively suggest that near-infrared light treatment can improve cognitive function by strengthening scavenging ability of mLVs through restoring mLEC function. In conclusion, lymphatic drainage potentiation by light promotes pathological remission and cognitive enhancement in aging and AD mouse models, which offers a potential amelioration strategy for neurodegenerative diseases.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hippocampus, meninges and meningeal lymphatic endothelial cells of 6-month 5xFAD male mice receiving light treatment vs. no-light treatment, as well as 6-month 5xFAD male mice vs. 6-month wild type mice.

first: Miao

last: Wang

first: Congcong

last: Yan

first: Xi

last: Li

first: Tianhao

last: Yang

first: Shengnan

last: Wu

first: Qian

last: Liu

first: Qingming

last: Luo


title: Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology [Multiome snRNA/snATAC]

city: Baltimore

first: Seth

last: Blackshaw

address: 733 N Broadway

department: Neuroscience

institute: Johns Hopkins University

summary: Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataract. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq, and CUT&RUN-seq to discover novel mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Further, we divulge a conserved epigenetic paradigm of cellular differentiation, defined by progressive loss of H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation.

overall_design: Embryonic day 4 (E4) and day 5 (E5) chicken eyes were profiled for combined single-nucleus RNAseq and ATACseq using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression library preparation workflow (10X Genomics, 1000285 & 1000230) following 10X Genomics protocol CG000338 Rev F. Eyes from 3 embryos were pooled per reaction.

first: Jared

last: Tangeman

first: Sofia

last: Rebull

first: Erika

last: Grajales-Esquivel

first: Jacob

last: Weaver

first: Stacy

last: Bendezu-Sayas

first: Michael

middle: L

last: Robinson

first: Salil

last: Lachke

first: Katia

last: Del Rio-Tsonis


title: TTP overexpression inhibits reconstitution potential of HSC but generates a dominant mitigating effect in collagen antibody-induced arthritis mice models

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

summary: Tristetraprolin (TTP), encoded by Zfp36 in mice, is one of the best characterized tandem zinc-finger mRNA binding protein involved in mRNA deadenylation and decay. TTPΔARE mice lack an AU-rich motif in the 3’ untranslated regions of TTP mRNA leading to increased TTP mRNA stability and more TTP protein, resulting in elevated mRNA decay rates of TTP targets.  We examined the effect of TTP overexpression on the hematopoietic system and found alterations in red blood cell and white blood cell frequencies, with loss of platelets and B220 cells and gains of eosinophils and T-cells. TTPΔARE mice also have skewed primitive populations in the bone marrow with increases in myeloid-biased HSCs, but loss of granulocyte/macrophage biased MPP3 in both young and mid-aged mice. These populations changes were associated with cell-specific transcriptional alterations, but surprisingly consistent upregulation of TNF and TGFB signaling pathways in both progenitor populations. HSCs with overexpression of TTP had decreased reconstitution potential but generate hematopoietic environments that mitigate the inflammatory response induced by collagen antibody-induced arthritis (CAIA) model- even when TTP overexpressing cells are present at low frequencies. We present an overall analysis of elevated TTP expression in the early hematopoietic compartments which drives reduced overall reconstitution potential of the HSCs but leads to a dominant repression of inflammation induced in a rheumatoid arthritis model.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hematopetic stem cells (HSCs) and TPPdeltaARE HSCs

first: Mayuri

last: Tanaka-Yano

first: Le

last: Zong

first: Isabel

last: Beerman


title: Evolutionary and Developmental Specialization of Foveal Cell Types in the Marmoset

status: Public on Dec 26 2023

city: Los Angeles

first: Yi-Rong

last: Peng

state: CA

address: 100 Stein Plaza Driveway, B-133

department: Department of Ophthalmology

institute: University of California, Los Angeles

summary: In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the degree of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high throughput single cell RNA sequencing (scRNA-seq) to profile retinal cells of the common marmoset (Callithrix jacchus), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults.

overall_design: Foveal and peripheral retina tissues were dissected from neonatal and adult marmoset retinas. The foveal piece (~1.5mm in diameter) of the retina containing the whole fovea area was dissected out and dissociated into individual cells for high throughput droplet-based single cell RNA sequencing (scRNA-seq, 10x Genomics). The peripheral area (any area 5mm away from the foveal center) was also dissociated into a single cell suspension and underwent two enrichment procedures. We first used CD73, a photoreceptor marker, to label photoreceptors and used a microbeads-conjugated secondary antibody to deplete all the CD73 labeled cells (1). Second, we enriched RGCs and ACs with CD90 positive selection via fluorescence-activated cell sorting (FACS). The peripheral cells after CD73 depletion or CD90 enrichment were used to generate scRNA-seq libraries (10X Genomics). Libraries were sequenced on the Illumina HiSeq 2500 platform.


title: Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology [scRNA-seq]

state: MD

overall_design: Whole chicken embryo eyes were collected for snRNA-seq via the split-pool barcoding method, using the Parse Biosciences Single Cell Whole Transcriptome Kit Chemistry Version 1 (Parse Biosciences, SB2001). An eye from each of 3 chickens were pooled per condition, across the following conditions: embryonic day 4, embryonic day 5, embryonic day 4 6 hours post-retinectomy, and  embryonic day 4 6 hours post-retinectomy and FGF2 treatment. All nuclei were processed in aggregate across 7 sublibraries. Sublibraries 1-3 were sequenced across 3 distinct sequencing lanes.


title: Growth, enzymatic, and transcriptomic analysis of xyr1 deletion reveals a major regulator of plant biomass-degrading enzymes in Trichoderma harzianum

first: Paul

last: Daly

address: 50 Zhongling St

institute: Jiangsu Academy of Agricultural Sciences

summary: The regulation of plant biomass degradation by fungi is critical to the carbon cycle, and applications in bioproducts and biocontrol. Trichoderma harzianum is an important plant biomass degrader, enzyme producer, and biocontrol agent, but few putative major transcriptional regulators have been deleted in this species. The T. harzianum ortholog of the transcriptional activator XYR1/XlnR/XLR-1 was deleted, and the mutant strains were analyzed by growth profiling, enzymatic activities, and transcriptomics on cellulose. From plate cultures, the Δxyr1 mutant had reduced growth on D-xylose, xylan, and cellulose, and from shake-flask cultures with cellulose, the Δxyr1 mutant had ~ 90% lower β-glucosidase activity, and no detectable β-xylosidase or cellulase activity. The comparison of the transcriptomes from 18 h shake-flask cultures on D-fructose, without a carbon source, and cellulose, showed major effects of XYR1 deletion whereby the Δxyr1 mutant on cellulose was transcriptionally most similar to the cultures without a carbon source. The cellulose induced 43 plant biomass-degrading CAZymes including xylanases as well as cellulases, and most of these had massively lower expression in the Δxyr1 mutant. Expression of a sub-set of carbon catabolic enzymes, other transcription factors, and sugar transporters was also lower in the Δxyr1 mutant on cellulose. In summary, T. harzianum XYR1 is the master regulator of cellulases and xylanases, as well as regulating carbon catabolic enzymes.

overall_design: Transcriptome analysis of Trichoderma harzianum wild type strain and Δxyr1 (Triha1_1126) mutant from mycelia from shake-flask cultures with either D-fructose, cellulose or without an added carbon source at 18h after transfer from D-fructose pre-cultures. Three biological replicate shake-flask cultures were analyzed.

first: Yishen

last: Zhao

first: Siqiao

last: Chen

first: Xian

last: Wen

first: Lunji

last: Wang

first: Wilfred

last: Anjago

first: Tianchi

last: Tian

first: Yajuan

first: Jinfeng

last: Zhang

first: Sheng

last: Deng

first: Min

last: Jiu

first: Pengxiao

last: Fu

first: Dongmei

last: Zhou

first: Irina

last: Druzhinina

first: Lihui

last: Wei


title: Dynamic complexity of genetic regulatory effects in response to a high cholesterol, high fat diet in baboons

city: Chicago

first: Wenhe

last: Lin

state: Illinois

address: 920 E 58th St

institute: University of Chicago

summary: Steady-state expression quantitative trait loci (eQTLs) explain only a fraction of disease-associated loci identified through genome-wide association studies (GWAS), while eQTLs involved in gene-by-environment (GxE) interactions have rarely been characterized in humans due to experimental challenges. Using a baboon model, we found hundreds of eQTLs that emerge in adipose, liver, and muscle after prolonged exposure to high dietary fat and cholesterol. Diet-responsive eQTLs exhibit genomic localization and genic features that are distinct from steady-state eQTLs. Furthermore, the human orthologs associated with diet-responsive eQTLs are enriched for GWAS genes associated with human metabolic traits, suggesting that context-responsive eQTLs with more complex regulatory effects are likely to explain GWAS hits that do not seem to overlap with standard eQTLs. Our results highlight the complexity of genetic regulatory effects and the potential of eQTLs with disease-relevant GxE interactions in enhancing the understanding of GWAS signals for human complex disease using nonhuman primate models.

overall_design: We obtained liver, muscle, and adipose tissue biopsy samples from 99 captive baboons before and after they were fed a high cholesterol, high fat (HCHF) diet for two years. There are a total of 588 samples before quality controls (QC) and 570 samples after QC.

first: Yoav

last: Gilad

first: Laura

last: Cox


title: PTEN-restoration abrogates brain colonization and perivascular niche invasion by melanoma cells

city: Charlottesville

first: Sarah

state: VA

address: 1340 Jefferson Park Avenue

department: Dept. of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

summary: Background: Melanoma brain metastases (MBM) continues to be a significant clinical problem with limited treatment options. Highly invasive melanoma cells migrate along the vasculature and perivascular cells may contribute to residual disease and recurrence. PTEN loss and hyperactivation of AKT occur in MBM; however, a role for PTEN/AKT in perivascular invasion has not been described. Methods: We used in vivo intracranial injections of murine melanoma and bulk RNA sequencing of melanoma cells co-cultured with brain endothelial cells (brECs) to investigate brain colonization and perivascular invasion. Results: We found that PTEN-null melanoma cells were highly efficient at colonizing the perivascular niche relative to PTEN-expressing counterparts. PTEN re-expression (PTEN-RE) in melanoma significantly reduced brain colonization and migration along the vasculature. We hypothesized this phenotype was mediated through vascular-induced TGFβ secretion, which drives AKT phosphorylation. Disabling TGFβ signaling in melanoma cells reduced colonization and perivascular invasion; however, introduction of constitutively-active myristolated-AKT (myrAKT) restored overall tumor size but not perivascular invasion. Conclusions: PTEN loss facilitates perivascular brain colonization and invasion of melanoma. TGFβ-AKT signaling partially contributes to this phenotype, but further studies are needed to determine the complementary mechanisms that enable melanoma cells to both survive and spread along the brain vasculature.

overall_design: To study differences in perivascular invasion by Pten-null vs. Pten-expressing melanoma cells, we co-cultured mCherry+ D4M.3A or SM1WT1 melanoma cells with GFP+ brain endothelial cells (brECs, b.End3). After FACS separating out these populations we performed bulkRNA sequencing on mono-cultured vs. co-cultured samples with n=4 per condition.

first: Andrew

last: Dudley


title: Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology [CUT&RUN]

first: Seth

last: Blackshaw

overall_design: Cleavage Under Targets and Release Using Nuclease sequencing (CUT&RUN-seq) was performed according to manufacturer protocol, with slight modification, as described. Chicken embryos were obtained from Michigan State University and lenses were dissected from embryonic day 4.5 chicken embryos. Dissected lenses were collected on ice and pooled into 3 biological replicates consisting of approximately 44 lenses each. Histone modifications and PRC2 complex members were assayed, as described.

first: Jared

last: Tangeman

first: Sofia

last: Rebull

first: Erika

last: Grajales-Esquivel

first: Jacob

last: Weaver

first: Stacy

last: Bendezu-Sayas

first: Michael

last: Robinson

first: Salil

last: Lachke

first: Katia

last: Del Rio-Tsonis


title: Identity and Nature of Neural Stem Cells in the Adult Human Subventricular Zone

city: Montreal

first: Kevin

last: Petrecca

address: 3801 Rue University

department: Neuro

institute: McGill

summary: The existence of neural stem cells (NSCs) in adult human brain neurogenic regions remains unresolved. To address this, we created a cell atlas of the adult human subventricular zone (SVZ) derived from fresh neurosurgical samples using single-cell transcriptomics. We discovered 2 adult radial glia (RG)-like populations, aRG1 and aRG2. aRG1 shared features with fetal early RG (eRG) and aRG2 were transcriptomically similar to fetal outer RG (oRG). We also captured early neuronal and oligodendrocytic NSC states. We found that the biological programs driven by their transcriptomes support their roles as early-lineage NSCs. Finally, we show that these NSCs have the potential to transition between states and along lineage trajectories. These data reveal that multipotent NSCs reside in the adult human SVZ.

overall_design:
SVZ samples were acquired from 15 patients undergoing brain tumor surgery. Their ages ranged from 38 to 72 years (Fig. 1A, fig. S1). SVZ regions that were normal on MRI and were to be removed during the course of surgery were sampled

***************************************************************
Raw data files not provided as there are privacy concerns regarding sequencing file (BAM, FASTQ)
***************************************************************

first: Salma

last: Baig

first: Javad

last: Nadaf

first: Redouane

last: Allache

first: Phuong

last: Le

first: Annisa

last: Djedid

first: Maryam

last: Safisamghabadi

first: Marie-Christine

last: Guiot


title: Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology.

first: Seth

last: Blackshaw

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

overall_design: Refer to individual Series


title: Epigenetic regulation of cardiac maturation by arginine methyltransferase Carm1 [ChIP-Seq 2]

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

summary: Genome-wide mapping of histone modification H3R17me2a in neonatal cardiomyocyte

overall_design: Histone H3R17me2a ChIP-seq of Carm1 KO and Wildtype neonatal heart cardiomyocyte

first: Haofei

last: Wang

first: Jiandong

last: Liu

first: Li

last: Qian


title: Epigenetic regulation of cardiac maturation by arginine methyltransferase Carm1 (ChIP-Seq)

summary: Genome-wide mapping of histone modification H3R17me2a in neonatal hearts

overall_design: Histone H3R17me2a ChIP-seq  on neonatal heart samples


title: Epigenetic regulation of cardiac maturation by arginine methyltransferase Carm1 (ATAC-Seq)

summary: Analysis of genome-wide chromatin accessibility of the neonatal control and Carm1 mutant hearts

overall_design: ATAC-seq libraries were generated using neonatal control and  Carm1 mutant heart samples


title: SNUPN deficiency causes splicing and mRNA expression dysregulation in primary dermal fibroblasts.

city: Istanbul

first: Nathalie

last: Billard

state: Istanbul

address: Istanbul- Bayrampasa

institute: Koc university

summary: Our study identified an atypical form of muscular dystrophy in patients with a germline deficiency of SNURPORTIN-1 (SPN1), a key adaptor protein for the nuclear import of spliceosomal small nuclear ribonucleoproteins (snRNPs). Through transcriptomic analysis of primary dermal fibroblast mutants compared to control lines, we discovered dysregulation in splicing and mRNA expression, providing valuable insights into the molecular mechanisms underlying the pathogenesis of SPN1.

overall_design: RNA samples extracted from 3 mutant and 2 control lines of primary dermal fibroblasts were subjected to deep transcriptome sequencing. Bioinformatics differential splicing and expression analyses were performed to reveal mis-splicing events and dysregulated genes, respectively.

last: Escande-Beillard

first: Marwan

last: Nashabat

first: Nasrin

last: Nabavizadeh

first: Hilal

middle: P

last: Saraçoğlu

first: Esra

last: Börklü


title: Epigenetic regulation of cardiac maturation by arginine methyltransferase Carm1 [RNA-Seq 2]

summary: Transcriptome profile of Carm1 KO and Wildtype neonatal heart cardiomyocyte

overall_design: mRNA-seq of Carm1 KO and Wildtype neonatal heart cardiomyocyte


title: Epigenetic regulation of cardiac maturation by arginine methyltransferase Carm1


title: Epigenetic regulation of cardiac maturation by arginine methyltransferase Carm1 (RNA-Seq)

summary: Genome-wide transcriptome analysis of the neonatal control and Carm1 mutant hearts

overall_design: RNA-seq libraries were generated on neonatal control and Carm1 mutant heart samples


title: Structural basis of ribosomal 30S subunit degradation by RNase R

status: Public on Dec 25 2023

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

summary: Protein synthesis is a major energy-consuming process of the cell, which requires controlled production and turnover of ribosomes. While the last years have seen major advances in our understanding of ribosome biogenesis, structural insight into the degradation of ribosomes has been lacking. Here we present native structures of two distinct small ribosomal 30S subunit degradation intermediates associated with the 3’ to 5’ exonuclease, RNase R. The structures reveal that RNase R binds initially to the 30S platform to facilitate degradation of the functionally important anti-Shine-Dalgarno sequence and decoding site helix 44. RNase R then encounters a roadblock when it reaches the neck region of the 30S, which is overcome by a major structural rearrangement of the 30S head, involving loss of ribosomal proteins. RNase R parallels this movement, relocating to the decoding site, by using its N-terminal helix-turn-helix domain as an anchor. In vitro degradation assays suggest that head rearrangement poses a major kinetic barrier for RNase R, but also that the enzyme alone is sufficient for complete 30S degradation. Collectively, our results provide a mechanistic basis for RNase R-mediated 30S degradation and reveal that RNase R targets orphaned 30S subunits using a dynamic anchored binding site switching mechanism.

overall_design: Rnase R is a 3' exonuclease which degrades the 16S rRNA within the 30S ribosomal subunit. To compare the truncation site from an in vivo pull down and an in vitro rection whereby recombinant Rnase R was mixed with isolated 30S subunits, we sequenced the extracted RNA in a high-througput reaction. For the in vivo sequencing the RNA from three independent IPs of endogenously Flag-tagged RNase R was extracted using Trizol. The in vitro sequencing was also carried out over three independent reactions.

first: Lyudmila

last: Dimitrova-Paternoga

first: Sergo

last: Kasvandik

first: Bertrand

last: Beckert

first: Tanel

last: Tenson

first: Daniel

middle: N

last: Wilson

first: Helge

last: Paternoga


title: Genome-wide analyses of NPR1 and HAC1 direct targets in Arabidopsis

city: Seoul

first: Se-Hun

last: Yun

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National Univ.

summary: Genome-wide direct targets of Arabidopsis NPR1 and HAC1 were identified by chromain immunoprecipitation followed by sequencing (ChIP-seq). For the study, we used Arabidopsis expressing NPR1:GFP or HAC1:mCherry under native NPR1 or HAC1 promoter, respectively. To identify direct targets both under salicylic acid-treated and untreated conditions, we performed ChIP-seq by using 2,6-dichloroisonicotinc acid (INA; synthetic SA analog)-treated and untreated NPR1:GFP or HAC1:mCherry transgenic Arabidopsis plants.

overall_design: For the rep1&2 NPR1:GFP ChIP-seq, chromatin was digested by sonication and immunoprecipitation (IP) was performed in condition containing 1% sodium dodecyl sulfate (SDS).  For the rep3&4 NPR1:GFP ChIP-seq, chromatin was digested by micrococcal nuclease (MNase) treatment and IP was performed in condition containing 0.02% SDS. For the rep1&2 HAC1:mCherry ChIP-seq, chromatin digestion and IP were performed as described for the rep3&4 NPR1:GFP ChIP-seq. Samples were treated either with INA (+INA) or water (-INA) and incubated for 12 hours before harvesting. Columbia-0 (Col) was used as a non-transgenic wild-type control.

first: Irfan

last: Khan

first: Bosl

last: Noh

first: Yoo-Sun


title: Anp32e protects against accumulation of H2A.Z at Sox motif containing promoters during zebrafish gastrulation

status: Public on Dec 24 2023

city: Rochester

first: Fanju

last: Meng

state: NY

address: 601 Elmwood Avenue

department: Biomedical Genetics

institute: University of Rochester Medical Center

summary: Epigenetic regulation of chromatin states is crucial for proper gene expression programs and progression during development, but precise mechanisms by which epigenetic factors influence differentiation remain poorly understood. Here we find that the histone variant H2A.Z accumulates at Sox motif-containing promoters during zebrafish gastrulation while neighboring genes become transcriptionally active. These changes coincide with reduced expression of anp32e, the H2A.Z histone removal chaperone, suggesting that loss of Anp32e may lead to increases in H2A.Z binding during differentiation. Remarkably, genetic removal of Anp32e in embryos leads to H2A.Z accumulation prior to gastrulation and developmental genes become precociously active. Accordingly, H2A.Z accumulation occurs most extensively at Sox motif-associated genes, including many which are normally activated following gastrulation. Altogether, our results provide compelling evidence for a mechanism in which Anp32e preferentially restricts H2A.Z accumulation at Sox motifs to regulate the initial phases of developmental differentiation in zebrafish.

overall_design: Genomic profiles of H2A.Z and Anp32e were examined by CUT&Tag in developing zebrafish embryos

first: Fabian

last: Halblander


title: Multisensory gamma stimulation promotes glymphatic clearance of amyloid

status: Public on Dec 23 2023

city: Cambridge

last: Sun

state: MA

address: 455 Main St

department: EECS

institute: Whitehead Institute

summary: The glymphatic movement of fluid through the brain powerfully clears metabolic waste. We observed multisensory 40 Hz stimulation promotes the influx of cerebrospinal fluid and the efflux of interstitial fluid in the cortex of the 5XFAD mouse model of Alzheimer’s disease, which was associated with increased aquaporin-4 polarization along astrocytic endfeet, dilated meningeal lymphatic vessels, and amyloid accumulation in cervical lymph nodes. Inhibiting glymphatic clearance abolished the removal of amyloid by multisensory 40 Hz stimulation. Using chemogenetic manipulation and a genetically encoded sensor for neuropeptide signaling, we found VIP+ interneurons facilitate glymphatic clearance by regulating arterial pulsatility. Our findings establish novel mechanisms to recruit the glymphatic system to remove brain amyloid.

overall_design: 6-month-old 5XFAD mice were presented with gamma stimulation or no stimulation for 60 minutes, allowed to rest for 60 minutes, then nuclei were prepared for snRNA-seq using 10X Genomics platform. Four replicates were prepared for mice receiving gamma stimulation and no stimulation control, and each replicate contained the cortices of three 6-month-old 5XFAD mice.

first: Mitchell

last: Murdock

first: Li-Huei

last: Tsai


title: Arginine reprograms metabolism in liver cancer via RBM39 [AA_overexpression/RBM39depletion]

city: Basel

first: Dirk

last: Mossmann

state: BS

address: Spitalstrasse 41

department: Biocenter

country: Switzerland

institute: University of Basel

summary: Metabolic reprogramming is a hallmark of cancer.  However, mechanisms underlying metabolic reprogramming and how altered metabolism in turn enhances tumorigenicity are poorly understood.  Here, we report that arginine levels are elevated in hepatocellular carcinoma (HCC) despite reduced expression of arginine synthesis genes, in murine and patient tumors.  Tumor cells accumulate high levels of arginine due to increased uptake and reduced arginine-to-polyamine conversion.  Importantly, the high levels of arginine promote tumor formation via further metabolic reprogramming, including changes in glucose, amino acid, nucleotide, and fatty acid metabolism.  Mechanistically, arginine binds RNA-binding motif protein 39 (RBM39) to control expression of metabolic genes.  RBM39-mediated upregulation of asparagine synthesis leads to enhanced arginine uptake, creating a positive feedback loop to sustain high arginine levels and oncogenic metabolism.  Thus, arginine is a second messenger-like molecule that reprograms metabolism to promote tumor growth.

overall_design:
As part of this study we performed gene expression profiling analysis using data obtained from
[1] RNA-seq of SNU-449 cells stably overexpressing arginase1 (ARG1) and agmatinase (AGMAT).These data we compared to control cells (SNU-449 infected with empty vector).
[2] RNA-seq of SNU-449 cells treated with indisulam combined with RBM39 siRNA.These data we compared to control cells (SNU-499 treated with DMSO combinded with non-targeting siRNA).
Please note that processed data was generated with two different analysis pipelines; [1] differential splicing and intron retention analysis data (*ASEs_contrasts_20230307.xlsx) [2] conventional differential expression analysis (*contrasts_20230307.xlsx)

first: Christoph

last: Müller

first: Sujin

last: Park

first: Brendan

last: Ryback

first: Marco

middle: E

last: Colombi

first: Nathalie

last: Ritter

first: Diana

last: Weissenberger

first: Eva

last: Dazert

first: Mairene

last: Coto-Llerena

first: Sandro

last: Nuciforo

first: Lauriane

last: Blukacz

first: Caner

last: Ercan

first: Veronica

last: Jimenez

first: Salvatore

last: Piscuoglio

first: Fatima

last: Bosch

first: Luigi

last: Terracciano

first: Uwe

last: Sauer

first: Markus

last: Heim

first: Michael

last: Hall


title: Gene-expression data for SKH1 mice receiving doxorubicin, hindlimb radiation therapy or both

city: St Paul

first: Davis

last: Seelig

state: MN

address: 1352 Boyd Ave.

department: Department of Veterinary Clinical Sciences

institute: University of Minnesota

summary: NanoString nCounter Glial Profiling Panel

overall_design: In this study, there is gene data from six SKH1 mice brains per treatment groups, doxorubicin treated mice (DOX), hindlimb radiation treated mice (RT), doxorubicin + hindlimb radiation treated mice (DOX-RT), and control mice (Control)

first: Kimberly

last: Demos-Davies

first: Jessica

last: Lawrence

first: Clara

last: Ferreira


title: Deep phenotyping of Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome [PBMC RNA-Seq]

status: Public on Dec 22 2023

city: Bethesda

first: Avindra

last: Nath

address: 10 Center Drive

institute: NIH/NINDS

summary: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling disorder that may occur following an infection, yet the clinical phenotype is poorly defined, the pathophysiology is unknown, and no disease-modifying treatments are available. We used rigorous criteria to recruit a cohort of post-infectious ME/CFS (PI-ME/CFS) volunteers (n=17) with matched healthy controls (n=21) to conduct deep clinical and biological phenotyping using an extensive battery of tests. Among the many physical and cognitive complaints, one defining feature of PI-ME/CFS was an alteration of effort preference, rather than physical or central fatigue, due to dysfunction of integrative brain regions potentially associated with central catechol pathway dysregulation, with consequences on autonomic functioning and physical deconditioning. Immune profiling suggested chronic antigenic stimulation with increase in naïve and decrease in switched memory B-cells. Alterations in gene expression profiles of peripheral blood mononuclear cells and metabolic pathways were consistent with cellular phenotypic studies and demonstrated differences according to sex. Together these clinical abnormalities and biomarker differences provide unique insight into the underlying pathophysiology of PI-ME/CFS, which may guide future intervention.

overall_design:
PBMC RNA Sequencing: RNA was extracted from PBMC’s of participants using miRNeasy Micro Kit (QIAGEN). RNA was quantified using Qubit 3.0 fluorometer (Thermo Fisher Scientific) and its integrity confirmed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Dual index libraries were constructed with at least one unique index per each patient library using the TruSeq Stranded Total RNA HT Kit (Illumina) to enable subsequent pooling of equal quantities of individual libraries. The integrity and ratio of pooled libraries was validated using Miseq system (Illumina); then, paired-end sequencing (2 × 75 base pairs (bp)) was performed on an HiSeq 3000 sequencer (Illumina) with the Illumina HiSeq 3000 SBS Hit.   Participants:  A total of 27 post-infectious Myalgic encephalomyelitis/chronic fatigue syndrome (PI-ME/CFS) volunteers underwent research evaluation at the National Institutes of Health (NIH) Clinical Center. Two participants withdrew after providing informed consent and completing a history and physical exam without undergoing any research investigations. Of the remaining 25 PI-ME/CFS participants, four were found to have previously undiagnosed medical conditions that were related to ME/CFS symptoms. This included one case each of desmoplastic small round cell tumor, atypical inflammatory myositis, primary biliary cholangitis, and parkinsonism. Of the remaining 21 PI-ME/CFS participants, four participants were determined not to have a demonstrable infectious association to their ME/CFS symptoms during the case adjudication process (Table S2C). Details about the case adjudication process can be reviewed below in Supplement, Methods. A total of 17 adjudicated PI-ME/CFS volunteers completed the initial deep phenotyping measurements; eight of these volunteers also completed the exercise stress measurements.   A total of 25 healthy volunteers (HVs) were recruited to serve as comparator volunteers. Of these, one volunteer withdrew prior to completing deep phenotyping measurements. Three volunteers were excluded after evaluation related to asymptomatic medical conditions were identified. One had leukodystrophy, another had pleocytosis in the cerebrospinal fluid, and the third had early onset dementia. A total of 21 healthy volunteer comparators completed the initial deep phenotyping measurements; nine of these comparators also completed the exercise stress measurements.
The,CHI,Consortium

first: Brian

last: Walitt

first: Komudi

last: Singh

first: Mark

last: Hallett

first: Steve

last: Jacobson

first: Kong

last: Chen

first: Yoshimi

first: Richard

last: Apps

first: Jennifer

last: Barb

first: Patrick

last: Bedard

first: Robert

last: Brychta

first: Ashura

middle: W

last: Buckley

first: Peter

middle: D

last: Burbelo

first: Brice

last: Calco

first: Brianna

last: Cathay

first: Li

first: Jinguo

first: Foo

last: Cheung

first: Snigdha

last: Chigurupati

first: Lisa

last: Chin

first: Benjamin

last: Coleman

first: Amber

last: Courville

first: Madeleine

last: Deming

first: Bart

last: Drinkard

middle: R

last: Feng

last: Ferrucci

first: Scott

last: Gabel

first: Angelique

last: Gavin

first: David

last: Goldstein

first: Shahin

last: Hassanzadeh

first: Sean

last: Horan

first: Silvina

middle: G

last: Horovitz

first: Kory

last: Johnson

first: Anita

last: Govan

first: Kristine

last: Knutson

first: Joy

last: Kreskow

first: Samuel

last: LaMunion

last: Levin

first: Jonathan


title: Conserved cell-type specific signature of resilience to Alzheimer’s disease nominates role for excitatory intratelencephalic cortical neurons

city: Bar Harbor

first: Maria

last: Telpoukhovskaia

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Alzheimer’s disease (AD), the leading cause of dementia, affects millions of people worldwide. With no disease-modifying medication currently available, the human toll and economic costs are rising rapidly. Under current standards, a patient is diagnosed with AD when both cognitive decline and pathology (amyloid plaques and neurofibrillary tangles) are present. Remarkably, some individuals who have AD pathology remain cognitively normal. Uncovering factors that lead to “cognitive resilience” to AD is a promising path to create new targets for therapies. However, technical challenges discovering novel human resilience factors limit testing, validation, and nomination of novel drugs for AD. In this study, we use single-nucleus transcriptional profiles of postmortem cortex from human individuals with high AD pathology who were either cognitively normal (resilient) or cognitively impaired (susceptible) at time of death, as well as mouse strains that parallel these differences in cognition with high amyloid load. Our cross-species discovery approach highlights a novel role for excitatory layer 4/5 cortical neurons in promoting cognitive resilience to AD, and nominates several resilience genes that include ATP1A1, GRIA3, KCNMA1, and STXBP1. This putative cell type has been implicated in resilience in previous studies on bulk RNA-seq tissue, but our single-nucleus and cross-species approach identifies particular resilience-associated gene signatures in these cells. These novel resilience candidate genes were tested for replication in orthogonal data sets and confirmed to be correlated with cognitive resilience. Based on these gene signatures, we identified several potential mechanisms of resilience, including regulation of synaptic plasticity, axonal and dendritic development, and neurite vesicle transport along microtubules that are potentially targetable by available therapeutics. Because our discovery of resilience-associated genes in layer 4/5 cortical neurons originates from an integrated human and mouse transcriptomic space from susceptible and resilient individuals, we are positioned to test causality and perform mechanistic, validation, and pre-clinical studies in our human-relevant AD-BXD mouse panel.

overall_design: After contextual fear conditioning paradigm to measure percent freezing (CFM.Total), frontal cortical regions of brains from AD-BXD female mice and their female non-transgenic littermates at ages 6 and 14 mo were processed for snRNA-seq analysis.

first: Niran

last: Hadad

first: Vivek

last: Philip

first: Catherine

last: Kaczorowski


title: Deep phenotyping of Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome

first: Avindra

last: Nath


title: Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish

city: Nagatsuta

first: Hiroaki

last: Komiya

state: Yokohama

department: School of Life Science and Technology

institute: Tokyo Institute of Technology

summary: Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development, growth, and homeostasis. However, developmental origins of osteoblasts and chondroblasts, lineage relationship, progenitor cells, and their differentiation potentials throughout animal life are not seamlessly understood. In this study, we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages, and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed, they never change their lineage identities throughout their lives, even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells, OPCs, which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration.

overall_design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin, we isolated sp7- mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 days post amputation (dpa) caudal fin by fluorescence-activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors (OMPs), chondrogenic mesenchymal progenitors (CMPs), and osteoblasts.

first: Yuko

last: Sato

first: Hiroshi

last: Kimura

first: Atsushi

last: Kawakami


title: Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via regulation of key regenerative pathways

city: Tampa

first: Xuewei

last: Wang

state: FL

address: 4001 E Fletcher Ave, ALZ 339

department: Molecular Medicine

institute: University of South Florida


title: Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via regulation of key regenerative pathways (RRBS)

summary: Current treatments for neurodegenerative diseases and neural injuries fall short of success. One primary reason is that neurons in the mammalian central nervous system (CNS) lose their regeneration ability as they mature. Here, we investigated the role of Ezh2, a histone methyltransferase, in regulation of mammalian axon regeneration. We found that Ezh2 declined in the mouse nervous system during maturation but was upregulated in adult dorsal root ganglion neurons to support spontaneous axon regeneration following peripheral nerve injury. In addition, overexpression of Ezh2 in retinal ganglion cells in the CNS promoted optic nerve regeneration via both histone methylation-dependent and -independent mechanisms. Further investigation revealed that Ezh2 supported axon regeneration by systematically silencing the transcription of genes regulating synaptic function and inhibiting axon regeneration, while simultaneously activating various axon regeneration promoting factors. In particular, our study demonstrated that the GABA transporter 2 encoded by the gene Slc6a13 acted downstream of Ezh2 to control axon regeneration. Our study suggested that modulating chromatin accessibility was a promising strategy to promote CNS axon regeneration.

overall_design: To study how Ezh2 and its mutant form Ezh2-Y726D support axon regeneration of retinal ganglion cells, we profiled the changes in the DNA methylation landscape of retinal ganglion cells induced by Ezh2 or Ezh2-Y726D overexpression and/or optic nerve crush with reduced representation bisulfite sequencing. We intravitreally injected AAV2-GFP, AAV2-Ezh2, or AAV2-Ezh2-Y726D and crushed the optic nerve after two weeks. Uninjured groups only received AAV2 injection but did not undergo optic nerve crush. Three days after the optic nerve crush (injured groups) or 17 days after AAV2 injection (uninjured groups), retinal ganglion cells were enriched from dissociated retinal cells.

first: Xue-Wei

first: Shu-Guang

last: Yang

first: Ming-Wen

last: Hu

first: Rui-Ying

first: Chi

last: Zhang

first: Anish

last: Kosanam

first: Arinze

last: Ochuba

first: Jing-Jing

last: Jiang

first: Ximei

last: Luo

first: Yun

last: Guan

first: Jiang

last: Qian

first: Chang-Mei

last: Liu

first: Feng-Quan

last: Zhou


title: Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via regulation of key regenerative pathways (RNA-Seq II)

overall_design: To study how Ezh2 and its mutant form Ezh2-Y726D support axon regeneration of retinal ganglion cells, we profiled the transcriptomic changes in retinal ganglion cells induced by Ezh2-Y726D overexpression with RNA-seq. We intravitreally injected AAV2-GFP (control) or AAV2-Ezh2-Y726D and crushed the optic nerve after two weeks. Three days after the optic nerve crush, retinal ganglion cells were enriched from dissociated retinal cells.


title: Activation and functions of Col6a1+ fibroblasts in colitis-associated canceer

city: Vari

first: Vasiliki

last: Koliaraki

state: Attiki

address: 34 Fleming street

country: Greece

institute: BSRC "Alexander Fleming"

summary: This study shows that Col6a1cre+ cells constitute a subpopulation of cancer-associated fibroblasts in colitis-associated cancer that partly maintains its homeostatic features, while its activation is characterized by the acquisition of a distinct proangiogenic signature, which could be associated with their initial perivascular location.

overall_design: 3’ RNA-Seq (QuantSeq) profiling of 2 sorted mesenchymal cell subpopulations (Col6a1Cre-GFP+, Col6a1Cre-Tomato+) from AOM/DSS-induced colitis-associated tumors. 3 replicates per group.

first: Niki

last: Chalkidi

first: Maria

last: Melissari


title: Deep phenotyping of Post-infectious Myalgic Encephalomyelitis/Chronic Fatigue Syndrome [Protein]

first: Avindra

last: Nath

overall_design: The proteome for 42 separate Cerebrospinal fluid (CSF) samples were profiled using the SOMAscan human proteomic assay. Samples included 21 individuals diagnosed with Chronic Fatigue Syndrome (10 Male, 11 Female) and 21 Controls (9 Male, 12 Female).

first: Brian

last: Walitt

first: Komudi

last: Singh

first: Mark

last: Hallett

first: Steve

last: Jacobson

first: Kong

last: Chen

first: Yoshimi

last: Akahata

first: Richard

last: Apps

first: Jennifer

last: Barb

first: Patrick

last: Bedard

first: Robert

last: Brychta

first: Ashura

last: Buckley

first: Peter

last: Burbelo

first: Brice

last: Calco

first: Brianna

last: Cathay

first: Li

first: Jinguo

first: Foo

last: Cheung

first: Snigdha

last: Chigurupati

first: Lisa

last: Chin

first: Benjamin

last: Coleman

first: Amber

middle: B

last: Courville

first: Madeleine

last: Deming

first: Bart

last: Drinkard

last: Feng

first: Luigi

last: Ferrucci

first: Scott

last: Gabel

first: Angelique

last: Gavin

first: David

last: Goldstein

first: Shahin

last: Hassanzadeh

first: Sean

last: Horan

first: Silvina

last: Horovitz

first: Kory

last: Johnson

first: Anita

last: Govan

first: Kristine

last: Knutson

first: Joy

last: Kreskow

first: Samuel

last: LaMunion


title: Trabectedin derails transcription-coupled nucleotide excision repair to induce DNA breaks in highly transcribed genes

city: Zurich

first: Shana

last: Sturla

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

institute: ETH Zurich

summary: Most genotoxic anticancer agents fail in tumors with intact DNA repair. Therefore, trabectedin, a unique agent more toxic to cells with active DNA repair, specifically transcription-coupled nucleotide excision repair (TC-NER), provides new therapeutic opportunities. To unlock the potential of trabectedin and inform its application in precision oncology, a full mechanistic understanding of the drug’s TC-NER-dependent toxicity is needed. Here, we determined that abortive TC-NER of trabectedin-DNA adducts forms persistent single-strand breaks (SSBs) by blocking the second of the two sequential NER incisions by XPG. We mapped the 3’-hydroxyl groups of SSBs originating from the first NER incision at trabectedin lesions, recording TC-NER on a genome-wide scale. We showed that trabectedin-induced SSBs primarily occur in transcribed strands of active genes and peak near transcription start sites. Frequent SSBs were also found outside gene bodies, revealing TC-NER connection to divergent transcription from promoters. This work advances trabectedin as a tool compound for precision oncology and for studying TC-NER and transcription.

overall_design: Genome-wide mapping of DNA breaks with GLOE-seq in U2OS WT, CSB knockout (-KO), XPC-KO and XPA-KO cells as well as in HAP1 WT cells that were exposed to trabectedin (50 or 20 nM) or DMSO (as a control) in 1 to 3 biological replicates per exposure-cell line combination. In addition, genome-wide mapping of DNA breaks with GLOE-seq in U2OS WT gDNA treated with the nicking endonuclease Nb.BsrDI.

first: Vakil

last: Takhaveev


title: HiCAR analysis of zebrafish fin regeneration identifies cis-regulatory chromatin reorganization in response to injury

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

summary: HiCAR (Hi-C on accessible regulatory DNA), which is a genome-wide profiling of chromatin accessibility and open chromatin anchored cis-regulatory element (cRE) interactions, identified 28690 calling loops from zebrafish caudal fins at three different time points (0, 1 and 4 day(s) post amputation (dpa)) including 5022 regeneration-responsive loops (17.5%).

overall_design: 10 caudal fins each of adult wild type zebrafish at 0, 1 and 4 dpa time points were pooled and three biological replicates were used for preparing HiCAR DNA libraries 10 caudal fins each of adult wild type zebrafish at 0, 1 and 4 dpa time points were pooled and three biological replicates were used for preparing HiCAR DNA libraries to find regeneration-responsive loops only in 1 and/or 4 dpa regenerating fins not in 0 dpa uninjured control fins..

first: Kenneth

last: Poss

first: Kazunori

last: Ando

first: Jianhong

last: Ou

first: Yarui

last: Diao

first: Xiaolin

last: Wei


title: Bulk RNA-seq analysis during fin regeneration of regeneration-associated silencer knockout zebrafish reveals its repressive ability silencing expression of nearby genes

summary: Bulk RNA-seq analysis during fin regeneration of regeneration-associated silencer (s1) knockout zebrafish identified several up-regulated genes near s1 from comparison of silencer knockout mutant fish and their WT siblings at three different time points (0, 1 and 4 day(s) post amputation (dpa)), indicating that s1 has repressive ability to control downregulation of the nearby genes.

overall_design: 10 caudal fins each of regeneration-associated silencer (s1) knockout zebrafish and their WT siblings at 0, 1 and 4 dpa time points were pooled and three biological replicates were used for preparing bulk RNA-seq DNA libraries to find differentially upregulated genes in s1 knockout fish at each timepoint.


title: Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via regulation of key regenerative pathways (ATAC-Seq)

first: Xuewei

last: Wang

overall_design: To study how Ezh2 and its mutant form Ezh2-Y726D support axon regeneration of retinal ganglion cells, we profiled the epigenetic changes in RGCs induced by Ezh2 or Ezh2-Y726D overexpression with RNA-seq. We intravitreally injected AAV2-GFP (control) or AAV2-Ezh2 and crushed the optic nerve after two weeks. Three days after the optic nerve crush, retinal ganglion cells were enriched from dissociated retinal cells.

first: Xue-Wei

first: Shu-Guang

last: Yang

first: Ming-Wen

last: Hu

first: Rui-Ying

first: Chi

last: Zhang

first: Anish

last: Kosanam

first: Arinze

middle: J

last: Ochuba

first: Jing-Jing

last: Jiang

first: Ximei

last: Luo

first: Yun

last: Guan

first: Jiang

last: Qian

first: Chang-Mei

last: Liu

first: Feng-Quan

last: Zhou


title: Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in Clostridioides difficile

status: Public on Dec 21 2023

first: Daniel

last: Pensinger

address: 1550 Linden Dr., MSB Rm3435

department: Department of Gastroenterology and Department of Medical Microbiology and Immunology

institute: UW-Madison

summary: The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. difficile in vitro and is correlated with C. difficile-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in C. difficile occurs under conditions where C. difficile also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into C. difficile cells and is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of butyrogenic pathway(s) in C. difficile coincides with alterations in toxin release and sporulation. Together, this work highlights butyrate as a marker of a C. difficile inhospitable environment to which C. difficile responds by releasing its diarrheagenic toxins and producing environmentally-resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how C. difficile growth is inhibited by butyrate and how butyrate alters C. difficile virulence in the face of a highly competitive and dynamic gut environment.

overall_design:
C. difficile 630 overnight cultures were back-diluted 1:50 in 20mL mRCM in 50mL conical tubes with 50 mM sodium butyrate or 50 mM sodium chloride adjusted to pH=6.5. Harvest was performed at OD600=0.3-0.5 for mid-log phase samples, at 24 hours post inoculation (early stationary phase) or at 48 hours post inoculation (late stationary phase).
At the appropriate time points, 5mL aliquots of the cultures were diluted 1:1 in chilled 1:1 Ethanol:Acetone to preserve RNA. These samples were then centrifuged for 5 minutes at 3000 x g at room temperature and cell pellets were frozen at -80˚C. Immediately prior to RNA extraction, cell pellets were centrifuged at 4˚C at 3000 x g for 1minute. Residual supernatant was removed from the cell pellets, which were subsequently washed with 5mL nuclease free PBS. Washed pellets were centrifuged at 4˚C at 3000 x g for 1minute, the supernatant was removed, and the resulting pellet was resuspended in 1mL TRIzol and processed using a TRIzol Plus RNA Purification Kit (Thermo) with on-column DNase treatment according to the manufacturer’s instructions. Purified RNA was frozen at -80C and RNA integrity was confirmed via BioAnalyzer (Agilent) prior to proceeding.
RNA-seq on high quality rRNA-depleted RNA extracts (12M paired end reads per sample) and transcript level quantification, count normalization, and differential expression analysis were performed using the C. difficile 630 reference genome (GCF_000009205.2_ASM920v2) for sequence alignments (SeqCenter, Pittsburgh, Pennsylvania, USA).

first: Horia

last: Dobrila

first: David

middle: M

last: Stevenson

first: Nicole

last: Hryckowian

last: Amador-Noguez

first: Andrew


title: Lhx3/4 initiates a cardiopharyngeal-specific transcriptional program in response to widespread FGF signaling

city: Swarthmore

first: Bradley

last: Davidson

state: PA

address: 500 College Ave

institute: Swarthmore College

summary: Individual signaling pathways, such as fibroblast growth factors (FGFs), can regulate a plethora of inductive events. According to current paradigms, signal-dependent transcription factors, such as FGF/MapK-activated Ets family factors, partner with lineage-determining factors to achieve regulatory specificity. However, many aspects of this model have not been rigorously investigated. One key question relates to whether lineage-determining factors dictate lineage-specific responses to inductive signals or facilitate these responses in collaboration with other inputs. We utilize the chordate model Ciona robusta to investigate mechanisms generating lineage-specific induction. Previous studies in C. robusta have shown that cardiopharyngeal progenitor cells are specified through the combined activity of FGF-activated Ets1/2.b and an inferred ATTA-binding transcriptional cofactor. Here we show that the homeobox transcription factor Lhx3/4 serves as the lineage-determining transcription factor that dictates cardiopharyngeal-specific transcription in response to pleiotropic FGF signaling. Targeted knockdown of Lhx3/4 leads to loss of cardiopharyngeal gene expression. Strikingly, ectopic expression of Lhx3/4 in a neuroectodermal lineage subject to FGF-dependent specification leads to ectopic cardiopharyngeal gene expression in this lineage. Furthermore, ectopic Lhx3/4 expression disrupts neural plate morphogenesis, generating aberrant cell behaviors associated with execution of incompatible morphogenetic programs. Based on these findings we propose that combinatorial regulation by signal-dependent and lineage-determinant factors represents a generalizable, previously uncategorized regulatory subcircuit we term cofactor-dependent induction. Integration of this subcircuit into theoretical models will facilitate accurate predictions regarding the impact of gene regulatory network rewiring on evolutionary diversification and disease ontogeny.

overall_design: To test hypotheses regarding properties of the C. robusta cardiopharyngeal lineage determinant Lhx3/4, we ectopically expressed the transcription factor in the C. robusta anterior neural plate lineage. Our control samples (in triplicate: C1, C2, C3) consist of RNA sequencing data from FACS-collected GFP+ cells from embryos electroporated with only Dmrt>GFP. The experimental samples (in triplicate: X1, X2, X3) consist of RNA sequencing data from FACS-collected GFP+ cells from embryos electroporated with Dmrt>GFP and Dmrt>Lhx3/4.  We used DESeq2 to analyze Lhx3/4-driven transcriptomic changes.

first: C. J.

last: Pickett

first: Hannah

last: Gruner