title: Detection of APOBEC3B-mediated RNA editing sites in T-47D cells [RNA-seq]

summary: RNA editing is a crucial post-transcriptional process that diversifies proteomic outcomes and influences gene expression. Particularly, the APOBEC3 family has emerged as a significant player in this mechanism, with APOBEC3A (A3A) showing notable roles in immune response and stress conditions. APOBEC3B (A3B), another family member, has garnered attention for its potential role in breast cancer genomic mutations. In this study, we employ an inducible expression cell model and a novel methodology for identifying differential variants in RNA (DVRs) to map A3B-mediated RNA editing sites in a breast cancer cell model. Our findings indicate that A3B engages in selective RNA editing and targets NEAT1 and MALAT1 long non-coding RNAs. Notably, the binding of these RNAs sequesters A3B’s catalytic activity, and thereby affects A3A’s activity through a feedback loop.

overall_design: To sample the RNA editing sites mediated by APOBEC3B, we conducted RNA-seq and WGS, followed by joint mutation calling and log ratio test to detect differentiated variants on RNA (DVRs).


title: Unraveling the Role of MIXL1 Activation in Endoderm Differentiation of Isogenic Human Induced Pluripotent Stem Cells [scRNA-seq]

status: Public on Aug 01 2024

city: Westmead

first: Nader

last: Aryamanesh

state: NSW

address: 214 Hawkesbury Rd

department: Bioinformatics

country: Australia

institute: CMRI

type: Expression profiling by high throughput sequencing

summary: Human induced pluripotent stem cells (hiPSC) possess the ability to differentiate into a multitude of tissue types but display heterogeneity in the propensity of differentiation into specific tissue lineages. An examination of isogenic hiPSC lines revealed variations in the endoderm propensity under directed differentiation conditions. Characterization of the transcriptome and proteome of the hiPSC lines showed that MIXL1 activity at the early differentiation stage correlated with the efficacy of generating definitive endoderm and further differentiation into endoderm derivatives. Enforced expression of MIXL1 in the endoderm-incompetent hiPSCs enhanced the propensity of endoderm differentiation, suggesting that modulation of key drivers of lineage differentiation can re-wire hiPSC to the desired lineage propensity for stem cell products.

overall_design: hiPSC lines were subjected= to definitive endoderm differentiation and single cell transciptomic signature was analysed at 0h, 24h and 96h of differentiation.

first: Pierre

last: Osteil

first: Hilary

last: Knowles

first: Nicole

last: Santucci

first: Patrick

last: Tam


status: Public on Sep 04 2024

city: New York

first: Xuanrong

last: Chen

state: New York

address: 1300 York Ave

country: USA

institute: Weill Cornell Medicine

summary: The androgen receptor (AR) is the central determinant of prostate tissue identity and differentiation, controlling normal, growth-suppressive prostate-specific gene expression. It is also a key driver of prostate tumorigenesis, becoming “hijacked” to drive oncogenic transcription. However, the regulatory elements determining the execution of the growth suppressive AR transcriptional program, and whether this can be reactivated in prostate cancer (PCa) cells remains unclear. Canonical androgen response element (ARE) motifs are the classic DNA binding element for AR. Here, we used a genome-wide strategy to modulate regulatory elements containing AREs to define distinct AR transcriptional programs. We find that activation of these AREs is specifically associated with differentiation and growth suppressive transcription, and this can be reactivated to cause death in AR+ PCa cells. In contrast, repression of AREs is well tolerated by PCa cells, but deleterious to normal prostate cells. Finally, gene expression signatures driven by ARE activity are associated with improved prognosis and luminal phenotypes in human PCa patients. This study demonstrates that canonical AREs are responsible for a normal, growth-suppressive, lineage-specific transcriptional program, that this can be reengaged in PCa cells for potential therapeutic benefit, and genes controlled by this mechanism are clinically relevant in human PCa patients.

overall_design: Gene expression profiling with RNA-seq in RWPE1 with inducible expression of MACC constructs.

first: Christopher

middle: E

last: Barbieri


title: PADI4-mediated citrullination of histone H3 stimulates HIV-1 transcription

status: Public on Aug 05 2024

city: Huddinge

first: Peter

last: Svensson

state: Stockholm

address: Hälsovägen 9

department: Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

type: Genome binding/occupancy profiling by high throughput sequencing

summary: HIV-1 infection establishes a reservoir of long-lived cells with integrated proviral DNA that can persist despite antiretroviral therapy (ART). The mechanisms governing the transcriptional regulation of the provirus are complex and incompletely understood. Here, we investigated the role of histone H3 citrullination, a post-translational modification catalyzed by protein-arginine deiminase type-4 (PADI4), in HIV-1 transcription and latency. We found that PADI4 inhibition by GSK484 reduced HIV-1 transcription after T cell activation in ex vivo cultures of CD4 T cells from viremic and ART treated people living with HIV-1 (PLWH). The effect was more pronounced in the viremic group. Using cell models of HIV-1 latency, we showed that PADI4-mediated citrullination of histone H3 occurred at the HIV-1 promoter upon T cell stimulation which facilitated proviral transcription. HIV-1 preferentially integrated into genomic regions marked by H3 citrullination and these integrated proviruses were less prone to latency compared to those in non-citrullinated chromatin. Inhibiting PADI4 led to compaction of the HIV-1 promoter chromatin and an increase of HP1a-covered heterochromatin, in a mechanism partly dependent on the HUSH complex. Our data reveal a novel mechanism of HIV-1 transcriptional regulation by PADI4 through H3 citrullination.

overall_design: CUT&Tag for histone H3cit in human Jurkat-derived cells. Cells were activated (or not) with PMA/ionomycin together (or not) with PADI4 inhibitor GSK484.

first: Luca

last: Love

first: Bianca

last: Jütte

first: Piotr

last: Nowak


title: Generation of cellular diversity through temporal patterning of radial glia during mouse corticogenesis I

status: Public on Sep 03 2024

city: Shanghai

first: XIAOSU

last: LI

state: Shanghai

address: 131 Dongan Road

country: China

institute: Fudan University

summary: Neural cell type diversity arises from both spatial and temporal patterning of neural stem cells. Although spatial patterning mechanisms have been extensively studied, temporal patterning mechanisms remain relatively unexplored. In this study, we addressed generation of diverse neural cell types through lineage progression of mouse cortical radial glia. The time series scRNA-seq and snATAC-seq of mouse cortical development revealed that radial glia temporally transitioned from neurogenesis to gliogenesis.  During gliogenic stages, various cell types were generated simultaneously along multidirectional lineage trajectories. We established comprehensive molecular maps for cortical lineage commitment and cellular diversification. The transcriptome and epigenome of cortical radial glia exhibit temporal dynamics, as revealed by scRNA-seq and snATAC-seq. Lhx2, a transcription factor with temporal dynamic chromatin binding activities, was identified as a key regulator of the neurogenesis-to-gliogenesis transition. It maintains neurogenic competence by establishing the active epigenetic state of its target genes.

overall_design: Time series scRNA-seq and snATAC-seq on purified cortical progenitor. scRNA-seq on Lhx2 cKO cortical progenitor. Lhx2 CUT&Tag-seq on cortical progenitor at E13, E15, and E18. ATAC-seq, H3K4me3, H3K27me3, and Polr2a CUT&Tag-seq of control and Lhx2 cKO cortices at E15.

first: Xiaosu

last: Li

first: Lin

last: Yang

first: Zhengang


title: The Drosophila Estrogen-Related Receptor acts within the larval fat body to promote triglyceride storage

status: Public on Aug 02 2024

city: Bloomington

first: Jason

middle: M

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

summary: Members of the Estrogen-Related Receptor (ERR) family of nuclear receptors (NR) serve a key role in coordinating triglyceride (TAG) accumulation with juvenile growth and development. In both insects and mammals, loss of ERR activity disrupts (TAG) storage during the post-embryonic growth phase, with loss-of-function mutations in mouseErraandDrosophila melanogaster dERRinducing a lean phenotype. However, the role of insect ERRs in controlling TAG accumulation remains poorly understood, as previous multiomic studies largely relied on whole animal analyses. Here we address this shortcoming by using tissue-specific approaches to determine how dERR regulates lipid metabolism within theDrosophilalarval fat body. We found that dERR autonomously promotes TAG accumulation within fat body cells by regulating expression of genes involved in glycolysis, the pentose phosphate pathway, lipid synthesis, andb-oxidation. As an extension of these results, we not only discovered thatdERRmutant fat bodies exhibit decreased expression of known HNF4 target genes but also found that dHNF4 activity is decreased indERRmutants. Overall, our findings indicate that dERR plays a multifaceted role in the larval fat body to coordinate lipid storage with developmental growth and hint at a conserved mechanism by which ERR and HNF4 homologs coordinately regulate metabolic gene expression

overall_design: RNA was isolated from both the fat body and whole animal homogenates of mid-L2 ERR[1/2] mutants and ERR[1/+] heterozygous controls

first: Tess

middle: D

last: Fasteen

first: Melody

last: Maniex

first: Robert

last: Policastro

first: Maria

last: Sterrett

first: Gabriel

last: Zentner


title: Subthreshold rejection activity in many kidney transplants currently classified as having no rejection.

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

summary: Most kidney transplant patients who undergo biopsies are classified as having no rejection based on consensus thresholds. However, we hypothesized that because these patients have normal adaptive immune systems, T cell-mediated rejection (TCMR) and antibody-mediated rejection (ABMR) may exist as subthreshold activity in some transplants currently classified as no rejection. Subthreshold molecular TCMR and/or ABMR activity molecular activity was detectable as elevated classifier scores in many biopsies classified as no rejection, with ABMR activity in many TCMR biopsies and TCMR activity in many ABMR biopsies. In biopsies classified as no rejection histologically and molecularly, molecular TCMR classifier scores correlated with increases in histologic TCMR features and molecular injury, lower eGFR, and higher risk of graft loss, and molecular ABMR activity correlated with increased glomerulitis and donor-specific antibody. No rejection biopsies with high subthreshold TCMR or ABMR activity had a higher probability of having TCMR or ABMR respectively diagnosed in a future biopsy. We conclude that many kidney transplant recipients have unrecognized subthreshold TCMR or ABMR activity, with significant implications for future problems.

overall_design: To examine this question, we studied genome-wide microarray results from 5086 kidney transplant biopsies (4170 patients). An updated archetypal analysis designated 56% of biopsies as no rejection. The existing 1745 samples from GSE124203 are re-analyzed.


title: Unraveling the Role of MIXL1 Activation in Endoderm Differentiation of Isogenic Human Induced Pluripotent Stem Cells [RNA-Seq]

first: Nader

last: Aryamanesh

overall_design: Five hiPSC lines from four isogenic groups (two males and two females) were subjected to definitive endoderm differentiation and chromatin accessibility was assessed 24h after induction by RNA-seq.

first: Pierre

last: Osteil

first: Nicole

last: Santucci

first: Patrick

last: Tam


title: Fibroblast-specific TGF-b signaling mediates dysfunction, fibrosis and hypertrophy in a mouse model of obesity-associated type 2 diabetes

status: Public on Aug 18 2024

city: NYC

first: Izabela

last: Tuleta

state: NY

address: 1300 Morris Park Avenue

department: Cardiology

institute: Albert Einstein College of Medicine

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

overall_design: Refer to individual Series


title: Stabilization of mitochondrial double stranded RNAs by SLIRP promotes positive feedback amplification of antiviral signaling.

status: Public on Jul 31 2024

city: Daejeon

first: Doyeong

last: Ku

address: Daehak-ro, 291

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: To investigate the gene expression upon dsRNA stress, we established HCT116 cell lines after 7h from transfection of poly I:C.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells after 7h from poly I:C transfection.

first: Namseok

last: Lee

first: Yoosik

last: Kim


title: A pan-KRAS inhibitor and its derived degrader elicit multifaceted anti-tumor efficacy in KRAS-driven cancers [bulk RNA-seq]

status: Public on Jul 30 2024

city: 上海市

first: 新婷

last: 夏

state: 上海市

address: 东川路500号

department: 生命科学学院

institute: 华东师范大学

summary: KRAS is the most frequently mutated oncogene in human cancers, but to date, only KRASG12C inhibitors have been FDA-approved. Small-molecule inhibitors that target other more prevalent KRAS mutations are in urgent clinical need. Here, we report a highly potent pan-KRAS inhibitor, MCB-294, that selectively targets KRAS, but not HRAS or NRAS. Molecular profiling studies show that MCB-294 binds to and inhibits several KRAS mutants, including G12D, G12C, G12V, thereby disabling KRAS oncogenic signaling. MCB-294 is well tolerated in mice and exhibits remarkable therapeutic efficacy against the growth of a comprehensive range of KRAS-driven cancer cell lines, patient-derived organoids, and tumor xenografts and prolongs mouse survival. By employing an MCB-294 derivative as the KRAS binder, we further identify a VHL-based pan-KRAS degrader, MCB-36, that efficiently degrades KRAS in vitro and in vivo through the ubiquitin-proteasome system. Importantly, MCB-294 and MCB-36 not only effectively kill KRASG12C inhibitor-resistant cells, but also reshape the tumor microenvironment by boosting T cell-mediated anti-tumor immunity. Taken together, our findings demonstrate a successful and feasible strategy for targeting pan-KRAS to impair multifaceted features of KRAS-driven cancers.

overall_design: To investigate the action of MCB-294 or MCB-36 on the modulation of sotorasib-resistance cell modle (MIA PaCa-2/SR), MIA PaCa-2 and MIA PaCa-2/SR treated with MCB-294 (30 nM, 3h) or MCB-36 (100 nM, 12h)  were harvested for bulk RNA-seq.

first: juanjuan

last: Feng

first: xuanzheng

last: Xiao

first: xinting

last: Xia


title: Energetic portrait of the amyloid beta transition state

status: Public on Jul 26 2024

city: Barcelona

first: Mireia

last: Seuma

state: Barcelona

address: Carrer de Baldiri Reixac, 10, 12

country: Spain

institute: Institute for Bioengineering of Catalonia

summary: In this study we use massively parallel combinatorial mutagenesis, a kinetic selection assay, and machine learning to better understand the nucleation reaction of amyloid beta (Aꞵ42), the protein that aggregates as a hallmark of Alzheimer’s disease (AD) and is mutated to cause familial AD.

overall_design: Systematic measurement of the nucleation of mutations at Amyloid beta 1-42 (AB1-42). We constructed mutagenesis libraries containing: double amino acid mutations at AB1-28 (N_terminal_Ab42_double_mutants), or double amino acid mutations at AB28-42 (C_terminal_Ab42_double_mutants), or combinatorial mutations with DTS codon mutagenesis (Combinatorial_1 and Combinatorial_2). The selection experiment to quantify amyloid nucleation for each library was performed in 3 biological replicates, each of them with one input sample (before selection) and one output sample (after selection).

first: Anna

last: Arutyunyan

first: Ben

last: Lehner

first: Benedetta

last: Bolognesi


title: Effects of PP121/ bufalin-induced differentiation on gene expression of neuroblastoma SK-N-AS and GIMEN cells

status: Public on Jul 23 2024

city: Boston

first: Lien

middle: Dieu

last: Nguyen

state: MA

address: 60 Fenwood Road, Hale Building for Transformative Medicine, Lab: 9006.009

department: Neurology

institute: Brigham and Women's Hospital

summary: Tumor cell heterogeneity in neuroblastoma, a pediatric cancer arising from neural crest-derived progenitor cells, poses a significant clinical challenge. In particular, unlike adrenergic (ADRN) neuroblastoma cells, mesenchymal (MES) cells are resistant to chemotherapy and retinoid therapy and thereby significantly contribute to relapses and treatment failures. Previous research suggested that overexpression or activation of miR-124, a neurogenic microRNA with tumor suppressor activity, can induce the differentiation of retinoic acid-resistant neuroblastoma cells. Leveraging our established screen for miRNA modulatory small molecules, we validated PP121, a dual inhibitor of tyrosine and phosphoinositide kinases, as a robust inducer of miR-124. A combination of PP121 and miR-132-inducing bufalin synergistically arrests proliferation, induces differentiation, and prolongs the survival of differentiated MES SK-N-AS cells for 8 weeks. RNA-seq and deconvolution analyses revealed a collapse of the ADRN core regulatory circuitry (CRC) and the emergence of novel CRCs associated with chromaffin cells and Schwann cell precursors. Using a similar protocol, we differentiated and maintained other MES neuroblastoma, as well as glioblastoma cells, over 16 weeks. In conclusion, our novel protocol suggests a promising treatment for therapy-resistant cancers of the nervous system. Moreover, these long-lived, differentiated cells provide valuable models for studying mechanisms underlying differentiation, maturation, and senescence.

overall_design: Comparing RNA profiles of naïve untreated cells vs. PP121/bufalin-differentiated cells at various time points

last: Krichevsky


title: Transcriptome sequencing analysis in glioma cells up- or down- regulated by lncRNA H19

city: Cheongju-si

first: Wanyeon

state: Chungbuk

address: Taeseongtabyeonro 250, Gangnaemyeon, Heungdeokgu

department: Biology Education

institute: Korea National University of Education

summary: To investigate the role of lncRNA H19 in glioma, transcriptome analysis was performed on H19 overexpressed, knocked down, and control groups in U87MG and A172.

overall_design:
Transcriptome sequencing analysis was performed in three groups: a group in which H19 was overexpressed, a group in which it was knocked down, and an untreated group. Six samples were analyzed using the cell lines U87MG and A172.
Examine glioma cells up- or down- regulated by lncRNA H19

first: Yeonsoo

last: Chae

first: Jungwook

last: Roh


title: High-Throughput Transcriptomics Screen of ToxCast Chemicals in U-2 OS Cells

status: Public on Aug 20 2024

city: Durham

first: Derik

middle: Evan

last: Haggard

state: North Carolina

address: 109 TW Alexander Drive

department: ORD-CCTE-SCDCD-DMMB

institute: US EPA

summary: New approach methodologies (NAMs) aim to accelerate the pace of chemical risk assessment while simultaneously reducing cost and dependency on animal studies. High Throughput Transcriptomics (HTTr) is an emerging NAM in the field of chemical hazard evaluation for establishing in vitro points-of-departure and providing mechanistic insight. In the current study, 1,201 test chemicals were screened for bioactivity at eight concentrations using a 24-hour exposure duration in the human- derived U-2 OS osteosarcoma cell line with HTTr. Assay reproducibility was assessed using three reference chemicals that were screened on every assay plate. The resulting transcriptomics data were analyzed by aggregating signal from genes into signature scores using gene set enrichment analysis, followed by concentration-response modeling of signatures scores. Signature scores were used to predict putative mechanisms of action, and to identify biological pathway altering concentrations (BPACs). BPACs were consistent across replicates for each reference chemical, with replicate BPAC standard deviations as low as 5.6×10-3 µM, demonstrating the internal reproducibility of HTTr-derived potency estimates. BPACs of test chemicals showed modest agreement (R2 = 0.55) with existing phenotype altering concentrations from high throughput phenotypic profiling using Cell Painting of the same chemicals in the same cell line.  Altogether, this HTTr based chemical screen contributes to an accumulating pool of publicly available transcriptomic data relevant for chemical hazard evaluation and reinforces the utility of cell based molecular profiling methods in estimating chemical potency and predicting mechanism of action across a diverse set of chemicals.

overall_design: In a previous study, we established experimental and computational workflows for HTTr screening in a human cell model (Harrill et al., 2021). The TempO-Seq human whole transcriptome assay (Yeakley et al., 2017) was used to identify biological pathway altering concentrations (BPACs) and characterize the biological activity of test chemicals. The present study applies those methods to a much larger chemical space. Here, we screened 1201 unique chemicals from the ToxCast chemical collection in U-2 OS cells using HTTr and the similar experimental conditions as described previously (Harrill et al., 2021).

first: Joseph

middle: L

last: Bundy

first: Logan

middle: J

last: Everett

first: Jesse

last: Rogers

first: Jo

last: Nyffeler

first: Gabrielle

last: Byrd

first: Megan

last: Culbreth

first: Laura

last: Word

first: Bryant

middle: A

last: Chambers

first: Sarah

last: Davidson-Fritz

first: Felix

last: Harris

first: Clinton

last: Willis

first: Katie

last: Paul-Friedman

first: Imran

last: Shah

first: Richard

last: Judson

first: Joshua

last: Harrill


title: Retinoic acid breakdown is required for proximodistal positional identity during axolotl limb regeneration

status: Public on Jul 22 2024

first: James

middle: R

last: Monaghan

address: 360 Huntington Ave.

institute: Northeastern University

summary: Regenerating limbs retain their proximodistal (PD) positional identity following amputation. This positional identity is encoded genetically by PD patterning genes, which instruct blastema cells to regenerate the appropriate PD limb segment. Retinoic acid (RA) is known to specify proximal limb identity, but how RA concentration is established in the blastema is unknown. Here, we show that RA breakdown via CYP26B1 is essential for determining the RA concentration within blastemas. CYP26B1 inhibition molecularly reprograms distal blastemas into a proximal identity, phenocopying the effects of administering excess RA. We identify Shox as an RA responsive gene that is differentially expressed between proximally and distally amputated blastemas. Ablation of Shox results in shortened limbs with proximal skeletal elements that fail to undergo endochondral ossification. These results suggest that PD positional identity is determined by RA degradation and that targets of RA have a critical role in skeletal element formation during limb regeneration.

overall_design: To understand the impact of excess endogenous retinoic acid on proximodistal patterning of the regenerating salmander forelimb, distal forelimb blastemas (mid-carpal amputation) were treated with increasing doses of talarozole (TAL) suspended in DMSO. Control distal and proximal (upper humerus amputation) forelimb blastemas were treated with vehicle (DMSO). Pools of 3 blastemas per sample (3 samples per condition) were collected at 14 days post amputation and immediately flash frozen in liquid nitrogen. Samples were stored at -80C until sent for sequencing.

first: Timothy

last: Duerr

first: Melissa

middle: N

last: Miller

first: Sage

last: Kumar

first: Dareen

last: Bakr

first: Jackson

last: Griffiths

first: Aditya

last: Gautham

first: Danielle

last: Douglas

first: S

last: Voss


title: The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia in a xenotransplantation model of Alzheimer’s disease [RNA-seq]

status: Public on Jul 08 2024

city: London

last: Marzi

address: Maurice Wohl Clinical Neuroscience Institute

country: United Kingdom

institute: King's College London

summary: Microglia play a key role in the response to amyloid beta in Alzheimer’s disease (AD). In this context, the major transcriptional response of microglia is the upregulation of APOE, the strongest late-onset AD risk gene. Of its three isoforms, APOE2 is thought to be protective, while APOE4 increases AD risk. We hypothesised that the isoforms functionally alter microglia by shaping their transcriptomic and chromatin landscapes. We used RNA- and ATAC-sequencing to profile gene expression and chromatin accessibility of human microglia isolated from a xenotransplantation model of AD. We identified widespread transcriptomic and epigenomic differences which are dependent on APOE genotype, and are corroborated across the profiling assays.

overall_design: To investigate the effects of the human APOE isoforms (APOE2, APOE3, APOE4) and the APOE-KO on the microglial response to amyloid beta pathology, we performed RNA-seq and ATAC-seq to profile the transcriptomic and epigenomic landscapes of human microglia xenotransplanted into the brains of the AppNL-G-F mouse model of Alzheimer's disease.

first: Kitty

middle: B

last: Murphy

first: Di

last: Hu

first: Leen

last: Wolfes

first: Renzo

last: Mancuso

first: Bart

last: De Strooper


title: Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts

status: Public on Jul 10 2024

city: Wako city

first: Shintaro

last: Iwasaki

address: 2-1, Hirosawa

department: CPR

country: Japan

institute: RIKEN

summary: Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis. However, the current method has substantial issues: contamination by rRNAs and the lack of appropriate methods to measure ribosome numbers in transcripts. Here, we overcomeovercame these hurdles through the development of “Ribo-FilterOut”, which is based on the separation of footprints from ribosome subunits by ultrafiltration, and “Ribo-Calibration”, which relies on external spike-ins of stoichiometrically defined mRNA-ribosome complexes. A combination of these approaches estimates the number of ribosomes on a transcript, the translation initiation rate, and the overall number of translation events before its decay, all in a genome-wide manner. Moreover, our method revealed the allocation of ribosomes under heat shock stress, during aging, and across cell types. Our strategy of modified ribosome profiling measures kinetic and stoichiometric parameters of cellular translation across the transcriptome.

sample_organism:
Escherichia coli
Arabidopsis thaliana
Saccharomyces cerevisiae
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design:
Ribosome profiling and RNA-seq of multiple cell lines to detect the global translation of each conditions.

UPDATE: [Jun-18-2025] In the titles and processed data file names for Samples GSM7430255 and GSM7430256, "DMSO" was replaced by "RocA3uM". In the titles and processed data file names for Samples GSM7430259 and GSM7430260, "RocA3uM" was replaced by "DMSO". The files associated with each GSMxxx did not change.

first: Kotaro

last: Tomuro

first: Mari

last: Mito

first: Takahito

last: Miyake

first: Siu

middle: Y

last: Chow

first: Masao

last: Doi

first: Yoshiho

last: Ikeuchi

first: Yuichi

last: Shichino

first: Hirotaka

last: Toh

first: Naohiro

last: Kawamoto


title: microRNA-1 Regulates Metabolic Flexibility by Programming Adult Skeletal Muscle Pyruvate Metabolism

status: Public on Aug 09 2024

city: Lexington

first: Ahmed

last: Ismaeel

state: Kentucky

address: 900 S Limestone St

department: Physiology

institute: University of Kentucky

summary: Metabolic flexibility refers to the ability of a tissue to adjust cellular fuel choice in response to conditional changes in metabolic demand and activity. A loss of metabolic flexibility is now recognized as a defining feature of various diseases and cellular dysfunction. In this study, using an inducible, skeletal muscle-specific knockout (KO) mouse, we found microRNA-1 (miR-1), the most abundant microRNA (miRNA) in skeletal muscle, was necessary to maintain whole-body metabolic flexibility. This was demonstrated by a loss of diurnal oscillations in whole-body respiratory exchange ratio and higher fasting blood glucose in miR-1 KO mice. Argonaute 2 enhanced crosslinking and immunoprecipitation sequencing (AGO2 eCLIP-seq) and RNA-seq analyses identified, for the first time, bona fide miR-1 target genes in adult skeletal muscle that regulated pyruvate metabolism. Comprehensive bioenergetic phenotyping combined with skeletal muscle proteomics and metabolomics showed that miR-1 was necessary to maintain metabolic flexibility by regulating pyruvate metabolism through mechanisms including the alternative splicing of pyruvate kinase (Pkm). The loss of metabolic flexibility in the miR-1 KO mouse was rescued by pharmacological inhibition of the miR-1 target, monocarboxylate transporter 4 (MCT4), which redirects glycolytic carbon flux toward oxidation. The maintenance of metabolic flexibility by miR-1 was necessary for sustained endurance activity in mice and in C. elegans. The physiological down-regulation of miR-1 in response to a hypertrophic stimulus in both humans and mice caused a similar metabolic reprogramming necessary for muscle cell growth. Taken together, these data identify a novel post-transcriptional mechanism of whole-body metabolism regulation mediated by a tissue-specific miRNA.

overall_design: At 4 months of age, HSA-MCM; miR-1-1f/f; miR-1-2f/f (HSA-miR-1) were treated with Vehicle (V, 15% ethanol in sunflower seed oil, n=4 female mice) or tamoxifen- to induce knockout (KO) of miR-1 (T, 2 mg/day, n=4 female mice) for 5 days. After an 8-week washout, total RNA was isolated from gastrocnemius muscles from V and T-treated (KO) for bulk RNA-sequencing.

first: A

first: J

last: McCarthy


title: Renal Proximal Tubule Cell-specific Megalin Deletion Induces Tubulointerstitial Nephritis in Mice Fed Western Diet

status: Public on Jul 04 2024

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

summary: Pharmacological inhibition of megalin (also known as low-density lipoprotein receptor-related protein 2: LRP2) attenuates atherosclerosis in hypercholesterolemic mice. Since megalin is abundant in renal proximal tubule cells (PTCs), PTC-LRP2 +/+ and -/- littermates in an LDL receptor -/- background were generated and fed a Western diet to determine effects of PTC-derived megalin on atherosclerosis. PTC-specific megalin deletion did not attenuate atherosclerosis in LDL receptor -/- mice in either sex. Serendipitously, we discovered that PTC-specific megalin deletion led to interstitial infiltration of CD68+ cells and tubular atrophy. The pathology was only evident in male PTC-LRP2 -/- mice fed the Western diet, but not in mice fed a normal laboratory diet. Renal pathologies were also observed in male PTC-LRP2 -/- mice in an LDL receptor +/+ background fed the same Western diet, demonstrating that the renal pathologies were dependent on diet and not hypercholesterolemia. By contrast, female PTC-LRP2 -/- mice had no apparent renal pathologies. In vivo multiphoton microscopy demonstrated that PTC-specific megalin deletion dramatically diminished albumin accumulation in PTCs within 10 days of Western diet feeding. RNA sequencing analyses demonstrated the upregulation of inflammation-related pathways in kidney. Overall, PTC-specific megalin deletion leads to tubulointerstitial nephritis in mice fed Western diet, with severe pathologies in male mice.

overall_design: Comparative gene expression analysis of RNA-seq data for the kidney of proximal tuble cell-specific LRP2 deficient mice and wild type littermates fed with Western type diet for either 2 or 12 weeks.


title: Impact of olive by-products based diets on the backfat transcriptome of growing Iberian pigs

status: Public on Jul 01 2024

city: Madrid

first: Patricia

last: Palma

address: Carretera de la Coruña, km 7,5

institute: INIA-CSIC

summary: Supplementing diets with olive by-products offers promising benefits for alleviating animal feeding stress without compromising growth. The aim of this study was to explore the transcriptome of backfat in Iberian pigs fed with two diets based in olive by-products. The pigs were divided in three diet groups: a Control (C) group, a dry olive pulp (DOP) group, which was fed a compound feed elaborated with olive pulp, and a wet crude olive cake (WCOC) group, which was fed a compound feed and olive cake silage supplied ad libitum. Subcutaneous fat biopsies were taken, and transcriptome analysis performed. Compared to a C group, we identified 411 and 924 genes as differentially expressed (DEG; q<0.05, Fold Change>1.5) between the DOP and WCOC diets, respectively. In DOP diet, functions related to polysaccharides metabolism were significantly activated, while WCOC exhibited activated biological processes associated with apoptosis and cellular death. Both diets showed inhibition of functions involved in inflammatory and immune responses, as well as reactive oxygen species production, although enriched by different DEGs. Furthermore, in the WCOC diet, functions related to cholesterol and lipid metabolism were suppressed. In both comparisons, the ADIPOQ gene was overexpressed, playing a key role in the majority of affected functions. In conclusion, our findings suggest that olive by-products may significantly influence the health status of animals, offering potential benefits in enhancing their overall well-being.

overall_design: A total of 44 Iberian pigs were divided in three diet groups: 1) control (C) group, 2) dry olive pulp (DOP) group, fed a compound feed elaborated with olive pulp, and 3) wet crude olive cake (WCOC) group, fed a compound feed and olive cake silage suppliedad libitum. Subcutaneous fat biopsies of five pigs per diet were collected from five pigs per diet for RNA extraction and subsequent RNA-seq analysis.

middle: P

last: Granados

first: Juan

last: García-Casco

first: Ramón

last: Peiró Pastor

first: Cristina

last: Óvilo

first: Miguel

last: Delgado

first: Fabián

last: García

first: Adrián

last: López

first: Elena

last: González Sánchez

first: María

last: Muñoz


title: Transcriptional profiling and multiple machine learning methods identified novel microglia biomarkers for Experimental Autoimmune Encephalomyelitis

status: Public on Jul 13 2024

city: Kunming

first: Yan

last: Wu

state: Yunnan

address: Xichang Road No. 295

institute: First Affiliated Hospital of Kunming Medical University

summary: Background: Microglia plays complex and crucial roles in multiple sclerosis (MS). This study aimed to explore the biological significance of microglia-associated genes in experimental autoimmune encephalomyelitis (EAE) . Methods:  Differentially expressed genes (DEGs) were screened with six machine learning (ML) methods, which were also utilized to validate the microglia-associated DEGs in three public databases. ceRNA and Protein–protein interaction (PPI) network analyses were utilized to identify the interaction of the 6 novel biomarkers with other molecules. Then, CIBERSORT and single-sample gene set enrichment analysis (ssGSEA) were employed to quantify the relative abundance of each immune cell infiltration, respectively. qRT-PCR was performed to test the expression of key DEGs in murine models. Results: A total of 247 DEmRNA, 499 DElncRNAs and 269 DEcircRNAs were identified. With screening strategy of five ML algorithms, 6 DEmRNAs were obtained including NGP, HIST1H2BJ, PBLD1, MBLN3, CD180 and F10. Then the 6 DEmRNAs were used as a multigene signature to construct models to differentiate EAE from normal microglia, and AUC value for each model was greater than 0.8. The diagnostic value of these 6 DEmRNAs were identified and further verified by qRT-PCR. Then, differential expression for five out of these 6 DEmRNAs, namely NGP, HIST1H2BJ, PBLD1, MBLN3, and F10 were confirmed. Using PPI analysis, DEmRNAs frequently interacting with transcription factors (TFs), potential drugs and RBPs were identified. With immune cell infiltration analyses, we found EAE microglia presented high levels of immune infiltration, especially Nature Killer (NK) cells and CD8+ T cells. We also reported circRNA (circRNA_00638) was predicted to bind to 76 RBPs. Conclusions: We identified and validated 6 novel microglia related genes and developed a multigene signature with ML methods to confirm their ability to accurately diagnose and characterize biological alterations in EAE microglia. The six key DEmRNAs might also be latent targets for immunoregulatory therapy.

overall_design:
To explore the transcriptional profiling as well as the interaction of key DEGs and other molecules, including circRNA, lncRNA, RBPs, immune cells of EAE microglia, we established EAE mice model and extracted brain microglia to compare with healthy cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 8 samples of EAE microglia and 8 samples of PBS control microglia

first: Yangbing

last: Han

first: Bo

last: Chen

first: Ping

last: Gan


title: The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia in a xenotransplantation model of Alzheimer’s disease [ATAC-seq]

first: Sarah

last: Marzi

summary: Microglia play a key role in the response to amyloid beta in Alzheimer’s disease (AD). In this context, the major transcriptional response of microglia is the upregulation of APOE, the strongest late-onset AD risk gene. Of its three isoforms, APOE2 is thought to be protective, while APOE4 increases AD risk. We hypothesised that the isoforms functionally alter microglia by shaping their transcriptomic and chromatin landscapes. We used ATAC- and ATAC-sequencing to profile gene expression and chromatin accessibility of human microglia isolated from a xenotransplantation model of AD. We identified widespread transcriptomic and epigenomic differences which are dependent on APOE genotype, and are corroborated across the profiling assays.

first: Kitty

last: Murphy

first: Di

last: Hu

first: Leen

last: Wolfes

first: Renzo

last: Mancuso

first: Bart

last: De Strooper


title: Unraveling the Role of MIXL1 Activation in Endoderm Differentiation of Isogenic Human Induced Pluripotent Stem Cells [ATAC-Seq]

status: Public on Aug 01 2024

city: Westmead

first: Nader

last: Aryamanesh

address: 214 Hawkesbury Rd

institute: CMRI

summary: Human induced pluripotent stem cells (hiPSC) possess the ability to differentiate into a multitude of tissue types but display heterogeneity in the propensity of differentiation into specific tissue lineages. An examination of isogenic hiPSC lines revealed variations in the endoderm propensity under directed differentiation conditions. Characterization of the transcriptome and proteome of the hiPSC lines showed that MIXL1 activity at the early differentiation stage correlated with the efficacy of generating definitive endoderm and further differentiation into endoderm derivatives. Enforced expression of MIXL1 in the endoderm-incompetent hiPSCs enhanced the propensity of endoderm differentiation, suggesting that modulation of key drivers of lineage differentiation can re-wire hiPSC to the desired lineage propensity for stem cell products.

overall_design: hiPSC lines WT and Mixl1-KO were subjected, in triplicate, to definitive endoderm differentiation and chromatin accessibility was assessed 24h after induction by ATAC-seq.

first: Pierre

last: Osteil

first: Nazmus

last: Salehin

first: Nicole

last: Santucci

first: Patrick

last: Tam


title: IL-13 decreases suceptibility to airway epithelial SARS-CoV-2 infection but increases disease severity in vivo

status: Public on Jun 28 2024

city: Iowa city

first: Alejandro

middle: Pezzulo

last: Colmenares

state: Iowa

address: 169 Newton Road

department: Internal medicine

institute: University of Iowa

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: The pioneer transcription factor Zelda facilitates the exit from regeneration and restoration of patterning in Drosophila

status: Public on Jun 26 2024

city: Urbana

first: Rachel

last: Smith-Bolton

state: Illinois

address: 601 S.Goodwin Ave

department: Cell and Developmental biology

institute: University of Illinois at Urbana Champaign

summary: For a damaged tissue to regenerate, the injured site must repair the wound, proliferate, and restore the correct patterning and cell types. We found that Zelda, a pioneer transcription factor largely known for its role in embryonic zygotic genome activation, is dispensable for normal wing development but crucial for wing disc patterning during regeneration. Impairing Zelda function during disc regeneration resulted in adult wings with a plethora of cell fate errors, affecting the veins, margins, and posterior compartment identity. Using CUT&RUN, we identified and validated targets of Zelda including the cell fate genes cut, Delta and achaete, which failed to return to their normal expression patterns upon loss of Zelda. In addition, Zelda  controls expression of factors previously established to preserve cell fate during regeneration like taranis and osa, which stabilizes engrailed expression during regeneration, thereby preserving posterior identity. Finally, Zelda ensures proper expression of the integrins encoded by multiple edematous wings and myospheroid during regeneration to prevent blisters in the resulting adult wing. Thus, Zelda is crucial for maintaining cell fate and structural architecture of the regenerating tissue.

overall_design: CUT&RUN was performed for the transcription factor Zelda during wing regeneration (2 days after damage) and normal wing development, which was endogenously GFP tagged. Experiment was performed with anti-GFP antibody (Abcam #ab290) in duplicates. As a control, w1118 regenerating and normally developing larave without any GFP tag were used with the anti-GFP antibody.

first: Anish

last: Bose

first: Keaton

last: Schuster

first: Chandril

last: Kodali

first: Surabhi

last: Sonam


title: FOXC2 pH-dependent SELEX-seq

status: Public on Jun 24 2024

city: San Francisco

first: Kyle

last: Kisor

address: 505 parnassus Ave

institute: UC San Francisco

summary: Intracellular pH (pHi) dynamics regulates diverse cell processes such as proliferation, dysplasia, and differentiation, often mediated by the protonation state of a functionally critical histidine residue in endogenous pH sensing proteins. How pHi dynamics can directly regulate gene expression and whether transcription factors can function as pH sensors has received limited attention. We tested the prediction that transcription factors with a histidine in their DNA binding domain (DBD) that forms hydrogen bonds with nucleotides can have pH-regulated activity, which is relevant to more than 85 transcription factors in distinct families, including FOX, KLF, SOX and MITF/Myc. Focusing on FOX family transcription factors, we used unbiased SELEX-seq to identify pH-dependent DNA binding motif preferences, then confirm pH-regulated binding affinities for FOXC2, FOXM1, and FOXN1 to a canonical FkhP DNA motif that are 2.5 to 7.5 greater at pH 7.0 compared with pH 7.5. For FOXC2, we also find greater activity for an FkhP motif at lower pHi in cells and that pH-regulated binding and activity are dependent on a conserved histidine (His122) in the DBD. RNA-seq with FOXC2 also reveals pH-dependent differences in enriched promoter motifs. Our findings identify pH-regulated transcription factor-DNA binding selectivity with relevance to how pHi dynamics can regulate gene expression for myriad cell behaviours.

overall_design: For SELEX-seq, a previously reported protocol (Riley et al. 2014) was used with modifications. We designed a library with a 16 base pair randomized region flanked by PCR sites GTTCAGAGTTCTACAGTCCGACGATCTGGNNNNNNNNNNNNNNNNTCGTATGCCGTCTTCTGCTTG. For each round of selective enrichment, final concentrations of 0.25 µM DNA library with 2.5 µM GST-FOXC2 were incubated for 30 min at RT in binding buffer (20 mM Hepes, 140 mM KCl, 0.05 mM TCEP-HCl) at either pH 7 or 7.8. Next, 30 µl of 50% pre-equilibrated glutathione Sepharose beads (Cytiva: 17075601) were added and samples were incubated end over end for 30 min at RT after which DNA-FOXC2-bead complexes were pelleted by centrifugation at 5000 rpm for 4 min. DNA-FOXC2-bead complexes were washed twice with 300 µl binding buffer and resuspended in 100 µl binding buffer prior to heat dissociation for 5 min at 95°C. Eluate DNA was clarified by centrifugation (10,000 rpm for 5 min) and PCR amplified with forward (SELEXF) and reverse (SELEXR) primers complementary to nucleotides flanking the randomized region. PCR products were cleaned using the MinElute PCR purification kit (Qiagen 28004) and the selection process was repeated four times with PCR products from prior rounds used as the starting library. 5’ and 3’ adapter overhangs were added by PCR to the initial starting library (R0) with all four rounds of selection (R1-4) used to prepare for addition of barcoded indexes. Indexes were added by PCR using the Nextera IDT UD Set D (Illumina 20027213) for multiplex sequencing

first: Diego

last: Ruiz

first: Matthew

last: Jacobson

first: Diane

last: Barber


title: Patchseq Data of T1D Donor Islets vs ND Matched Controls

status: Public on Jun 25 2024

city: Edmonton

last: MacDonald

state: Alberta

address: 6-126 Li Ka Shing Centre

institute: University of Alberta

summary: Will be updated closer to manuscript finalization. Patchseq allows for combined electrical and transcriptomic data to be obtained at single cell resolution. Here we performed patchseq on islet cells from human donors

overall_design: Isolated human islets were dispersed to single cells, and whole cell patch clamp electrophysiology was performed. Following, the cell was sent for scRNA-seq (SmartSeq). XXH12 wells were left empty and A3A11 and V2A11 failed to sequence. Since they were empty fastq files, they have not been uploaded based on GEO's recommendations.

first: Theodore

last: dos Santos

first: Cara

last: Ellis

first: Jessica

last: Ewald

first: Robert

middle: C

last: Jones

first: Joan

last: Camunas-Soler

first: Stephen

last: Quake


title: FOXC2-HIS122 and pH-dependent gene expression

overall_design: To investigate genes in which expression is dependent on FOXC2-His122 and pH, we established control (high pH) and clonal NHE1-KO (low pH) MDA-MB-436 cells. Next, we collected RNA from three biological replicates each from both control and NHE1-KO cells untransfected or transfected with FOXC2-WT, or pH-independent FOXC2 mutants H122K and H122N. To establish which genes are dependent on both FOXC2-His122 and pH, we filtered for genes that are only differentially expressed between control and NHE1-KO in the FOXC2-WT  condition but not untransfected or FOXC2- H122K, H122N.


title: Architecture of the genome-wide transcriptional regulatory network reveals the dynamic biological functions and divergent evolutionary trajectory in Pseudomonas syringae

status: Public on Jun 21 2024

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: The model Gram-negative plant pathogen Pseudomonas syringae utilizes hundreds of transcription factors (TFs) to manipulate its functional processes, including virulence and metabolic pathways to control its infection to host plants. Although the molecular mechanisms of regulators have been studied for decades, the comprehensive understanding throughout the genome-wide TFs in P. syringae remains uncertain. Here, we set out to investigate the binding characteristics of 170 of all 301 annotated TFs using ChIP-seq. To further explore and delineate the physiological and pathogenic roles of TFs in P. syringae, we integrated both the 118 different position weight matrix (PWM) motifs of 100 TFs analyzed by HT-SELEX previously and more than 26000 direct interactions of 170 TFs here, mapped the hierarchical regulatory network not only between TFs but also within TFs and target genes. We next investigated the co-association statistics across the 26000 interactions and identified the high co_x0002_association scores of bottom TFs in the hierarchical network. The evolution analysis revealed the functional variability of TFs between different pathovars of P. syringae. Topological modularity network of all ChIPed TFs and their targets exhibited the various biological functions. Overall, our work provided the global transcriptional regulatory network of genome-wide TFs in P. syringae, including 35 virulence_x0002_associated and metabolic TFs, which promoted the development of effective treatment and prevention strategies for the related infectious diseases.

sample_organism: Pseudomonas syringae pv. tomato str. DC3000

sample_organism: Pseudomonas savastanoi pv. phaseolicola 1448A

sample_organism: Pseudomonas syringae pv. actinidiae str. Shaanxi_M228

overall_design:
Chromatin immunoprecipitation sequencing (ChIP-seq) for 170 transcription factors in Pseudomonas syringae 1448A
The name of each sample consists of three parts: one is the strain label, the second is the locus_tag of TF, and the last -number represents the biological replicate.  For example, PSPPH_0001-1 indicates the first biological replicate of TF 0001 in the PSPPH strain (1448A). Control samples are EV/HACK labelled.

last: Deng


title: Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro

status: Public on Jul 29 2024

city: Chapel Hill

first: Daniel

last: Dominguez

state: NC

address: 120 Mason farm

department: Pharmacology

institute: UNC Chapel Hill

summary: While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we examined interspecies differences in RNA-protein interactions using the conserved neuronal RNA-binding protein, Unkempt (UNK) as model. We find that roughly half of mRNAs bound in human are also bound in mouse. Unexpectedly, even when transcript-level binding was conserved across species differential motif usage was prevalent. To understand the biochemical basis of UNK-RNA interactions, we reconstituted the human and mouse UNK-RNA interactomes using a high-throughput biochemical assay. We uncover detailed features driving binding, show that in vivo patterns are captured in vitro, find that highly conserved sites are the strongest bound, and associate binding strength with downstream regulation. Furthermore, subtle sequence differences surrounding motifs are key determinants of species-specific binding. We highlight the complex features driving protein-RNA interactions and how these evolve to confer species-specific regulation.

sample_organism:
Pan troglodytes
Homo sapiens
Mus musculus
synthetic construct

overall_design:
Natural sequence RNA bind-n-seq (nsRBNS) and 100vertebrate RNA bind-n-seq (100vertRBNS) for unkempt (UNK) zinc fingers 1-6
Please note that all organism/species included in the *100vertRBNS samples are listed in the Series supplementary 'organisms.txt' file.

first: Sarah

last: Harris

first: Maria

middle: S

last: Alexis

first: Gilbert

last: Giri

first: Francisco

middle: F

last: Cavazos Jr

first: Jernej

last: Murn

last: Aleman

first: Christopher

last: Burge

first: Yue

last: Hu


title: The immune landscape and mechanism of hepatitis B virus surface antigen clearance [CITEseq]

city: Shanghai

first: Jianhua

last: Li

address: NO.131 DONGAN RD., FUXING BUILDING 306

institute: Fudan University

summary: Hepatitis B virus (HBV) surface antigen (HBsAg) clearance constitutes the hallmark of resolution of acute infection and is a therapeutic goal for functional cure of chronic hepatitis B. Here, we reveal the immunological landscape and mechanism of HBsAg clearance in mice. After acquiring nonopsonized HBsAg, B cells prime CD4+ T cell responses by CCR5- and EBI2-guided interaction with CD4+ T cells at follicular and interfollicular regions, respectively. Monocyte-derived macrophages transport complement-opsonized HBsAg to follicular dendritic cells (FDCs) to maintain germinal center reaction. Batf3+ XCR1+ conventional type 1 DCs (cDC1s) acquire and present HBsAg by MHC-I cross-dressing to drive CD8+ T cell responses in liver. We map the antigen-presenting cell (APC)-T cell crosstalk landscape and identify key costimulatory signals. The immune responses in patients with acute HBV infection are revealed by a single-cell transcriptome atlas. These findings revolutionize our understanding of anti-HBV immune responses and would lead to immunotherapeutic strategies for HBsAg clearance.

overall_design: To study the heterogeneity of CD4+ T cell differentiation fate in response to HBsAg, we adoptively transferred OT-II T cells into congenic WT hosts and profiled FACS-sorted OT-II T cells form the spleen, dLN and liver by scRNA-seq at day 7 after injection with pHBV1.3/OVA323-339. To identify the APC subsets and underlying mechanisms of cellular interaction responsible for HBsAg-specific CD8+ T cell responses in liver, we performed scRNA-seq on sorted CD11chighMHCII+ DCs, hepatocytes and OT-I T cells from liver at days 0 and 2.5 after the hydrodynamic injection of pHBV1.3/OVA257-264.

first: Xiaofang

first: Wenxuan

last: Sun

first: Xiaolan

last: Xu

first: Lu

last: Bai

first: Qirong

last: Jiang

first: Chengmeng

last: Jin

first: Jiangxia

last: Liu

first: Bisheng

last: Shi

first: Jiming

last: Zhang

first: Zhenghong

last: Yuan


title: Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development [human ATAC-seq]

city: Los Angeles

first: Andrew

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

summary: Mammalian kidneys maintain fluid homeostasis through the cellular activity of nephrons and the conjoined collecting system. Each epithelial network originates from distinct progenitor cell populations that reciprocally interact during development. To extend our understanding of human and mouse kidney development, we profiled chromatin organization (ATAC-seq) and gene expression (RNA-seq) in developing human and mouse kidneys. Data were analyzed at a species level and then integrated into a common, cross-species multimodal data set. Comparative analysis of cell types and developmental trajectories identified conserved and divergent features of chromatin organization and linked gene activity, revealing species- and cell-type specific regulatory programs. Identification of human-specific enhancer regions linked through GWAS studies to kidney disease highlights the potential of developmental modeling to provide clinical insight.

overall_design:
Human donor fetal kidneys were obtained, dated and dissected by the Obstetrics and Gynecology Maternal Fetal Medicine Division of University of Southern California. Fetal embryonic age is estimated based on first day of last menstrual period (LMP).  Non-nucleotide, processed feature-barcode information is provided.
***Controlled access to raw fastq files is available through dbGaP***

first: Sunghyun

last: Kim

first: Kari

last: Koppitch

first: Riana

middle: K

last: Parvez

first: JinJin

last: Guo

first: MaryAnne

last: Achieng

first: Jack

last: Schnell

first: Nils

middle: O

last: Lindström


title: Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development [mouse scRNA-seq]

overall_design: C57BL6/J mice pups were harvested at day of birth (postnatal day 0) and sexed by urogenital track.


title: Proteasome inhibition sensitizes anaplastic Wilms tumor to actinomycin D

status: Public on Jun 20 2024

city: Dallas

first: Kenneth

last: Chen

state: TX

address: 5323 Harry Hines Blvd

department: Pediatrics

institute: UT Southwestern

summary: Wilms tumor is the most common kidney cancer in children, and anaplastic Wilms tumor is the most chemoresistant histological subtype. Here we explore how anaplastic Wilms tumor cells evade the common chemotherapeutic drug actinomycin D, which inhibits ribosomal biogenesis. We found that, when ribosomal capacity is limited by actinomycin D treatment, anaplastic Wilms tumor cells preferentially translate proteasome components and upregulate proteasome activity. Accordingly, increased proteasome levels are associated with anaplastic histology and with worse prognosis in Wilms tumor. Lastly, we show that the proteasome inhibitor bortezomib sensitizes cells to actinomycin D treatment both in vitro and in vivo.

overall_design: WiT49 cells were treated with actinomycin D (actD) or vehicle (DMSO), for varying lengths of time, in three replicates per condition, then subjected to ribosome profiling and RNA sequencing

first: Patricia

last: Tiburcio


title: Gestational exposure to environmental chemicals and epigenetic alterations in the placenta and cord blood mononuclear cells

status: Public on Jun 19 2024

city: Philadelphia

first: Jagadeesh

last: Puvvula

state: Pennsylvania

address: 423 Guardian Drive

department: Department of Biostatistics, Epidemiology, and Informatics

institute: University of Pennsylvania

type: Methylation profiling by genome tiling array

summary: This study includes 75 pregnant individuals, where associations between 37 endocrine disrupting chemical biomarkers and methylation intensities were assessed using multiple linear regression. Methylation intensities were quantified from cord blood mononuclear cells and cord blood. The DNA methylation profiles were generated using the Illumina Infinium HumanMethylation450 Beadchip that measured about 450,000 CpGs.

overall_design: We profiled the methylome from cord blood mononuclear cells and placenta tisse from up to 75 pregnant individuals. This study follows cross sections desgin where exposure biomarkers were quantified from maternal urine at the delivery visit.

first: Aimin


title: Characterization of a suspension Vero cell line for viral vaccine production

status: Public on Jun 18 2024

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

country: France

institute: U1208, INSERM

summary: Vero cells, as approved by the World Health Organization, have been the most commonly used continuous cell line for viral vaccine production over the last 25 years, but their adherent phenotype continues to limit productivity. Adapting to a suspension culture would overcome this restriction and reduce production costs. First, a Vero suspension isolate was obtained and metabolically characterized. Second, RNA sequencing analysis was used to identify differentially expressed genes between adherent and suspension cells, which revealed complete downregulation of adhesion and matrix-associated genes. Additionally, signaling pathways involving Wnt and other tyrosine kinase receptors were identified as potential leads for growth optimization. In particular, supplementation with fibroblast growth factor 2 allowed for a 20% increase in cell density. Finally, a comparative viral productivity assay revealed a 30% increase in poliovirus production in suspension Vero cells compared to adherent cells depending on the serotype, as well as a 140% increase in respiratory syncytial virus production and a 150% increase in yellow fever virus production.This work establishes the potential of the suspension Vero cell line as a new cell platform for viral vaccine production.

overall_design: We established a Vero cell line that can grow in suspension. To understand the mechanism of adaptation to this new method of culture, we performed a gene expression profiling analysis of the parental adherent cell line and the new suspension isolate at three timepoints. We then determined differentially expressed genes between the two cell lines.

last: Pain

first: Léa

last: Bourigault

first: Christian

last: Jean


title: The immune landscape and mechanism of hepatitis B virus surface antigen clearance [RNA-Seq]

first: Jianhua

last: Li

overall_design: HBsAg-specific S129G1HL B cells with/without co-transferred OT-II T cells in the spleens were FACS-sorted from mice at 0 h, 18 h, day 1 and day 2.5 after pHBV1.3/OVA323-339 hydrodynamically injection, and used for RNAseq.

first: Xiaofang

first: Wenxuan

last: Sun

first: Xiaolan

last: Xu

first: Lu

last: Bai

first: Qirong

last: Jiang

first: Chengmeng

last: Jin

first: Jiangxia

last: Liu

first: Bisheng

last: Shi

first: Jiming

last: Zhang


title: Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development

first: Andrew

last: McMahon

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

overall_design: Refer to individual Series


title: The integrated stress response fine-tunes stem cell fate decisions in response to serine deprivation and tissue injury [scRNA-seq]

city: New York

first: Jesse

middle: Stephen Swyer

last: Novak

state: New York

address: 1230 York Ave.

institute: Weill Cornell Institutional MD-PhD Program/The Rockefeller University

summary: Epidermal stem cells constantly rejuvenate the skin’s barrier, which excludes harmful microbes and prevents dehydration. In routine wounds, underlying hair follicle stem cells (HFSCs), normally dedicated to hair regeneration, must also reconstruct and thereafter maintain the overlying epidermis. How these fate choices are balanced to restore physiologic function to damaged tissue remains poorly understood.  Here, we uncover the non-essential amino acid serine as a surprising rheostat in this process. Utilizing diet and HFSC-specific loss-of-function studies, we show that under serine-depleted conditions, HFSCs delay hair growth, and upon injury skew their fate towards epidermal re-epithelialization while concomitantly limiting hair growth. Combining temporal single-cell RNA sequencing, genetics and pharmacological intervention, we show that serine deficiency augments an injury-activated integrated stress response (ISR), boosting re-epithelization and rapidly restoring the skin’s barrier at the wound edge. Our findings integrate injury, the ISR, metabolism, tissue fate-selection and repair, offering potential for dietary and pharmacologic intervention to accelerate wound healing.

overall_design: Mouse hair follicle stem cells from unwounded HFSCs and HFSCs/progeny from 3 and 5 days post wounding (dpw) were isolated from Sox9-CreER;R26-LSL-YFP;Phgdh +/+ or Phgdh fl/fl mice and transcriptomally analyzed.

first: Douglas

last: Barrows

first: Ji-Dung

last: Luo

first: Thomas

last: Carroll


title: The integrated stress response fine-tunes stem cell fate decisions in response to serine deprivation and tissue injury [RNA-seq]

overall_design:
Mouse hair follicle stem cells from HFSCs in telogen and anagen from K15-CrePGR; Shh+/- were isolated and transcriptomically analyzed.

Reanalyzed samples were submitted to GEO previously in GSE67404 (third-party reanalysis) and in GSE123913 (self-reanalysis).

first: Ya-Chieh

last: Hsu


title: Targeting T cell plasticity by pooled single cell CRISPR-screening in preclinical models of kidney and gut inflammation

status: Public on Jun 14 2024

city: Hamburg

first: Malte

last: Hellmig

state: Hamburg

address: Martinistraße 52

department: III. Department of Medicine

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary:
Treatment of autoimmune diseases demands a shift from unspecific immunosuppression towards targeted therapies. This could be achieved by turning pro-inflammatory T helper (Th) cells into anti-inflammatory subsets. However, the molecular pathways involved in T cell plasticity and stability are not fully understood. Single cell CRISPR-screens are a powerful tool to simultaneously analyze the impact of multiple genes on cellular phenotypes. To investigate the molecules involved in T cell plasticity in disease settings, we established in vivo single cell CRISPR droplet sequencing (iCROP-seq). By applying this technique to in vivo models of inflammatory diseases in the kidney and intestine, we demonstrate that CRISPR-induced alterations in T cell polarization can be identified and ranked according to corresponding transcriptional perturbations. In particular, we targeted pro-inflammatory Th17 cells in models of immune-mediated diseases and quantified polarization biases into Th1 and regulatory T cells. These findings uncover Th17 to Th1 cell plasticity in the human kidney in the context of renal autoimmunity. iCROP-seq will facilitate the identification of therapeutic targets by highly efficient functional stratification of genes and pathways in a disease- and tissue-specific manner.
Processed data file from the alignment with the cellranger software can also be found at Figshare (https://doi.org/10.6084/m9.figshare.28547528).

overall_design: Splenocytes were obtained from Il17a-Cre x Cas9-GFP mice and enriched for CD4+ T cells. With these cells a Th17 polarization was performed. After polarization the cells were transduced with lentiviral particles containing vectors for guide-RNAs and blue fluorescent protein (eBFP2). Transduced cells were then injected in Rag-1-deficient mice. 3 days after cell transfer crescentic glomerulonephritis was induced by i.p. injection of sheep serum against the glomerular basement membrane. Lymphozytes from the kidney were isolated and analysed using scRNAseq. In the disease model of experimental colitis, 14 days prior the injection of the transducted cells into  Rag-1-deficient mice, the mice were gavaged with colitogenic bacteria. Intestinal lymphozytes were then isolated and analysed using scRNAseq.

first: Leon

middle: U

last: Enk

first: Kristoffer

last: Riecken

first: Christoph

last: Kilian

first: Paul

last: Datlinger

first: Saskia

last: Jauch-Speer

first: Tobias

last: Neben

first: Zeba

last: Sultana

first: Varshi

last: Sivayoganathan

first: Alina

last: Borchers

first: Hans-Joachim

last: Paust

first: Yu

last: Zhao

first: Nariaki

last: Asad

first: Shuya

first: Theodora

last: Agalioti

first: Penelope

last: Pelczar

first: Thorsten

last: Wiech

last: Bock

last: Huber

first: Samuel

first: Stefan

last: Bonn

first: Nicola

last: Gagliani

first: Boris

last: Fehse

first: Ulf

last: Panzer

first: Christian

last: Krebs


title: Temporal dynamics of gene expression during metamorphosis in two distant Drosophila species

status: Public on Jun 17 2024

city: Moscow

first: Aleksandra

middle: M

last: Ozerova

address: Skolkovo Innovation Center, Bolshoy Boulevard, 30, p.1

department: Life sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: Complete metamorphosis of holometabolous insects is a complex biological process characterized by profound morphological, physiological, and transcriptional changes. To reveal the temporal dynamics of gene expression during this critical developmental transition, a detailed analysis of the developmental transcriptomes of two Drosophila species, Drosophila melanogaster and Drosophila virilis, was conducted. We confirm partial recapitulation of the embryonic transcriptional program in pupae, but instead of the traditional hourglass model, which posits maximal conservation at mid-embryonic stages, at different stages of pupae we observe a more complicated pattern of alternating low and high diversity, resembling an inverted hourglass, or "spindle". This observation challenges the notion of a singular conserved phylotypic period during holometabola ontogeny and underscores the complexity of developmental processes during complete metamorphosis. Notably, recently formed genes (specific to insects) exhibit pronounced expression peaks during mid-pupal development, underscoring their potential role in developmental transitions.

sample_organism:
Drosophila melanogaster
Drosophila virilis

overall_design: The dataset includes RNA sequencing samples from wild-type Drosophila melanogaster (Oregon-R) and Drosophila virilis (Strain 9), representing the subgenera Sophophora and Drosophila. Collections included phylotypic embryonic stage, larvae, stages P1 to P5, intermediate, and late pupal stages, as well as five-day-old adult males. All samples were gathered in three biological replicates.

first: Dina

last: Kulikova

first: Mikhail

last: Evgen’ev

last: Gelfand


title: Responses of human MAIT cells to CA7S

status: Public on Jun 12 2024

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: To investigate the effect of cholic acid sulfate to MAIT cells, PBMCs were stimulated with 5-OP-RU and CA7S and scRNA sequencing was performed. Inflammatory genes were induced by 5-OP-RU, while wound healing related genes were inducesed by CA7S. This analysis showed that cholic acid sulfate may contributes to maintenance of MAIT cells.

overall_design: PBMCs were unstimulated or stimulated with 5-OP-RU or with CA7S overnight. CD161+MR1-5-OP-RU tetramer+ cells were sorted and analyzed by single-cell TCR- and RNA-seq.

first: Emi

last: Ito

first: Yu-Chen

last: Liu

last: Okuzaki

first: Sho

last: Yamasaki


title: Precise measurement of molecular phenotypes with barcode-based CRISPRi screens

city: Berkeley

first: Joseph

middle: Heimlich

last: Lobel

state: CA

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: UC berkeley

summary: Uncovering the genetic basis of molecular processes is essential for understanding a broad range of biological phenomena. CRIPSR-Cas9 approaches enable this discovery through programable and systematic profiling of regulatory genes underlying diverse cellular behaviors. A key challenge for dissecting genetic networks is expanding CRISPR-based screens to interrogate specific phenotypes with high precision. Here, we use a quantitative, sequencing-based CRISPRi platform to enhance the scope and sensitivity of genome-wide screens. We first systematically explore how technical variations distort guide effects and correct for these factors by using RNA reporters and normalizers expressed from closely matched promoters. We then combine this platform with a recombinase-based integration system to interrogate protein and RNA-level phenotypes. We find our approach accurately captures known regulators of protein or RNA quality control with high accuracy and minimal background. These barcode-based CRISPR systems provide a powerful and generalizable platform for dissecting critical cellular regulatory pathways.

overall_design: We perform barcode-based CRISPRi screens across various conditions and identify methods to reduce background

middle: H

first: Nicholas

middle: T

last: Ingolia


title: RNA-seq analysis of age-specific growth characteristics in the rumen of Hanwoo (Korean native cattle) steers

status: Public on Jun 02 2024

city: Wanju

first: Yejee

last: Park

address: Kongjwipatjwi-ro 1500

institute: National Institute of Animal Science

summary: Hanwoo cattle are a Korean breed renowned for their cultural significance and high-quality beef, characterized by low cholesterol and high unsaturated fat ratio. Growth is divided into a growing phase focused on development and a fattening phase for marbling. Proper feed management, considering genetic and environmental factors, is vital for maximizing growth potential. The rumen plays a crucial role in digestion and gene expression regulation, with rumen fermentation being central to nutrient absorption and cattle health. In this study, we conduct transcriptome analysis of the rumen at eight timepoints. Our goal is to identify genetic factors that influence the growth of Hanwoo steers to enhance our understanding of the rumen’s functions and roles during their growth. In this RNA-sequencing analysis of Hanwoo steer rumen, differential gene expression was examined over eight timepoints, highlighting significant genetic changes, particularly between 12 and 26 months. Weighted gene co-expression network analysis identified and organized as three modules: turquoise, blue, and yellow. The turquoise module, linked to immune response, showed down-regulation in genes at 30 months. The blue module, associated with steroid metabolism, was notably up-regulated at 26 months. The yellow module’s genes showed a consistent increase in expression with growth. These modules and their functional annotations provide a deeper understanding of the biological processes during Hanwoo growth, highlighting the intricate relationship between gene expression and cattle development. The growth stages of Hanwoo steers were explored in our investigation utilizing rumen transcriptome data. The rumen plays critical role in their development, particularly during the growing and fattening phases. Proper feed management, considering the rumen’s function, is essential for optimal growth. Transcriptome analysis helps identify genes associated with growth and provides insights for cattle breeding and management practices. Understanding the complex connection between gene expression and Hanwoo development is essential for maximizing productivity and health.

overall_design: whole mRNA sequencing profiles of 61 Hanwoo steer's rumen

first: Woncheol

first: Sunsik

last: Jang


title: The immune landscape and mechanism of hepatitis B virus surface antigen clearance

first: Jianhua

last: Li


title: RNA regulation by the cell-cell adhesion component PLEKHA7

status: Public on Jun 03 2024

city: Charleston

first: Antonis

last: Kourtidis

state: SC

address: 173 Ashley Avenue

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

summary: We have identified PLEKHA7 as a cell-cell adhesion protein that interacts with and regulates RNAi compelxes, miRNAs and mRNAs at adherens junctions of well-differentiated epithelial cells. This study was conducted to identify global effects of PLEKHA7 depletion on total RNA expression in colon epithelial cells

overall_design: Colon epithelial Caco2 cells that stably express either a non-target (NT) shRNA or an shRNA targeting PLEKHA7 (shP7) were lysed and total RNA was extracted and used for deep RNA sequencing.

first: Mary

last: Bridges

first: E

last: Hazard

first: Robert

last: Wilson

first: Gary

last: Hardiman


title: Mapping genetic interactions in the SLC Transporter Superfamily.

city: Vienna

first: Giulio

last: Superti-Furga

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Transporters mediate and control the flux of molecules across compartmental membranes. The human genome encodes 1500 genes with transport functions, of which the solute carriers (SLCs) form the largest superfamily with more than 450 members. Over 250 different SLCs are expressed in a typical human cell, many exhibiting overlapping expression patterns and substrate specificities. The collective role of these often seemingly redundant transporters in defining cellular outcomes, such as cell survival, remains unclear. Here, we performed pooled combinatorial KO screens to identify  genetic interactions between 258 expressed SLCs, and between a subset of SLCs and selected metabolic enzymes under different growth conditions using both CRISPR-Cas12a and -Cas9 double knockout systems in the colorectal carcinoma cell line HCT116.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Pooled combinatorial KO screens with proliferation read out.

first: Gernot

last: Wolf

first: Philipp

last: Leippe

first: Svenja

last: Onstein


title: Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis [Xenium]

status: Public on Jun 04 2024

city: Phoenix

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

summary: Large-scale changes in the structure and cellular makeup of the distal lung are a hallmark of pulmonary fibrosis (PF), but the spatial contexts that contribute to disease pathogenesis have remained uncertain. Using image-based spatial transcriptomics, we analyzed the gene expression of 1.6 million cells from 35 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characterized the localization of PF-emergent cell types, established the cellular and molecular basis of classical PF histopathologic features and identified a diversity of distinct molecularly defined spatial niches in control and PF lungs. Using machine learning and trajectory analysis to segment and rank airspaces on a gradient of remodeling severity, we identified compositional and molecular changes associated with progressive distal lung pathology, beginning with alveolar epithelial dysregulation and culminating with changes in macrophage polarization. Together, these results provide a unique, spatially resolved view of PF and establish methods that could be applied to other spatial transcriptomic studies.

overall_design:
Sample names were generated based on their collection site (Vanderbilt University-'VU'; Translational Genomics Research Institute-'T'), disease status (healthy donor-'HD'; interstitial lung disease-'ILD'), unique number assigned to the patient and where applicable, whether the sample was taken from a 'less affected' or 'more affected' tissue section as determined by percent pathology scores. Replicate healthy samples were labeled 'A' and 'B' to distinguish (for example, VUHD116A and VUHD116B), and replicate disease samples with the same 'less affected' or 'more affected' designation were labeled '1' and '2' (for example, VUILD105MA1 and VUILD105MA2).

UPDATE [May-08-2025]:
- GSM7990534_output-XETG00048__0003400__TILD117MA__20230313__191400_transcripts.csv.gz
was replaced by
GSM7990534_output-XETG00048__0003400__TILD117MA1__20230313__191400_transcripts.csv.gz
- GSM8505453_TILD117MA_transcripts.csv.gz
was replaced by
GSM8505453_TILD117MA2_transcripts.csv.gz

UPDATE [June-06-2025]: The processed data were updated.

first: Annika

last: Vannan

first: Ruqian

last: Lyu

first: Arianna

middle: L

last: Williams

last: Negretti

first: Evan

middle: D

last: Mee

last: Hirsh

first: Samuel

first: David

last: Nichols

first: Chase

middle: J

last: Taylor

first: Vasiliy

middle: V

last: Polosukhin

first: A

last: McCall

first: Jason

last: Gokey

first: Heejung

last: Shim

first: Lorraine

last: Ware

first: Matthew

last: Bacchetta

first: Ciara

last: Shaver

first: Timothy

last: Blackwell

first: Jennifer

last: Sucre

first: Jonathan

middle: A

last: Kropski

first: Davis

last: McCarthy

middle: E


title: Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development [mouse snATAC-seq]

first: Andrew

middle: P

last: McMahon

overall_design:
C57BL6/J mice pups were harvested at day of birth (postnatal day 0) and sexed by urogenital track.
filtered_peak_bc_matrix_fragments_singlecell.tar.gz

first: Sunghyun

last: Kim

first: Kari

last: Koppitch

first: Riana

last: Parvez

first: JinJin

last: Guo

first: MaryAnne

last: Achieng

first: Jack

last: Schnell

first: Nils

last: Lindström


title: Multi-omics analysis of aggregative multicellularity

status: Public on May 30 2024

city: Gothenburg

first: Bart

last: Edelbroek

address: Medicinaregatan 3B

department: Bioinformatics and Data Centre, Core Facilities

institute: University of Gothenburg

summary: The extent to which mRNA and protein levels correlate is still not fully known, especially during development, when cells undergo a major transition in gene expression. One organism with particular development is Dictyostelium discoideum, during which it transitions from free-living unicellular to multicellular. Previously the transcriptome has been thoroughly studied during multicellular development, however the proteome and its correlation to the transcriptome during this transition is not fully understood. We present paired transcriptomics and proteomics performed in a time series during aggregative multicellularity. From the analysis, the majority of transcripts were identified as differentially expressed, and we could quantify roughly a third of the proteome during early multicellular development. The proteome and transcriptome correlate relatively highly during steady-state, however this decreases as soon as multicellular aggregation is initiated. Correlation is particularly low at the gene-level during development. We find that dynamically regulated mRNA often leads to linear up- or downregulation of the protein, and that there is a time lag of approximately 2 to 4 hours between mRNA and protein.

overall_design: To study the transcriptome during multicelllular aggregation, mRNAseq was performed on D. discoideum AX4 cells undergoing the transition from single cellular to multicellular. Time points were taken every 2h up to 10h.

first: Jakub

last: Westholm

first: Fredrik

last: Soderbom


title: Overexpression of MG53 in mouse intestinal organoids

status: Public on May 21 2024

city: hangzhou

first: Yumeng

last: Pei

state: zhejiang

address: Xihu district Zhuan Tang street

institute: Zhejiang university

summary: Emerging evidence suggests that priming intestinal stem cell (ISC) lineages towards secretory progenitor cells is beneficial for maintaining gut homeostasis against inflammatory bowel disease (IBD). However, the mechanism driving such biased lineage commitment remains elusive. Here we show that MG53, also named as TRIM72, plays and important role in maintaining intestinal epithelium integrity against various insults-induced IBD. Specifically, MG53 deficiency leads to exacerbated IBD manifestations caused by various injuries in mice, whereas MG53 overexpression in ISCs is sufficient to ameliorate intestinal damage.

overall_design: We isolated intestinal organoids from MG53-TG mice and littermates wild type.

first: Meng

last: Fang

first: Xinli

last: Hu

first: Rui-ping

last: Xiao


title: Transcriptome comparison between Old vs young rat retinae

status: Public on May 31 2024

city: Pittsburgh

first: Yuanyuan

last: Chen

state: PA

address: 1622 Locust Street,

department: Ophthalmology

institute: University of Pittsburgh

summary: Visual decline in the elderly is often attributable to retinal aging, which predisposes the tissue to pathologies including age-related macular degeneration. Currently, effective oral pharmacological interventions for retinal degeneration are limited. Utilizing the Fischer 344 rat model of aging, we evaluated the efficacy of 8-aminoguanine (8-AG), a compound previously shown for multi-organ protection, against age-related retinal degeneration. Remarkably, administration of 8-AG at a dosage of 5 mg/kg body weight via drinking water from 22 months of age for a duration of 8 weeks resulted in substantial retinal preservation evidenced by an increase in retinal thickness, a greater number of photoreceptors with longer outer segments, and enhanced electroretinogram signals.  RNA sequencing and subsequent analyses revealed pronounced anti-inflammatory effects by 8-AG on both adaptive and innate immune responses within the aged retina.

overall_design: To compare the transcriptome changes affected by aging and by 8-AG treatment, we collected retina and RPE/choroids separetly from young (4 months old), aged (24 months old) and 8-AG treated (24 months old) Fischer344 rats. Specifically, 5 mg/kg body weight of 8-AG was treated daily to the aged rats starting at 22 monthls of age by suppementing the compound in the drinking water. The drinking water was refresehd daily and the treatment lasted 8 weeks and animals were euthanized at 24 months of age for tissue collection. mRNA seq was performed for both retina and RPE/choroids samples.

last: Cen

first: Abhishek

last: Vats


title: Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development [human snRNA-seq]

first: Andrew

last: McMahon

summary: Mammalian kidneys maintain fluid homeostasis through the cellular activity of nephrons and the conjoined collecting system. Each epithelial network originates from distinct progenitor cell populations that reciprocally interact during development. To extend our understanding of human and mouse kidney development, we profiled chromatin organization (ATAC-seq) and gene expression (RNA-seq) in developing human and mouse kidneys. Data were analyzed at a species level and then integrated into a common, cross-species multimodal data set. Comparative analysis of cell types and developmental trajectories identified conserved and divergent features of chromatin organization and linked gene activity, revealing species- and cell-type specific regulatory programs. Identification of human-specific enhancer regions linked through GWAS studies to kidney disease highlights the potential of developmental modeling to provide clinical insight.

overall_design:
Human donor fetal kidneys were obtained, dated and dissected by the Obstetrics and Gynecology Maternal Fetal Medicine Division of University of Southern California. Fetal embryonic age is estimated based on first day of last menstrual period (LMP).  Non-nucleotide, processed feature-barcode information is provided.
***Controlled access to raw fastq files is available through dbGaP***

last: Kim


title: Endotoxin stimulates lipolysis in bovine adipocytes

status: Public on May 20 2024

city: East Lansing

first: G. Andres

last: Contreras

state: MI

address: 736 Wilson Road Room D202, Michigan State University

department: Large Animal Clinical Sciences

institute: Michigan State University

summary: As cows progress from pregnancy to lactation, the adipose tissues (AT) undergo adaptations characterized by the mobilization of free fatty acids (FFA) through lipolysis to address energy deficiencies. Typically, in clinically healthy cows, the intensity of lipolysis decreases during lactation. However, when the release of FFA surpasses tissue requirements, it leads to the accumulation of lipid-derived products, heightening the susceptibility of cows to metabolic and infectious diseases. A second factor correlated to disease incidence in dairy cows is the presence of bacterial endotoxins in blood. The last is implicated in AT lipolysis and dysfunction  in mammals. However, the mechanisms by which endotoxin activates lipolysis and affects the formation of lipid derived products in bovine adipocyte remains unknown. We hypothesize that endotoxin triggers AT dysfunction by increasing the synthesis and release of lipid-derived products with proinflammatory potential.  Preadipocytes were obtained from subcutaneous AT of multiparous Holstein cows (n=9). Adipogenesis was induced for 7 d and cells were incubated with endotoxin  [lipopolysaccharide 1µg/mL (LPS)] for up to 7 h. Beta-adrenergic receptor agonist isoproterenol (ISO; 1 µM) was used as an activator of canonical lipolysis. The antilipolytic effect of insulin was evaluated alone or in combination with LPS. Lipolysis was evaluated by the release of glycerol in the media. RNA from adipocytes was sequenced in Illumina NextSeqData, and Differential Expressed Genes (DEG) identified. Enrichment and network analyses were performed in Ingenuity Pathways (IPA). Our findings provide evidence supporting the higher abundance of lipid-derived products with proinflammatory activity and dysfunction related to inflammatory activation.

overall_design: To investigate the proinflammatory effect of endotoxins in bovine adipocytes and its role on the formation of lipid-derived products

first: Miguel

last: Chirivi

first: Madison

last: Smith

first: G


title: WNT3 Promotes Chemoresistance in Oral Squamous Cell Carcinoma via Activating the Canonical β-catenin Pathway

status: Public on May 15 2024

city: Fuzhou

first: Kairui

last: Sun

state: Fujian

address: Jiaotong Road 88

department: School and Hospital of Stomatology

institute: Fujian Medical University

summary: Oral squamous cell carcinoma (OSCC) represents a major malignancy in the oral and maxillofacial region. The primary therapeutic agents, 5-fluorouracil (5FU) and oxaliplatin (OXA), often encounter the challenge of chemoresistance, leading to treatment failure. The WNT/β-catenin signaling pathway, closely tied with chemoresistance, offers a promising therapeutic avenue. This study delves into this potential connection. 5FU-resistant and OXA-resistant cell lines were established by gradually elevating the drug concentration in the culture medium. Differential gene expressions between parental and resistant cells were analyzed by RNA sequencing analysis, which was then substantiated via RT-qPCR and western blot. The influence of the WNT signaling on OSCC drug resistance was ascertained through WNT3 knockdown or overexpression. The WNT inhibitor, MSAB, was probed for its capacity to boost the efficacy of 5FU or OXA. Through transcriptome sequencing, successfully derived 5FU-resistant and OXA-resistant cell lines revealed a conspicuous activation of the WNT/β-catenin signaling pathway in the drug-resistant cells. WNT3 was identified as a pivotal factor contributing to chemoresistance in OSCC. Counteracting β-catenin notably augmented the therapeutic potency of 5FU and OXA. Our study underscored the activation of the WNT/β-catenin signaling pathway in resistant OSCC cell lines. By modulating WNT signaling activity, drug resistance in OSCC cells may be effectively circumvented.

overall_design: To elucidate the chemoresistance mechanism, we established 5FU-resistant and OXA-resistant cells. We extracted RNA and employed RNA-seq to identify key differentially expressed genes between parental and resistant cells.

first: Xuyang

last: Zhang

first: Ruihuan

last: Gan

first: Dali

last: Zheng

first: Youguang

last: Lu


title: Multi-level proteomics profiling of virus restrictive and -permissive cellular environments reveal regulatory factors of virus infection

city: Glasgow

first: Honglin

address: Centre for Virus Research

institute: Centre for Virus Research

summary: Virus proliferation inside host cells relies on a diverse range of host machineries and is also restricted by the host through antiviral factors. The configuration of virus-dependency and antiviral factors determine the permissiveness of host cells to virus infection, however, overall differences between highly permissive and restrictive cellular states remain largely unexplored. Here we employed integrated omics analysis combining RNA-seq, proteomics, and phosphoproteomics to study determinants of virus permissiveness on a model system comprising multiple cellular states: highly permissive cells (HEK293T), steady-state cells (HEK293), and restrictive cells (interferon alpha (IFN-a) stimulated HEK293) due to their similar genetic background and distinct permissiveness. Our in-depth proteomics map across cellular states revealed pathway-level depletion of innate immune response and enrichment of anabolic processes in HEK293T cell. RNA-seq and proteomics results depicted dynamic regulations of IFN-α response across early/late timepoints, highlighting a group of robustly upregulated antiviral factors. In addition, phosphoproteomics uncovered extensive alterations of phosphorylation in IFN-a response. Integrated analysis of multi-level omics results identified putative regulators of infection, and we experimentally validated their roles in virus infection.

overall_design: This RNA-seq data is part of our integrated omics analysis that aim to identify determinants of virus permissiveness across distinct cellular states. RNA-seq was performed with steady-state cells (HEK293), and restrictive cells (IFN-α stimulated HEK293 cells), comparing gene expression changes between unstimulated, early timepoint (4 h) IFN-α stimulation, and late timepoint (20 h) IFN-α stimulation in HEK293 cell line. Integration of sequencing results and our proteomics analysis facilitated identification of virus regulating factors in human cells.

first: Quan

last: Gu


title: Effect of Trp53 and Rb1 knockout and Myc overexpression on fallopian tube epithelial organoids

status: Public on May 07 2024

city: Shinjuku

first: Tomohiro

last: Tamura

state: Tokyo

address: Shinanomachi 35

department: Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory

institute: Keio University School of Medicine

summary: Refractory high-grade serous carcinoma (HGSC) is one of the most severe clinical problems in gynecology, but we have barely grasped the underlying mechanism of aggressiveness and chemo-resistance. We performed gene set variation analysis and comprehensive log-rank tests on TCGA advanced serous ovarian cancer datasets. As a result, regulation of small GTPase signaling prominently correlated with poor prognosis uniquely in BRCA1/2-unmutated HGSC patients, and eventually, pathway clustering analysis discovered aberrant RAS/PI3K crosstalk as peculiar poor prognostic signature of BRCA1/2-unmutated HGSC patients. To elucidate the mechanism of poor progression triggered by RAS/PI3K, we utilized our syngeneic HGSC organoid models newly established from murine fallopian tube epithelium by making Myc overexpressing, and knocking out Trp53 and Rb1. After that, we knocked out Nf1 and Pten to induce aberrant RAS/PI3K crosstalk in the primitive HGSC model. In-vivo evaluation and growth comparison indicated that aberrant RAS/PI3K crosstalk transformed Brca1/2-unmutated HGSC modeling cells into aggressive phenotypes. Chemo-sensitivity assay also showed that the genetic manipulation made Brca1/2-unmutated HGSC modeling cells more tolerant to anti-tumor agents. To investigate biological processes that induce the aggressive and chemo-resistant phenotype, we performed gene set enrichment analysis among our HGSC models. The result showed that aberrant RAS/PI3K crosstalk induces cell cycle acceleration and downregulation of apoptosis in the HGSC cells, which backed up aggressive phenotype and chemo-resistance in our HGSC models. In conclusion, aberrant RAS/PI3K crosstalk transforms Brca1/2-unmutated HGSC modeling cells more aggressive and chemo-resistant, which was well recapitulated by our HGSC modeling organoids. The integration of our computational approach and experimental models will lead us to detect peculiar therapeutic targets against refractory HGSC.

overall_design: To investigate the biological changes caused by TRP53 and RB1 knockout and MYC overexpression in fallopian tube epithelium, we established murine fallopian tube epithelial organoids and performed a transcriptomic analysis. Genotypes were as follows; RPM: Rb1-/-Trp53-/-MycOE, RPMN: Rb1-/-Trp53-/-MycOE + Nf1KO, RPMP: Rb1-/-Trp53-/-MycOE + PtenKO, RPMNP: Rb1-/-Trp53-/-MycOE + Nf1KO + PtenKO. A control sample was normal fallopian tube epithelial organoids established from an Rb1fl/flTrp53fl/flMycLSL/LSL mouse.

first: Shimpei

last: Nagai

first: Kenta

last: Masuda

first: Keiyo

last: Imaeda


title: Lipid-Associated Macrophages Reshape BAT Cell Identity in Obesity

city: Rome

first: Andrea

last: Ninni

address: Via della ricerca scientifica 1

department: Biology

country: Italy

institute: University of Rome "Tor Vergata"

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

overall_design: Refer to individual Series


title: Preclinical efficacy of targeting epigenetic mechanisms in AML with 3q26 lesions and EVI1 overexpression. [ATAC-Seq]

status: Public on May 06 2024

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

summary: AML with chromosomal alterations involving 3q26 overexpress the transcription factor (TF) EVI1, associated with therapy refractoriness and inferior overall survival in AML. Consistent with a CRISPR screen highlighting BRD4 dependency, treatment with BET inhibitor (BETi) repressed EVI1, LEF1, c-Myc, c-Myb, CDK4/6, and MCL1, and induced apoptosis of AML cells with 3q26 lesions. Tegavivint (TV, BC-2059), known to disrupt binding of nuclear β-catenin and TCF7L2/LEF1 with TBL1, also inhibited co-localization of EVI1 with TBL1 and dose-dependently induced apoptosis in AML cell lines and patient-derived (PD) AML cells with 3q26.2 lesions. TV treatment repressed EVI1, attenuated enhancer activity at ERG, TCF7L2, GATA2 and MECOM loci, abolished interactions between MYC enhancers, repressing AML stemness while upregulating mRNA gene-sets of interferon/inflammatory response, TGF-β signaling and apoptosis-regulation. Co-treatment with TV and BETi or venetoclax induced synergistic in vitro lethality and reduced AML burden, improving survival of NSG mice harboring xenografts of AML with 3q26.2 lesions.

overall_design: Paired end ATAC-Seq of an EVI1-expressing AML sample treated with BC2059 for 16 hours.

first: Warren

last: Fiskus

first: Kapil

middle: N

last: Bhalla


title: Preclinical efficacy of targeting epigenetic mechanisms in AML with 3q26 lesions and EVI1 overexpression [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) and Hi-ChIP for the histone modification H3K27Ac in AML191 cells treated with tegavivint for 16 hours.