title: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans

status: Public on Jan 29 2024

city: Fort Collins

first: Taiowa

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

summary: Canonical small interfering RNAs (siRNAs) are generated by the cleavage of double-stranded RNA (dsRNA) by the ribonuclease Dicer. siRNAs are found in plants, animals, and some fungi where they bind to Argonautes to direct RNA silencing. In this study, we characterized the canonical Dicer-dependent siRNAs of C. elegans. We identified thousands of endogenous loci, representing dozens of unique elements, that give rise to low to moderate levels of siRNAs, called 23H-RNAs. These loci include repetitive elements, alleged coding genes, pseudogenes, non-coding RNAs, and unannotated features, many of which adopt hairpin structures. Using protein-small RNA co-immunoprecipitation, we identified the Argonautes that associate with 23H-RNAs and using mRNA-sequencing we explored their roles in gene regulation.

overall_design: mRNA and small RNA high-throughput sequencing were done on wild-type and rde-1(ram40) mutant strains of C. elegans, along with small RNA sequencing from various transgenic strains containing GFP fusions to Argonaute proteins. Samples were either untreated or subjected to RNAi targeting oma-1, nrfl-1, dcr-1, or rde-1. RNA was isolated from cell lysates or Argonaute co-immunoprecipitates from C. elegans cultured at 20˚C. mRNA sequencing data was analyzed with a custom pipeline utilizing fastp, RSEM, STAR, and DESeq2. Small RNA data was analyzed with the tinyRNA pipeline complemented by custom Python scripts.


title: Helicobacter pylori infection induces DNA breaks at replication-coupled fragile sites by inducing dNTP depletion in CagA-independent manner

status: Public on Feb 15 2024

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

summary: Helicobacter pylori (H.pylori) infection is a significant risk factor for gastric cancer (GC) development. A growing body of evidence suggests a causal link between infection with H.pylori and increased DNA breakage in the host cells. While several mechanisms have been proposed for this damage, their relative impact on the overall bacterial genotoxicity is unknown. Moreover, the link between the formation of DNA damage following infection and the emergence of cancerous structural variants (SV) in the genome of infected cells remained unexplored. To resolve these gaps, we constructed high-resolution map of genomic H.pylori-induced recurrent break sites. Our data indicated that these sites are ubiquitous across cell types, localized at replication-related fragile sites, and their breakage is dependent on replication. Consistent with that, we found that H.pylori inflicts nucleotide depletion, and that rescuing the nucleotide pool largely reduced H.pylori-induced DNA breaks. Intriguingly, we found that this genotoxic mechanism operates independently of the H.pylori virulence factor, CagA, which was previously implicated in increasing DNA damage by downregulating the DNA damage response. Finally, we show that sites of recurrent H.pylori-mediated breaks coincide with chromosomal deletions observed in patients with intestinal-type GC, and that this link potentially elucidates the persistent transcriptional alterations observed in cancer driver genes. These findings establish the link between H.pylori genotoxicity, and its oncogenic potential.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 14 samples of END-seq profile:  H.pylori infected (3 samples) and uninfected (3 samples) human gastric cell line AGS, and H.pylori infected (6 samples) and uninfected (6 samples) mouse pre-B vAbl cell line, treated or untreated with STI-571 (3 each).

first: Hadas

last: Sibony-Benyamini

first: Rose

last: Jbara

first: Tania

last: Shubash

first: Alexander

last: Brandis

first: Tamar

last: Leshem

first: Avi

last: Peretz

first: Layan

last: Abu-Rahmun

first: Michal

last: Easton Mor

first: Shira

last: Perez


title: Fine needle aspiration of human lymph nodes reveals cell populations and soluble interactors pivotal to immunological priming

status: Public on Feb 23 2024

city: Oxford

first: Nicholas

last: Provine

address: Roosevelt Way

department: Pandemic Sciences Institute

country: United Kingdom

institute: University of Oxford

type: Expression profiling by high throughput sequencing

summary: Lymph node (LN) fine needle aspiration (LN FNA) represents a powerful technique for minimally invasive sampling of human LNs in vivo and has been used effectively to directly study aspects of the human germinal center response. However, systematic deep phenotyping of the cellular populations and cell-free proteins recovered by LN FNA has not been performed. Thus, we studied human cervical LN FNAs as a proof-of-concept and used single-cell RNA-sequencing and proteomic analysis to benchmark this compartment, define the purity of LN FNA material, and facilitate future studies into this immunologically pivotal environment. Our data provide evidence that LN FNAs contain bone fide LN-resident innate immune populations, with minimal contamination of blood material. Examination of these populations reveals unique biology not predictable from equivalent blood-derived populations. LN FNA supernatants represent a specific source of lymph- and lymph node-derived proteins, and can, aided by transcriptomics, identify likely receptor-ligand interactions. This represents the first description of the types and abundance of immune cell populations and cell-free proteins that can be efficiently studied by LN FNA. These findings are of broad utility for understanding LN physiology in health and disease, including infectious or autoimmune perturbations, and in the case of cervical nodes, neuroscience.

overall_design: cervical lymph node fine needle aspirates and matched peripheral blood from four healthy human volunteers was used for single-cell RNA-sequencing by the 10x Genomics 5' platform (gene expression and surface proteins)

first: Provine

last: Nicholas


title: Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord [Spinal spatial]

status: Public on Jan 11 2024

city: Chengdu

first: Donghang

last: Zhang

state: Sichuan

address: No.37, guoxue lane, wuhou district, chengdu city, sichuan province

country: China

institute: West China Hospital of Sichuan University

summary: Despite the recognized importance of the spinal cord in sensory processing, motor behaviors, and neural diseases, the underlying organization of neuronal clusters and their spatial location remain elusive. Recently, several studies have attempted to define the neuronal types and functional heterogeneity in the spinal cord using single-cell or single-nucleus RNA sequencing in animal models or developing humans. However, molecular evidence of cellular heterogeneity in the adult human spinal cord is limited. Here, we classified spinal cord neurons into 21 subclusters and determined their distribution from nine human donors using single-nucleus RNA sequencing and spatial transcriptomics. Moreover, we compared the human findings with previously published single-nucleus data of the mouse adult spinal cord, which revealed an overall similarity in the neuronal composition of the spinal cord between the two species while simultaneously highlighting some degree of heterogeneity. Additionally, we examined the sex differences in the spinal neuronal subclusters. Several genes, such as SCN10A and HCN1, showed sex differences in motor neurons. Finally, we classified human DRG neurons using spatial transcriptomics and explored the putative interactions between DRG and spinal cord neuronal subclusters. In summary, these results illustrate the complexity and diversity of spinal neurons in humans and provide an important resource for future research to explore the molecular mechanisms underlying spinal cord physiology and diseases.

overall_design: Spatial transcriptomics and single-nucleus transcriptomic profiles of spinal cord in 9 human donors

first: Yali

last: Chen

first: Yiyong

last: Wei

first: Hongjun

first: Yujie

last: Wu

first: Lin

first: Jin

last: Li

first: Changhong

last: Miao

last: Liu

first: Tao

last: Zhu

first: Cheng

last: Zhou


title: Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord [DRG Spatial]


title: RNA-seq in mESCs with and without TIP60

status: Public on Jan 30 2024

city: Illkirch

first: Manuel

last: Mendoza

address: 1 rue Laurent Fries

country: France

institute: INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY

summary: Transcript buffering entails the reciprocal modulation of mRNA synthesis and degradation rates, ensuring a constant RNA concentration amidst changes in cellular conditions. While an increasing body of research supports a global, non-sequence-specific linkage between mRNA synthesis and degradation, the underlying mechanisms remain elusive. To explore this, we investigated alterations in RNA metabolism following the acute depletion of TIP60/KAT5, the transcriptional coactivator and acetyltransferase subunit of the NuA4 complex, in mouse embryonic stem cells. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling, we show that TIP60 activates transcription of numerous genes, with substantially fewer genes undergoing transcriptional repression. Surprisingly, specific RNA species' transcription changes triggered by TIP60 depletion were counterbalanced by compensatory adjustments in RNA export and/or stability within the nucleus and in RNA stability within the cytoplasm. These discoveries imply that transcript buffering operates on a gene-specific level and suggest that cells continually monitor RNA molecule counts in nuclear and cytoplasmic compartments to maintain cellular homeostasis.

overall_design: Total RNA extraction. 6 samples, 2 conditions (TIP60-AID transgenic mESC line treated with auxin for 24h or DMSO)

first: Faezeh

last: Forouzanfar


title: TT-seq in mESCs with and without TIP60

overall_design: Purification of newly synthesized RNA coupled with genome-wide sequencing. 6 samples, 2 conditions (TIP60-AID transgenic mESC line treated with auxin for 24h or DMSO)


title: Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord [Spinal snRNA-seq]


title: Response to tumor- infiltrating lymphocyte adoptive therapy is associated with preexisting CD8+T- myeloid cell networks in melanoma [bulk RNAseq]

status: Public on Feb 05 2024

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

summary: Adoptive cell therapy (ACT) using ex vivo–expanded tumor-infiltrating lymphocytes (TILs) can eliminate or shrink metastatic melanoma, but its long-term efficacy remains limited to a fraction of patients. Using longitudinal samples from 13 patients with metastatic melanoma treated with TIL-ACT in a phase 1 clinical study, we interrogated cellular states within the tumor microenvironment (TME) and their interactions. We performed bulk and single-cell RNA sequencing, whole-exome sequencing, and spatial proteomic analyses in pre- and post-ACT tumor tissues, finding that ACT responders exhibited higher basal tumor cell–intrinsic immunogenicity and mutational burden. Compared with nonresponders, CD8+ TILs exhibited increased cytotoxicity, exhaustion, and costimulation, whereas myeloid cells had increased type I interferon signaling in responders. Cell-cell interaction prediction analyses corroborated by spatial neighborhood analyses revealed that responders had rich baseline intratumoral and stromal tumor–reactive T cell networks with activated myeloid populations. Successful TIL-ACT therapy further reprogrammed the myeloid compartment and increased TIL-myeloid networks. Our systematic target discovery study identifies potential T-myeloid cell network–based biomarkers that could improve patient selection and guide the design of ACT clinical trials.

overall_design: Melanoma tumors gene expression profiling pre and post TIL adoptive cell therapy

first: Alexandre

last: Harari

first: Denarda

last: Dangaj

first: George

last: Coukos


title: Repairing of isoaspartyl residues by PCMT1 alleviates renal fibrosis through the repression of TGF-β1/TGFBR2/Smad signaling pathway

status: Public on Jan 01 2024

city: Shanghai

first: Yutong

last: Hou

address: 227 South Chongqing Road

institute: SJTU

summary: Protein L-isoaspartyl/D-aspartyl Methyltransferase (PCMT1) plays a pivotal role in repairing a spontaneous post-translational modification (PTM) of L-isoaspartyl residues resulted from asparagine deamidation or aspartate isomerization. This PTM is particularly important for extracellular matrix (ECM) proteins because their low turnover rate and are susceptible to factors that could accelerate such modification. Therefore, it becomes imperative to comprehensively investigate the impact of PCMT1 on ECM homeostasis and its associated pathological alterations. In this study, we revealed that secreted PCMT1 repairs the isoaspartyl residues of the TGFBR2 protein on the cell membrane to suppress TGF-β1/Smad pathway. Through this novel PTM regulation, PCMT1 played essential roles in combating renal fibrosis, as lack of PCMT1 worsened tubular injury, collagen deposition, myofibroblast activation, and macrophage infiltration in total kidney and tubular contexts in a mouse model of chronic kidney disease. Moreover, PCMT1 level decreased in fibrotic kidney tissues and inversely related to kidney function in mice and in humans. Our study highlights the important function of PCMT1 in modifying proteins in the extracellular space and identified a novel role of PCMT1 in regulating TGF-β1 pathway in renal fibrosis. This study holds the potential of innovative therapeutic avenue for the mitigation of renal fibrosis.

overall_design: To further elucidate the comprehensive transcriptome-wide transcriptional alterations resulting from PCMT1 deficiency, we conducted whole transcriptome sequencing in HK-2 WT and PCMT1-KO cells. Moreover, RNA sequencing was also carried out on kidney tissues from WT and Pcmt1-/- mice to achieve the same objective. We also conducted RNA sequencing on the kidney tissues from Pcmt1 fl/fl and Pcmt1 tKO mice after modeling of unilateral ureteral obstruction (UUO).

first: Jia

last: Xia


title: HuR inhibition reduces post-ischemic cardiac remodeling by dampening inflammatory gene expression and the innate immune response

city: Columbus

first: Michael

last: Tranter

state: OH

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

country: USA

institute: The Ohio State University

summary: In this study, we applied a novel small molecule inhibitor of HuR to define the functional role of HuR in the acute response to I/R injury and gain a better understanding of the HuR-dependent mechanisms during post-ischemic myocardial remodeling. Our results show an early post-ischemic increase in HuR activity that is necessary for inflammatory gene expression in cardiomyocytes. Despite the early reductions inflammatory gene expression, HuR inhibition has no effect on initial infarct size at 24-hours post-I/R. However, in agreement with previously published work by our group using a pressure overload model, we do see a protection with regard to pathological remodeling and cardiac function at two weeks post-I/R upon HuR inhibition. RNA-sequencing analysis of neonatal rat ventricular myocytes (NRVMs) post-LPS treatment to model damage associated molecular pattern (DAMP)-mediated activation of toll like receptors (TLRs) demonstrates a broad HuR-dependent regulation of pro-inflammatory chemokine and cytokine gene expression in cardiomyocytes. Importantly, we show that conditioned media from NRVMs pre-treated with HuR inhibitor loses the ability to induce inflammatory gene expression in bone marrow derived macrophages (BMDMs) compared to NRVMs treated with LPS alone. Functionally, HuR inhibition in NRVMs also reduces their ability to induce endocrine migration of peripheral blood monocytes in vitro and reduces post-ischemic macrophage infiltration to the heart in vivo. In summary, these results suggest a HuR-dependent expression of pro-inflammatory gene expression by cardiomyocytes that leads to subsequent monocyte recruitment and macrophage activation in the post-ischemic myocardium.

overall_design: Neonatal rat ventricular myocytes (NRVMs) treated with LPS to mimic toll-like receptor (TLR) receptor signaling via damage associated molecular patterns (DAMPs) that often occurs during in vivo I/R injury. NRVMs were treated with LPS with or without HuR inhibition (KH-3) and RNA-sequencing was performed at two hours post-treatment.

first: Samuel

last: Slone


title: Characterization of stress-susceptible cells and gene in mouse brain via Spatial Transcriptomics

status: Public on Feb 09 2024

city: Beijing

first: TING

last: WANG

address: Haidian District, Beijing

institute: Beijing Institute of Basic Medical Sciences

summary: Spatial transcriptome analysis of brain sections from non-stressed controls (CON), susceptible mice (SUS) and resistant mice (RES) was performed to investigate spatial patterns of gene expression in multiple brain regions to gain new insights into stress susceptibility.

overall_design: Animals were subjected to 10 days of chronic social defeat stress and then phenotypes were acquired using social interaction tests.Fresh brain tissue was collected 1.5 hours after the last CSDS exposure of mice, and we obtained three coronal sections(Bregma2.0~2.1) from the left brain of Control, susceptible, resilient mouse by cryosections of mouse brains. After that Spatial transcriptome (ST) sequencing was performed.

first: Ting

last: Wang

first: Zhihong

last: Song

first: Haitao


title: Atypical somatic small RNAs in Anopheles

city: Moscow

first: Sergei

last: Funikov

state: Moscow

address: Vavilov str. 32

country: Russia

institute: Engelhardt Insitute of Molecular Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs of the Piwi-interacting RNA class (piRNA) play a key role in controlling the activity of transposable elements (TEs) in the animal germ line. In some arthropod species, including mosquitoes, the vectors of malaria and other pathogens, the piRNA pathway is active not only in the gonads, where it controls TE activity, but also in somatic tissues, where its targets and functions are less clear. It is thought that the piRNA pathway in somatic tissues is involved in the antiviral response and the modulation of TE activity. Here, we studied the features of small RNA production in head and thorax somatic tissues of Anopheles coluzzii focusing on the small RNAs processed from protein-coding gene mRNAs. We revealed tissue and sex specificity in the production of small RNAs derived from the genic transcripts. Genic small RNAs of 24-30 nt in length are atypical RNAs that lack the hallmarks of piRNAs. The majority of these short RNAs are derived from mitochondrial and nuclear genes involved in energy metabolism. We discuss the peculiarities of the piRNA biogenesis in Anopheles species which may result in the production of genic small RNAs in the somatic tissues.

overall_design: Deep-sequencing of small RNAs (18-32 nt) of Anopheles coluzzii somatic tissues and sexes.


title: BS-seq of WT, slnor, and sldml2

status: Public on Dec 31 2023

city: Shenzhen

first: yujing

last: lin

address: No. 1088 Xueyuan Avenue, Nanshan District, Shenzhen City, Guangdong Province

institute: Southern University of Science and Technology

type: Methylation profiling by high throughput sequencing

summary: Using WGBS-seq to study the methylation level of genes in WT, slnor, and sldml2 mutants

overall_design: Examination of methylation level using WGBS-Seq

first: Ying

last: Gao

first: Yujing

last: Lin

first: Min

last: Xu

first: Hanxiao

last: Bian

first: Chi

last: Zhang

first: Jingyu

first: Hanqing

first: Yaping

first: Qingfeng

last: Niu

first: Jinhua

last: Zuo

first: Da-Qi

last: Fu

first: Yu

last: Pan

first: Kunsong

last: Chen

first: James

last: Giovannoni

first: Harry

last: Klee

first: Zhaobo

last: Lang

first: Bo


title: Spatial transcriptomics and single-nucleus RNA-sequencing reveal a transcriptomic atlas of human spinal cord

first: Donghang

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

overall_design: Refer to individual Series


title: Bulk RNA-seq of Sox9-deficient intrahepatic biliary epithelial cells

city: Augusta

first: Sergei

last: Bombin

institute: Augusta University

summary: To define the regulatory role of Sox9 in intrahepatic biliary epithelium, we conducted bulk RNA-seq on biliary epithelial cells (BECs) from adult control (Sox9fl/fl) and conditional Sox9 knockout (Sox9cKO; Sox9fl/fl:Albumin-Cre) mice. Livers were dissociated to single cells and BECs isolated by FACS based on CD326 positivity. CD31+ and CD45+ cells were excluded by FACS. Gallbladder and extrahepatic tissues were excluded by dissection. RNA was isolated using Ambion RNAqueous Micro kit and libraries were made using Takara SMARTer Stranded Total RNA-seq Kit v3 Pico.

overall_design: Differential expression analysis of 3 Sox9cKO and 3 Control samples of BEC cells

first: H

middle: R

last: Hrncir

first: S

first: A

middle: D

last: Gracz


title: Chronic oral administration of nicotine affects transcriptomic profiling in conditional Presenilin 1/2 knockout mice and wild type mice

last: Meng

address: 3663 Zhongshan Rd(N.)

institute: East China Normal Univeristy

summary: we found that chronic oral (3 months) administration of nicotine had different effects on transcriptomic profiling in prefrontal forebrain cortex of wildtype (WT) and Presenilin 1/2 double knockout mice.

overall_design: 8-month-old Presenilin 1/2 double knockout mice (DKO) and the wildtype mice (WT) were exposed to nicotine by drinking water at the dose of 100 μg/ml (DKO-N and WT-N, respectively) or water (DKO-B and WT-B, respectively) ad libitum for 3 months, after the behavior tests, the prefrontal forebrain cortex of the four groups of mice were collected for RNA-seq.

first: Youwen

last: Si


title: Single cell RNA-seq of Sox9-deficient intrahepatic biliary epithelial cells

summary: To define the regulatory role of Sox9 in intrahepatic biliary epithelium, we conducted single cell RNA-seq on biliary epithelial cells (BECs) from adult control (Sox9fl/fl) and conditional Sox9 knockout (Sox9cKO; Sox9fl/fl:Albumin-Cre) mice. Livers were dissociated to single cells and BECs isolated by FACS based on CD326 positivity. CD31+ and CD45+ cells were excluded by FACS. Gallbladder and extrahepatic tissues were excluded by dissection. Sorted cells were fixed according to manufacturer instructions using Parse Whole Cell Fixation kit. Fixed cells were frozen and stored at -70C for less than 6mo, prior to being used in split-pool combinatorial barcoding according to manufacturer instructions. Barcoding and library construction was carried out with the Parse Evercode Whole Transcriptome v2 kit.

overall_design: Clustering and differential expression analysis of Sox9cKO and control samples of biliary epithelial cells


title: Mapping the cellular landscape of Atlantic salmon head kidney by single cell and single nucleus transcriptomics

status: Public on Jan 12 2024

city: Ås

first: Adriana Magalhaes

middle: Santos

last: Andresen

state: Other

address: Elizabeth Stephansens v. 1

country: Norway

institute: Veterinærinstituttet

summary: Comparison of two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar)

overall_design: Head kidney samples from two Atlantic salmon were utilized for single-cell RNA sequencing (sc), while two samples were used for single-nucleus RNA sequencing (sn). Single cells and nuclei were isolated accordingly. Libraries were generated using the 10x Genomics platform, and sequencing was performed using Illumina NextSeq500 (sc) and NovaSeq 6000 (sn) for paired-end reads.

first: Adriana

middle: M

first: Richard

middle: S

last: Taylor

first: Unni

last: Grimholt

first: Rose

last: Daniels

first: Jianxuan

last: Sun

first: Ross

last: Dobie

first: Neil

middle: C

last: Henderson

first: Samuel

middle: A

last: Martin

first: Daniel

middle: J

last: Macqueen

first: Johanna

middle: H

last: Fosse


title: A dataset of single-cell transcriptomic atlas of Bama pigs and potential marker genes across seven tissues

status: Public on Dec 22 2023

city: chengdu

first: chen

last: long

state: sichuan

address: 211 Huimin Road, Wenjiang District

department: animal science and technology

institute: Sichuan Agricultural University

summary: The use of single-cell sequencing technology for single-cell transcriptomics studies in pigs is expanding progressively. However, the comprehensive classification of cell types across different anatomical tissues and organs of pigs in multiple datasets remains relatively limited. This study centers on an investigation using single-cell sequencing technology in Bama pigs, where unique marker genes and their corresponding transcriptomic profiles have been identified for diverse cell types across distinct anatomical tissues and organs, encompassing subcutaneous fat, visceral fat, skeletal muscle, liver, spleen, lung, and kidney. Using comprehensive data analyses, we discovered the widespread cellular diversity inherent in different anatomical tissues and organs of Bama pigs. This study not only provides a pivotal dataset for physiological research on Bama pigs but also contributes to the verification and prediction of key marker genes in the single-cell transcriptomics of these tissues and organs. Furthermore, the data and methodologies that were used in this study underscore our commitment to enhancing the authenticity of cell type identification and ensuring the consistency in cell type allocation.

overall_design: We selected tissues from the liver, spleen, lung, kidney, psoas major muscle (PMM), subcutaneous adipose tissue (SAT), and greater omentum (GOM) of Bama pigs. These meticulously cleaned tissue samples were sealed and preserved in liquid nitrogen until they underwent a cellular extraction procedure, subsequently sequenced on the 10× Genomics platform.

first: Long

last: Chen

first: Bo

last: Zeng

last: Jin

first: Mingzhou

last: Li


title: Single-cell RNA transcriptome reveals heterogeneity and dynamics of cells during skeletal muscle development in different chicken breeds

status: Public on Dec 25 2023

first: Xiong

middle: Zhi

address: Wuhou District

institute: Southwest Minzu University

summary: Different chicken breeds exhibit distinct muscle phenotypes resulting from selective breeding, but little is known about the molecular mechanisms responsible for this phenotypic difference. Skeletal muscle is composed of a large number of heterogeneous cell populations. Differences in differentiation and interaction of cell populations play a key role in the difference of skeletal muscle phenotype. Here, skeletal muscle single-cell RNA sequencing in three developmental stages was performed on Daheng broiler (cultivated breed) and Tibetan chicken (native breed).

overall_design: Leg musculatures were collected from the male embryos were dissected at embryonic (E) 10, E14, and E18 of Daheng broiler and Tibetan chicken. For each group, pooled skeletal muscle samples isolated from at least three embryos were dissociated into single cell suspension, resulting a total of 6 samples for single-cell RNA sequencing.

first: Jie

first: Zhixiong


title: Unstable EBV latency drives inflammation in multiple sclerosis patient derived spontaneous B cells [EBV WGS]

status: Public on Dec 21 2023

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Epstein-Barr virus (EBV) is an etiologic risk factor, and likely prerequisite, for the development of multiple sclerosis (MS). However, the role of EBV infected B cells in the immunopathology of MS is not well understood. Here, we characterized spontaneous lymphoblastoid cell lines (SLCLs) isolated from MS patients and healthy controls (HC) ex vivo to study EBV and host gene expression in the context of an individual’s endogenous EBV. SLCLs derived from MS patient B cells during active disease had higher EBV lytic gene expression than SLCLs from MS patients with stable disease or HCs. Host gene expression analysis revealed activation of pathways associated with hypercytokinemia and interferon signaling in MS SLCLs and differential expression of several genes, including upregulation of forkhead box protein 1 (FOXP1), which contributes to EBV lytic gene expression. In addition, we demonstrate that antiviral approaches targeting EBV replication decreased inflammatory cytokine production and diminished autologous CD4+ T cell responses. These data suggest that dysregulation of intrinsic B-cell control of EBV gene expression drives a pro-inflammatory, pathogenic B cell phenotype that can be attenuated by suppressing EBV lytic gene expression.

overall_design: Genomic DNA was extracted from spontaneous lymphoblastoid cell lines derived from MS patients (n=7) and healthy controls (n=2). DNA was extracted from SLCLs using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). The Illumina DNA preparation kit was used for sequencing library preparation according to the manufacturer’s instructions. Sequencing was done with an Illumina NextSeq 500 system in high-output mode to generate a total of ∼4 × 108 paired-end 75-bp reads. Fastq reads were aligned against the EBV genome (accession NC_007605.1) using the BWA algorithm. Analysis of heterogeneous sites was performed following the procedure described by Čejková et al.. The consensus EBV genome for each sample was extracted using samtools59. Circus plots were generated using the R BioCircos package. Proteins were translated from nucleotide sequences using Geneious prime 2022.2 (https://www.geneious.com). Nucleotide and protein sequences were aligned using MAFFT  v7.407 and visualized using Geneious prime 2022.2. Reference EBNA1 regions, in addition to the sequence from NC_007605.1, were obtained by querying each SLCL-derived sequence against nr using tblastn and taking differentially occurring sequences between matches for the three groups of samples (HC, AMS, SMS). One representative for each of three groups of identical sequences was kept. A phylogenetic tree of the 13 resulting sequences (9 samples, 4 reference) was constructed using PhyML with default parameters and visualized using iTOL.

first: Samantha

last: Soldan

first: Paul

last: Lieberman

first: Noam

last: Auslander

first: Steven

last: Jacobson


title: Sub-chronic administration of AM6545 enhances cognitive performance and induces hippocampal synaptic plasticity changes in naïve mice

status: Public on Dec 01 2023

city: Barcelona

first: Andrés

last: Ozaita

address: Dr Aiguader, 88

department: Department of Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

summary: Using RNA sequencing, we perform gene expression profile of five male mice treated with vehicle and five male mice sub-chronically treated with AM6545 at a dose of 1 mg/kg. To evaluate hippocampal modifications promoted by peripheral CB1R modulation, we analyze at transcript level hippocampal synaptoneurosomes fractions.

overall_design: mRNA profiles of hippocampal synaptoneurosomes from wild-type mice after sub-chronic AM6545 or vehicle administration.

first: Araceli

last: Bergadà-Martínez

first: Lucía

last: de los Reyes-Ramírez


title: scRNAseq of aqueous immune cells in human uveitis

status: Public on Dec 14 2023

city: Saint Louis

first: Joseph

middle: B

last: Lin

state: MO

address: 660 South Euclid Ave, MSC-8096-06-07

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine

summary: We profiled using single cell RNA sequencing the immune cells of the aqueous humor from patients with uveitis.

overall_design: We sampled 100-200 ul of the inflamed anterior chamber fluid using a 25- to 30-gauge needle. We pelleted cells by centrifugation (400 x g, 5 min) to remove the aqueous fluid and cryopreserved cells in fetal bovine serum containing 10% DMSO. To profile cells by single cell RNA sequencing, we used the 10x Genomics 5'v2 gene expression kit.

first: Lynn

last: Hassman


title: RNA-seq data  for Sulfolobus islandicus REY15A Δcbp1 strain and the parental strain E234

status: Public on Dec 07 2023

city: London

first: Finn

last: Werner

address: Gower Street

department: Institute of Structural and Molecular Biology

institute: University College London

first: Fabian

last: Blombach

first: Michal

last: Sýkora


title: Response to tumor- infiltrating lymphocyte adoptive therapy is associated with preexisting CD8+T- myeloid cell networks in melanoma [full scRNAseq]

first: David

last: Barras

overall_design: Baseline melanoma tumor gene expression profiling by full viable sorted 3' single cell RNAseq

first: Alexandre

last: Harari

first: Denarda

last: Dangaj

first: George

last: Coukos


title: Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS [ATAC-seq]

status: Public on Dec 29 2023

city: Bethesda

first: Mingming

last: Zhao

address: 9000 Rockville Pike

institute: national institutes of health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: IL-4 activates tissue resident macrophages (TRMs) to mediate tissue repair and clearance of nematode infections in mice, but most studies have been performed on the C57BL/6 background. The natural genetic variation between C57BL/6 and BALB/c mouse strains can result in differences in allergic responses, parasite resistance, monocyte to macrophage conversion and response to IL-4 activation. Here, we investigated in vivo IL-4 activation in TRMs of the peritoneal cavity from C57BL/6 and BALB/c mice and find that C57BL/6 TRMs are surprisingly more transcriptionally responsive to IL-4 stimulation, with greater association of induced genes with super enhancers, induced enhancers and topologically associating domains (TAD) boundaries. IL-4-directed epigenomic remodeling showed NF-κB motif enrichment only in C57BL/6 TRMs. This resulted in an enhanced synergistic response upon in vitro lipopolysaccharide (LPS) exposure in IL-4 activated C57BL/6 TRMs but not for BALB/c, despite unstimulated BALB/c TRMs having a stronger transcriptional response to LPS than C57BL/6 TRMs. Single cell RNA sequencing (scRNAseq) analysis of mixed bone marrow chimeric mice indicates that transcriptional differences between C57BL/6 and BALB/c TRMs is cell intrinsic within the same tissue environment. Hence, genetic variation alters IL-4-induced cell intrinsic epigenetic reprogramming between C57BL/6 and BALB/c TRMs to regulate the magnitude of synergistic responses to LPS exposure.

overall_design:
8 samples were anlysied (Ctrl and IL4 treatment in each strain, 2 replicates per samples)

UPDATE: [09-30-2024] The GSM7904801_BL6_Ctrl_1.genrich.RPM.bw file was renamed to GSM7904804_BL6_IL4_2.genrich.RPM.bw, and vice versa.

first: Verena

last: Link

first: Katherine

last: Hornick

first: Justin

last: Lack

first: Yasmine

last: Belkaid

first: Dragana

last: Jankovic

first: P'ng

last: Loke


title: Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS


title: Unstable EBV latency drives inflammation in multiple sclerosis patient derived spontaneous B cells

first: Priyankara

last: Wickramasinghe

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4


title: Human Renal Cells and Skin Fibroblast from Individuals with Nephropathic Cystinosis and their Controls

status: Public on Dec 08 2023

city: San Francisco

first: Swastika

last: Sur

state: CA

address: 513 Parnassus Ave

department: Surgery

institute: UCSF

summary: Transcriptional profiling of normal and cystinotic human renal proximal tubular epithelial cells (RPTECs) and skin fibroblasts with and without cysteine dimethyl ester (CDME). CDME- loaded RPTECs and fibroblasts did not transcriptionally mimic the cystinotic phenotype suggesting that CDME- loading is a poor surrogate in vitro model. Results highlight marked transcriptional differences between cystinotic RPTECs and fibroblasts from the same individual. Many genes are significantly dysregulated in cystinotic RPTECs (n=1,926; FDR<0.05) and fibroblasts (n=745; FDR<0.05), with 219 overlapping genes associated with DNA integrity loss and damage. Transcriptional microarray analysis identified that the majority of cystinosis affected genes belong to one large cluster, crucial for normal lysosomal and mitochondrial function.

overall_design:
Six-condition experiments, normal, cystinosis, normal+CDME for both, RPTEC and fibroblast, cell types. Biological replicates: 6 Normal RPTECs, 8 Cystinosis RPTECs, 4 normal+CDME RPTECs, 6 normal fibroblast, 8 cystinosis fibroblasts, 4 normal+CDME fibroblasts.
*** Submitter statement concerning missing raw data: the hard drive that housed raw data files got corrupted and it is unretreiveable. ***

first: Maggie

last: Kerwin

first: Silvia

last: Pineda

first: Poonam

last: Sansanwal

first: Tara

middle: K

last: Sigdel

first: Marina

last: Sirota

first: Minnie

last: Sarwal


title: Transcriptome analysis of the mouse fetal and adult rete ovarii and surrounding tissues

status: Public on Nov 07 2023

city: Aurora

first: Jennifer

last: McKey

address: 1775 Aurora Ct Barbara Davis Center, M20-3202G

institute: CU Anschutz medical campus

summary: The rete ovarii (RO) is an epithelial structure that arises during fetal development in close proximity to the ovary, and persists throughout adulthood in mammals. However, the functional significance of the RO remains elusive and it has been absent from recent discussions of female reproductive anatomy. The RO comprises three distinct regions: the intraovarian rete (IOR) within the ovary, the extraovarian rete (EOR) in the periovarian tissue, and the connecting rete (CR) linking the EOR and IOR. We hypothesize that the RO plays a pivotal role in maintaining ovarian homeostasis and responding to physiological changes. To uncover the nature and function of RO cells, we conducted transcriptome analysis, encompassing bulk, single-cell, and nucleus-level sequencing of both fetal and adult RO tissues using the Pax8-rtTA; Tre-H2B-GFP mouse line, where all RO regions express nuclear GFP. This study presents three datasets, which highlight RO-specific gene expression signatures and reveal differences in gene expression across the three RO regions during development and in adulthood. The integration and rigorous validation of these datasets will advance our understanding of the RO's roles in ovarian development, female maturation, and adult female fertility.

overall_design: This study employs comprehensive bulk, single cell and single nucleus transcriptome analysis to uncover gene expression signatures of the fetal and adult rete ovarii (RO) in mice.

first: Dilara

middle: N

last: Anbarci

first: Rebecca

last: O'Rourke

first: Blanche

last: Capel


title: Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms

status: Public on Nov 08 2023

first: Shiming

last: Chen

state: Missouri

address: 517 South Euclid Avenue

department: Department of Ophthalmology & Visual Sciences

institute: Washington University in St Louis

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct


title: Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease

status: Public on Dec 04 2023

city: Gaithersburg

first: Prabha

last: Chandrasekaran

state: Maryland

address: 8348 Hawkins Creamery Rd

institute: ehealth&Informatics, LLC

summary: Background and aims: Gene mutations or variants leading to insufficient reactive oxygen species (ROS) production have been associated with inflammatory bowel disease (IBD). In particular, 40-50% of patients with chronic granulomatous disease have IBD (CGD-IBD). CGD is caused by inherited defects in any one of the 5 subunits forming the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex 2 (NOX2), leading to severely reduced or absent phagocyte-derived ROS production. While conventional IBD therapies can treat CGD-IBD, their benefits must be weighed against the risk of infection in this immune compromised population. Understanding the impact of NOX2 defects on the composition and function of the intestinal microbiota may lead to the identification of treatments for CGD-IBD.   Methods: We evaluated GI symptom and quality of life scores, and clinical biomarkers of local (i.e. fecal occult blood and calprotectin) and systemic (i.e. CBC, CRP, ESR, and albumin) inflammation in a cohort of 79 patients with CGD, 8 mutation carriers and 17 healthy controls followed at the National Institutes of Health (NIH). We profiled the intestinal microbiome by 16S rRNA (V4 region) sequencing and the stool metabolome by mass spectrometry in all fecal samples, and further validated our findings by profiling the stool microbiome in a second cohort of 36 patients with CGD recruited from 11 centers across North-America through the Primary Immune Deficiency Treatment Consortium (PIDTC). Predictive functional profiling of the microbial communities based on 16S rRNA sequencing was also performed.  Results: After controlling for significant variables, we show decreased alpha diversity and identified distinct intestinal microbiome and metabolomic profiles in patients with CGD compared to healthy individuals. In particular, we observed enrichment for Erysipelatoclostridium spp., Sellimonas spp. and Lachnoclostridium spp. in stool samples from patients with CGD. Despite differences in alpha and beta diversity in samples from the NIH compared to the PIDTC cohort, there were several bacterial taxa that correlated significantly between both cohorts. We further demonstrate that patients with active IBD and/or a history of IBD have a distinct microbiome and metabolomic profile compared to patients without CGD-IBD and identified bacterial taxa to be evaluated as potential markers of disease severity, as well as targets for future therapeutic interventions.  Conclusions: Intestinal microbiome and metabolomic signatures distinguished patients with CGD and CGD-IBD and identified microbial and metabolomic candidates to be further evaluated as potential targets to improve the management of patients with CGD-IBD.

first: Chandrasekaran

last: Prabha

first: Han

last: Yu

first: Zerbe

last: Christa

first: Heller

last: Theo

first: Kreuzburg

last: Samantha

first: Marciano

middle: E

last: Beatriz

first: Siu

last: Yik

first: Jones

last: Drew

first: DeRavin

last: Suk See

first: Malech

middle: L

last: Harry

first: Kang

last: Elizabeth

first: Leiding

middle: W

last: Jennifer

first: Danielle

last: Arnold

first: Logan

last: Brent

first: Dvorak

last: Christopher

first: Togerson

last: Troy

first: Marsh

last: Rebecca

first: Pulsipher

last: Michael

first: Stenger

first: Haddad

last: Elie

first: Parikh

last: Suhag

first: Mousallem

middle: I

last: Talal

first: Kapoor

last: Neena

first: Rayes

last: Ahmad

first: Kapdia

last: Malika

first: Burroughs

last: Lauri

first: Sharat

last: Chandra

first: Heimall

first: Murguia-Favela

last: Luis

first: Barnum

last: Jessie

first: Broglie

last: Larisa

first: Pai

last: Sung-Yun

first: Notarangelo

last: Luigi

first: Griffith

last: Linda

first: Kohn

last: Donald

first: Puck

first: Cowan


title: Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms [Spec-seq]

first: Shiming

last: Chen

summary: Homeodomain transcription factors (HD TFs) are instrumental to vertebrate development. Mutations in HD TFs have been linked to human diseases, but their pathogenic mechanisms remain elusive. Here we use Cone-Rod Homeobox (CRX) as a model to decipher the disease-causing mechanisms of two HD mutations, p.E80A and p.K88N, that produce severe dominant retinopathies. Through integrated analysis of molecular and functional evidence in vitro and in knock-in mouse models, we uncover two novel gain-of-function mechanisms: p.E80A increases transactivation of canonical CRX target genes in developing photoreceptors; p.K88N alters CRX DNA-binding specificity resulting in binding at ectopic sites and severe perturbation of CRX target gene expression. Both mechanisms produce novel retinal morphological defects and hinders photoreceptor maturation distinct from loss-of-function models. This study reveals the distinct roles of E80 and K88 residues in CRX HD regulatory functions and emphasizes the importance of transcriptional precision in normal development.

overall_design: Two Spec-seq libararies containing monomeric HD motif variants on the sense or antisense strand were designed to profile the binding specificity of WT and mutant CRX HDs. The two libraries were mixed in equal molar ratio in the Spec-seq experiments.

first: Yiqiao

last: Zheng


title: RNA-seq for U937 cell line in either the absence or presence of ZNF217

status: Public on Oct 30 2023

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for U937 cell line in either the absence or presence of ZNF217

overall_design: 2 U937 samples with no treatment and 2 U937 samples with ZNF217 knockdown

first: Jian

last: Pan

first: Bi

last: Zhou


title: Super-Enhancer-regulated gene ZNF217 promotes AML progress


title: CUT-TAG for AML cell lines

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore CUT-TAG results in AML cell lines.

overall_design: CUT-TAG for ZNF217, MEF2D, FOXP1, RUNX2 and ELF1


title: RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma [RIP-seq]

status: Public on Oct 20 2023

city: Urumqi

first: Jingzhan

last: Zhang

state: Xinjiang

address: NO. 91, Tianchi Road, Tianshan District

department: Dermatology

institute: People’s Hospital of Xinjiang Uygur Autonomous Region

summary: In order to clarify the post-transcriptional regulatory network of RPS27 in KS. We constructed a transcriptomic binding network using iRIP-seq. The KS lesions of the other two patients were used for separately.

overall_design: iRIP captures both direct and indirect RNA-RPS27 interactions. IP was performed using flag-tagged RPS27; two independent iRIP replicates were performed, and the cDNA libraries were sequenced on an Illumina NovaSeq system. ompared with the input group, reads in the IP group were enriched in the coding sequence and noncoding exon regions. The Piranha method was used for peak calling.

first: Xiaojing

last: Kang


title: RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma [RNA-seq]

summary: RNA-seq technology was used to investigate the differentially expressed genes and regulated alternative splicing events in Kaposi's sarcoma lesions and adjacent non-tumor tissues. We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  Kaposi's sarcoma lesions and adjacent non-tumor tissues


title: RNA-seq for MV4-11 cell line in either the absence or presence of ZNF217

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for MV4-11 cell line in either the absence or presence of ZNF217

overall_design: 2 MV4-11 samples with no treatment and 2 MV4-11 samples with ZNF217 knockdown


title: RNA-binding protein RPS27 and gene expression regulation in Kaposi’s sarcoma

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

overall_design: Refer to individual Series


title: Diffrential expression of adipose tissue immune cells after normal diet and high-fat diet induced obesity by RNA-seq analysis

status: Public on Oct 01 2023

city: Memphis

first: Udai

middle: P

last: Singh

state: TN

address: 881 Madison Avenue

department: Pharmacy

institute: University of Tennessee Health Science Center

summary: We determine the role of high fat diet and normal diet induced obesity, progression of differential expression in altering immune response function by RNAseq analysis . We identified several genes that are either upregulated or downregulated upon HFD feeding as compared to ND.

overall_design: We observed several genes upregulated or downregulated in adipose tissue derived immune cells from mice fed with HFD. Gpnmb, CDK18, CTSK, Fam83f, SBK2, Siglec15, Nptx1, Mmp9, Muc1, Timd4, Mmp3, FbIn7, and fat3 are differentially mediated as compared to ND, suggesting that obesity and low grade chronic inflammation may result from altered gene expression mediated by HFD induction.

first: Mousumi

last: Mandal

first: Sonia

last: Kiran


title: Characterization of rice-yellow stem borer interaction

status: Public on Oct 15 2023

city: Hyderabad

first: Ramesh

middle: Venkata

last: Sonti

state: Telangana

address: Habsiguda

country: India

institute: CSIR-Centre for Cellular and Molecular Biology

summary: Yellow stem borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), is a major pest of rice in India, that can lead to 20-60% loss in rice production. Effective management of YSB infestation is challenged by the non-availability of adequate source of resistance and poor understanding of resistance mechanisms, thus necessitating studies for generating resources to breed YSB resistant rice and to understand rice-YSB interaction. Here we performed transcritpomics profiling of rice lines with contrasting response to YSB. RNA-sequencing of the susceptible (SM) and tolerant (SM92 lines revealed multiple genes to be differentially regulated upon YSB infestation. Comparative transcriptome analysis revealed a putative candidate gene that was predicted to encode an alpha-amylase inhibitor. Analysis of the transcriptome and metabolite profiles further revealed a possible link between phenylpropanoid metabolism and YSB tolerance.

overall_design: Rice plants in reproductive stage were infested with YSB larvae and the zone of infestation (~2cm stem cuts) were collected at 72hours post infestation from the susceptible and tolerant lines. Uninfested samples were collected as controls and subjected to RNA isoaltion and seqeuncing.

first: Hitendra

last: Patel

first: Padmakumari

last: AP

first: Sheshu Madhav

last: Maganti

first: Gokulan

last: CG


title: Multiomic chromatin accessibility and gene expression in peripheral blood predicts future decompensation in hospitalized adults with COVID-19

status: Public on Oct 17 2023

city: Durham

first: Julie

last: Steinbrink

state: NC

address: 315 Trent Drive

department: Center for Applied Genomics and Precision Medicine

institute: Duke University

summary: To elucidate host response elements that define impending decompensation during SARS-CoV-2 infection, we enrolled subjects hospitalized with COVID-19 who were matched for disease severity and comorbidities at the time of admission and initial sampling. We then performed combined single-cell RNA sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) on peripheral blood mononuclear cells (PBMCs) from the time of admission and compared subjects who improved from their initial low-level oxygen requirement (no change from initial WHO Ordinal category 4/5) to those who later clinically decompensated and required invasive mechanical ventilation or died (WHO Ordinal score 7/8). Chromatin accessibility and transcriptomic immune profiles were markedly altered at admission in patients who will go on to develop critical illness. The greatest immunologic signals were seen in CD4+ T cells, inflammatory T cells, dendritic cells, and NK cell subsets, where an aggregate multiomic signature score calculated at admission offered strong prediction of future clinical deterioration (area under the receiver operating characteristic curve (auROC) 0.91). Epigenetic and transcriptional changes in PBMCs reveal unique, early, and conserved aspects of the immune response before typical clinical signals of decompensation are apparent and thus provide novel biomarkers that can predict future disease severity.

overall_design: COVID-19 subjects were matched for disease severity and comorbidities at the time of admission and initial sampling. Combined single-cell RNA sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) on peripheral blood mononuclear cells (PBMCs) from the time of admission were performed and compared subjects who improved from their initial low-level oxygen requirement to those who later clinically decompensated and required invasive mechanical ventilation or died.

first: Micah

middle: T

last: McClain

first: Ilya

last: Zhbannikov

first: Lisa

last: Satterwhite

first: Ricardo

last: Henao

first: Nicholas

last: Giroux

first: Shengli

last: Ding

first: Thomas

last: Burke

first: Purushothama

middle: R

last: Tata

first: Ephraim

last: Tsalik

first: Christina

last: Nix

first: Jorge

last: Prado Balcazar

first: Elizabeth

last: Petzold

first: Xiling

last: Shen

first: Christopher

last: Woods


title: Modified C-type natriuretic peptide normalizes tumor vasculature and improves solid tumor therapies

status: Public on Oct 16 2023

first: Serge

middle: Y.

last: Fuchs

address: 316 Hill Veterinary School

institute: University of Pennsylvania

summary: Deficit of oxygen and nutrients in the tumor microenvironment (TME) triggers abnormal angiogenesis that produces dysfunctional and leaky blood vessels, which fail to adequately perfuse tumor tissues. Resulting hypoxia, exacerbation of metabolic problems and generation of immunosuppressive TME undermine the efficacy of cancer treatment. These problems can be partially alleviated by angiogenesis inhibitors. Here we propose an alternative agonist-based normalization approach utilizing a derivative of the C-type natriuretic peptide (dCNP). This well-tolerated agent stimulated formation of highly functional tumor blood vessels to reduce hypoxia. Administration of dCNP also inhibited stromagenesis and reinvigorated the anti-tumor immune responses. Treatment with dCNP decelerated growth of primary tumors and suppressed their metastases. Moreover, inclusion of dCNP into the chemo-, radio- or immune-therapeutic regimens increased their efficacy against solid tumors. These results demonstrate the proof of principle for using activators of normalized angiogenesis to improve therapies against solid tumors and characterize dCNP as the first in class amongst such agents.

overall_design: To investigate the role of dCNP on tumor microenvironment reprograming, we injecetd MC38 cancer cells into C57BL/6J mice and these tumor bearing mice were treated with vehicle or dCNP for 10 days. Afterward, tumors were collecetd and RNA was extracted for bulk RNA sequencing.

first: Zhen

last: Lu

last: Miao

first: Menghao

last: You

middle: Y


title: Deep indel mutagenesis reveals the impact of insertions and deletions on protein stability and function

status: Public on Sep 28 2023

first: Magdalena

last: Topolska

state: Barcelona

address: C/ del Dr. Aiguader, 88

department: Systems and Synthetic Biology

institute: Centre for Genomic Regulation

summary: Amino acid insertions and deletions (indels) are an abundant class of genetic variants.   However, compared to substitutions, the effects of indels are not well understood and poorly predicted.  Here we address this shortcoming by performing deep indel mutagenesis (DIM) of structurally diverse proteins. Indel tolerance is strikingly different to substitution tolerance and varies extensively both between different proteins and within different regions of the same protein. Although state of the art variant effect predictors perform poorly on indels, we show that both experimentally-measured and computationally-predicted substitution scores can be repurposed as good indel variant effect predictors by incorporating information on protein secondary structures. Quantifying the effects of indels on protein-protein interactions reveals that insertions can be an important class of gain-of-function variants. Our results provide an overview of the impact of indels on proteins and a method to predict their effects genome-wide.

overall_design: DNA-seq of PCR amplicon

first: Antoni

last: Beltran

first: Ben

last: Lehner


title: A Novel HIF-2α/ARNT Signaling Pathway Protects Against Microvascular Dysfunction and heart failure After Myocardial Infarction

status: Public on Sep 29 2023

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

summary: Experiments were conducted with mice carrying an inducible EC-specific Hif2α-knockout (ecHif2α–/–) mutation, with mouse cardiac microvascular endothelial cells (CMVECs) isolated from the hearts of ecHif2α–/– mice after the mutation was induced, and with human CMVECs and umbilical-vein endothelial cells transfected with ecHif2α siRNA. After MI induction, echocardiographic assessments of cardiac function were significantly lower, while measures of cardiac microvascular leakage (Evans blue assay), plasma IL6 levels, and cardiac neutrophil accumulation and fibrosis (histology) were significantly greater, in ecHif2α–/– mice than in control mice, and RNA-sequencing analysis of heart tissues from both groups indicated that the expression of genes involved in vascular permeability and collagen synthesis was enriched in ecHif2α–/– hearts. In cultured ECs, ecHif2α deficiency was associated with declines in endothelial barrier function (electrical cell impedance assay) and the reduced abundance of tight-junction proteins, as well as an increase in the expression of inflammatory markers, all of which were largely reversed by the overexpression of ARNT. We also found that ARNT, but not Hif2α, binds directly to the IL6 promoter and suppresses IL6 expression.

overall_design: To assess the functional role of HIF2α in ischemic heart injury, we ligated the proximal left anterior descending coronary artery to induce MI in tamoxifen inducible adult ecHIF2α-/- and control (Hif2aflox/flox) mice. Total RNA from controls and Hif2α-/- heart tissues was isolated 28 days after MI using RNeasy Fibrous Tissue Mini Kit (74704, Qiagen, MD) according to the manufacturer’s protocol.

first: Karim

last: Ullah

first: Lizhuo

last: Ai

first: Lifeng

last: Liu

first: Qin

last: Zhang

first: Kaichao

last: Pan

first: Zainab

last: Humayun

first: Albert

last: Sitikov

first: Qiaozhu

last: Su

first: Qiong

last: zhao

first: Willard

last: Sharp

first: Yun

last: Fang

first: David

last: Wu

first: James

last: Liao

first: Rongxue


title: Gene expression data in total mRNA from human SKMEL28 melanoma cell line shCont, shp16, shp16+shATR. Light and heavy polysome fractions for shCont and shp16.

status: Public on Sep 24 2023

city: Pittsburgh

first: Katherine

last: Aird

address: 5051 Centre Ave.

institute: University of Pittsburgh School of Medicine

summary: p16/CDKN2A is a critical cell cycle regulator and tumor suppressor that is lost in ~50% of all human cancers. Recent studies have identified roles of p16 outside of the cell cycle. Understanding the fundamental biology of p16 loss in cancer may provide novel targets to exploit for therapy.

overall_design: To investigate the transcriptonal and translational differences upon p16 loss, we knocked down p16 with or without knockdown of ATR in SKMEL28 human melanoma cell lines. We isolated total mRNA and fractionated light (0-2) and heavy (>2) ribosome fractions. All samples were done in triplicate. Comparative gene expression profiling analysis for SKMEL28 shGFP (control) and shp16.

middle: M

first: Raquel

last: Buj

first: Naveen

last: Tangudu


title: Human inhibitory interneuron cell therapy for chronic focal epilepsy

status: Public on Oct 10 2023

city: South San Francisco

first: Robin

last: Zhou

state: California

address: 170 Harbor Way

institute: Neurona Therapeutics

summary: Mesial temporal lobe epilepsy (MTLE) is the most common type of focal seizure disorder. In MTLE, seizures typically originate from a sclerotic hippocampus. Approximately one-third of patients do not respond to anti-seizure drugs and have few effective therapeutic options. Surgery to resect or ablate the affected temporal lobe is one such option, but it is not indicated or adequate for all individuals and can have adverse effects. Here, we report the development of an alternative cell therapy strategy for drug-resistant MTLE. The cell therapeutic is derived from a clinical-grade human embryonic stem cell line, and composed of cryopreserved post-mitotic medial ganglionic eminence (MGE)-type GABAergic inhibitory neurons of a predominantly pallial interneuron lineage. Single-dose intrahippocampal delivery of cryopreserved human pallial interneurons in a chronic mouse model of drug-resistant MTLE resulted in consistent and stable suppression of mesiotemporal seizures, with most animals becoming seizure-free. The grafted human interneurons distributed locally, matured, and persisted in the sclerotic hippocampus throughout the 8.5-month study. Pathological hallmarks of MTLE, such as hippocampal granule cell dispersion and sclerosis, were significantly reduced, and epileptic animal survival rates increased, after administration of the human interneurons. Suppression of seizure activity and amelioration of neuropathology were dose-dependent and suggested a broad therapeutic dosing range. No ectopic tissue or teratoma formation was detected after cell transplantation. Furthermore, behavioral abnormalities were not observed at any dose on a battery of assays. These findings support further development of human pallial MGE-type GABAergic interneuron cell therapy for the treatment of drug-resistant focal epilepsies.

overall_design: A clinical-grade human embryonic stem cell line (D0) was used for differentiation. They are differentiated into neuronal progenitors first (D14), then into MGE interneurons. Nine batches of differentiation were made and their cell compositions were analyzed by using 10X Genomics scRNA-seq platform.

first: Marina

last: Bershteyn


title: Comparison of global gene expression profile associated with inhalation anesthesia between sevoflurane and desflurane

status: Public on Oct 03 2023

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Division of Biomedical Sciences, Research Center for Genomic Medicine

country: Japan

institute: Saitama Medical University

summary: Comparative gene expression profiling analysis of RNA-seq data for livers from rats subjected to inhalational anesthesia with either sevoflurane or desflurane and their controls that were treated with sevoflurane or desflurane only briefly until the loss of their consciousness.

overall_design:
4 samples

Submitter states: There is 6-hour gap in the timing of tissue harvesting between control and anesthetized rats. To eliminate the effect of circadian rhythm on alteration in gene expression levels, we re-conducted the same RNA-sequencing experiment using new samples in which tissue harvesting had been conducted at approximately the same timing of the day (actually 3:00 pm) for all the samples. These data were submitted in GSE24436.

first: Takehiro

last: Nogi

first: Kousuke

last: Uranishi

first: Masataka

last: Hirasaki


title: Single-cell CRISPR screening characterizes transcriptional deregulation in T-cell acute lymphoblastic leukemia

status: Public on Sep 30 2023

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive leukemia caused by accumulation of genetic alterations in T-cell progenitors. For many genes it remains unknown how loss-of-function mutations contribute to disease development. Single-cell CRISPR screening in ex vivo pro-T cells allowed us to study the transcriptomic impact of such alterations. A first CRISPR screen targeted 17 well-studied regulators and defined the core transcriptional signatures, such as NOTCH1, MYC, STAT5 and E2F. Additionally, Spi1 was identified as an essential gene associated with the MYC regulon. A second screen targeted 42 poorly characterized genes and identified gene clusters with E2F/MYC and STAT/NOTCH1 signatures having opposing roles. Bcl11b inactivation conferred the strongest growth advantage and was associated with JAK/STAT upregulation, corresponding with publicly available T-ALL patient data. Bcl11b inactivation cooperated with mutant JAK3 in transforming pro-T cells to cytokine-independent growth. With this data, we characterized tumor suppressors and oncogenes in T-ALL, thereby providing insight in the mechanisms of leukemia development.

overall_design: ex-vivo murine ProT cells were transduced with a CRISPR library and analysed using the 10x genomics feature-barcoding technology (capture of both mRNA and CRISPR guides)

first: Demeyer

last: Sofie

first: Cools

last: Jan

first: Meyers

last: Sarah


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia.

status: Public on Sep 25 2023

city: New York

first: Javier

last: Rodriguez Hernaez

state: New York

address: East 30th Street. 8th Floor

institute: NYU Langone Health


title: TLX3 ex vivo model identifies TLE4 as a co-repressor in T-ALL

status: Public on Sep 16 2023

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological disease originating from the malignant transformation of T-cell progenitors caused by the accumulation of genetic aberrations. One fifth of T-ALL patients are characterized by the ectopic expression of the homeobox transcription factor TLX3, which is normally not expressed in hematopoietic cells. Strikingly, this TLX3 positive subgroup of T-ALL has a high frequency of FLT3 mutations. Co-expression of TLX3 and FLT3-ITD in ex vivo pro-T cells conferred IL7 independent growth, confirming that TLX3 expression and FLT3 signaling cooperate to transform T-cells and make them less dependent on extracellular signals. After inducing TLX3 expression for 24 hours in Pro-T cells, transducin-like enhancer of split 4 (Tle4) was detected to be downregulated. Interestingly, T-ALL patients also present a strongly decreased expression of TLE4 specific to TLX3 and TLX1 subtypes. Family members of the transcriptional corepressor TLE4 have been described to interact and thus, inhibit transcription factors, through their interaction with an Engrailed-homology 1 (Eh1) domain. Generation of a point mutation in the Eh1 domain present at the N-terminus of TLX3 allowed us to show that TLE4 has a repressive effect on TLX3 activity. Together, we propose a TLX3+FLT3-ITD Pro-T cell model and use this to illustrate that low expression levels of TLE4 are favourable for the oncogenic function of TLX3.

overall_design:
In a ProT-CreER cell model, we introduced FTL3-ITD and TLX3 (with a V5 tag), performed 3'end RNA-sequencing and compared this with the WT ProT CreER cells.
In a ProT-CrER cell model, we induced TLX3 with tamoxifen over 24h and compared them with the non-treated (DMSO) ProT cells. We performed 3'end RNA-sequencing
In a ProT-CreER cell model TLX3 and TLX1 were induced with tamoxifen over 24/48h and compared with the non-induced condition (DMSO). 3'end RNA-sequencing was performed.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) with TLX3 antibody in DND-41 cells
RNA sequencing of ProT-cells with overexpression of TLX3, introduction of FLT3-ITD and overexpression of TLE4, and combinations of these.

first: Quentin

last: Van Thillo

first: Lukas

last: Lauwereins

first: Jan

last: Cools

first: Alexandra

last: Veloso


title: NFIC1 inhibited the migration and invasion of MDA-MB-231 cells through increasing S100A2 induced inactivation of MEK/ERK pathway

status: Public on Sep 23 2023

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

summary: To investigate the underlying mechanism through which NFIC1 inhibited the migration and invasion of MDA-MB-231 cells, we used RNA sequencing to discover the NFIC1-regulated genes that could mediate the inhibition.

overall_design: Total RNA obtained from MDA-MB-231 cells transiently transfected with pcDNA3.1 (Control) or pcDNA3.1-NFIC1 (NFIC1).

first: Jing

last: Zhang

first: Chanjuan

last: Jin

first: Zehua

last: Liang

first: Zhaoying

last: Wang

first: Yueru

last: Shi

first: Mingyue

last: Fan

first: Youzhong

last: Wan


title: Down-stream targets of TGFβ/BMP signaling in C. elegans exposed to microbiota CeMbio using RNAseq

status: Public on Oct 31 2023

city: Berkeley

first: Michael

last: Shapira

address: Valley Life Sciences Building

department: Integrative Biology

institute: University of California, Berkeley

summary: Only recently, the natural gut microbiome of the model organism Caenorhabditis elegans has been described. C. elegans harbors a distinct gut microbiome that is shaped by environmental conditions, age, and host genotype. However, there is not much known about the genetic factors on the molecular level that the worm employs in order to keep its microbiota at bay.  Previously, we have shown that TGFβ/BMP immune signaling is able to control the gut microbiome of C. elegans in particular in regards to Enterobacter species. We now aimed to identify the downstream targets of TGFβ/BMP immune signaling that implement the changes in microbiome composition. Hence, we exposed TGFβ mutants, dbl-1(nk3) and sma-3(e491), overexpression strain ctIs40 [dbl-1(+) + sur-5::GFP], and wild-type N2 to a synthetic microbiota community, CeMbio, and an E. coli OP50 control, and performed RNAseq. CeMbio is a collection of 12 diverse bacterial strains, previously isolated from wild C. elegans, C. elegans grown in microcosms, or substrates with C. elegans.   Using the R packages edgeR and limma we are currently analyzing the data to understand the involvement of TGFβ/BMP signaling in host-microbiome interaction.

overall_design: worm strains dbl-1(nk3), sma-3(e491), ctIs40 [dbl-1(+) + sur-5::GFP], and N2 exposed to either E. coli OP50 or CeMbio in 3 biological replicates

first: Barbara

last: Pees


title: Comparing the gene expression profile between wildtype and gal80Δ mutant of S. cerevisiae in fructose and fructose-palatinose mixture

status: Public on Oct 19 2023

city: Edinburgh

first: Peter

middle: S

last: Swain

address: CH Waddington Building, Mayfield Road

department: School of Biological Sciences

institute: University of Edinburgh

summary: We wanted to find out (1) which genes are affected by the active Gal4 in the gal80Δ mutant in fructose, and (2) which MAL genes are affected by the active Gal4 in the fructose-palatinose mixture.

overall_design: 36-sample RNA-seq of three timepoints (fructose mid-log, 10h after mid-log and 16h after mid-log), two strains (wildtype & gal80Δ) and two conditions (0.1% fructose & 0.1%fructose+0.9% palatinose), in three biological replicates. The timepoints are chosen such that 10h after mid-log, fructose is running out; 16h after the mid-log, wildtype cells have highly activated MAL genes. The conditions are chosen because (1) 0.1% fructose does not repress the expression of GAL or MAL genes; (2) the growth rate of the wildtype and gal80Δ are similar in 0.1% fructose.

first: Yu

last: Huo

first: Edward

last: Wallace


title: Transcriptomic profiling of CDCP1 knock-down in human cardiac fibroblasts (HCFs)

status: Public on Sep 22 2023

city: Rochester

first: Duan

last: Liu

email: liud25@gmail.com, liu.duan@mayo.edu

state: MN

address: 200 1st ST SW

department: MPET

institute: Mayo Clinic

summary: To investigate the function of CDCP1 in regulation of HCF proliferation, we cultured primary HCFs and transfected with non-targeting siRNA and CDCP1 siRNAs. Total RNA samples were extracted for RNA-seq to identify transcriptome-wide gene expression changes in the HCFs after CDCP1 knock-down (KD).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCF cells with and wihout CDCP1 KD.

first: Vishakantha

last: Murthy

first: Thanh

last: Nguyen


title: Rapamycin mitigates Valproic Acid-induced teratogenicity in human and animal models by suppressing AP-1-mediated senescence

status: Public on Sep 05 2023

city: brisbane

first: Giovanni

last: Pietrogrande

state: QLD

address: Corner College and Cooper Rds, Bldg 75, AIBN

country: Australia

institute: University of Queensland

summary: Valproic acid (VPA) is an effective and widely used anti-seizure medication but is teratogenic when used during pregnancy, affecting brain and spinal cord development for reasons that remain largely unclear.  Here we designed a genetic recombinase-based SOX10 reporter system in human pluripotent stem cells that enables tracking and lineage tracing of Neural Crest cells (NCCs) in a human organoid model of the developing neural tube. We found that VPA induces extensive cellular senescence and promotes mesenchymal differentiation of human NCCs at the expense of neural lineages. We next show that the clinically-approved drug, Rapamycin, inhibits AP1-mediated senescence and restores aberrant NCC differentiation trajectory in human organoids exposed to VPA. Notably, in vivo validation in developing zebrafish highlighted the therapeutic promise of this approach. Collectively our data identifies a novel mechanism for VPA-associated neurodevelopmental teratogenicity and a potential pharmacological preventative strategy. The results exemplify the power of genetically modified human stem cell-derived organoid models for drug discovery and safety testing.

overall_design: Spinal cord organoids controls, VPA, VPA+Rapamycin, in triplicate


title: High-resolution spatial transcriptomics of hormone-induced ovulation in mice

status: Public on Aug 21 2023

city: Ithaca

first: Iwijn

last: De Vlaminck

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

summary: The rupture of ovarian follicles during ovulation is a crucial and intricate process essential for procreation, yet the molecular mechanisms behind this process are not fully understood. Here, we use high-resolution spatial transcriptomics to reveal the spatiotemporal regulation of cell-type-specific molecular programs driving follicle maturation and rupture during hormone-induced ovulation.

overall_design: High-resolution spatial transcriptomics of immature and preovulatory murine ovaries

first: Madhav

last: Mantri

first: Hanxue

middle: H

first: Manny

last: Spanos

first: Yi

middle: A

last: Ren


title: Investigating multigenerational epigenetic adaptation of the hepatic wound-healing response

status: Public on Sep 06 2023

city: Basel

first: Remi

last: Terranova

address: Fabrikstrasse 2

institute: Novartis Biomedical Research

summary: The possibility that ancestral environmental conditions and exposures could result in effects inherited across generations, with potential impact for human health, has been long debated. Here, we comprehensively investigate transgenerational effects of the hepatotoxicant carbon tetrachloride (CCl4) on the hepatic wound-healing response in male rats. Detailed microscopic and clinical pathology evaluations do not support adaptive phenotypic suppression of the hepatic wound-healing response or a greater fitness of animals with ancestral liver injury exposure as originally reported. We produced RNAseq libraries on the F2 liver samples to further characterize any adaptive effect based on molecular changes.

overall_design: Treatment of three generations of Sprague Dawley rats.Treatment of F0 and F1 with either 100% olive oil or 50% (v/v) CCl4 in olive oil via oral gavage three times a week for 6 weeks followed by 2 weeks recovery before mating. Treatment of F2 with either 100% olive oil, 8% (v/v) CCl4 in olive oil or 50% (v/v) CCl4 in olive oil via oral gavage three times a week for 6 weeks; sampling of liver after 39 days.  Isolation of total RNA from rat liver tissue, n=7 per group, 12 different treatment conditions (F0-control/F1-control/F2-control, F0-control/F1-control/F2-treated_CCl4_8%,   F0-control/F1-control/F2-treated_CCl4_50%, F0-control/F1-treated/F2-control, F0-control/F1-treated/F2-treated_CCl4_8%,   F0-control/F1-treated/F2-treated_CCl4_50%, F0-treated/F1-control/F2-control, F0-treated/F1-control/F2-treated_CCl4_8%, F0-treated/F1-control/F2-treated_CCl4_50%, F0-treated/F1-treated/F2-control, F0-treated/F1-treated/F2-treated_CCl4_8%, F0-treated/F1-treated/F2-treated_CCl4_50%)


title: YTHDF1 deletion in macrophages aggravates LPS-induced inflammation

status: Public on Aug 08 2023

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

summary: To investigate the effect of YTHDF1 on LPS-induced inflammation, we performed RNA-seq with the total RNA extracted from peritoneal macrophages (PMs) with or without YTHDF1 deletion. Ythdf1-/- or wild type mice were intraperitoneally injected with 6% starch broth. Three days later, PMs were isolated and cultured overnight. Then, the PMs were treated by LPS (1 μg/mL) or PBS for 6 hours, followed by RNA extraction and RNA-seq.

overall_design: We isolated peritoneal macrophages (PMs) from WT and Ythdf1-/- mice after intraperitoneally injected with 6% starch broth for three days. Cells were cultured overnight and then stimulated with LPS (1 μg/mL) or PBS for 6 hours, followed by RNA extraction and RNA-seq. Triplicates were performed for each gruop.

first: Hao

last: Li


title: Multimodal hierarchical classification allows for efficient annotation of CITE-seq data

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: Single-cell RNA sequencing (scRNA-seq) is an invaluable tool for profiling cells  in complex tissues and dissecting activation states that lack well-defined surface   protein expression. For immune cells, the transcriptomic profile captured by scRNA-  seq cannot always identify cell states and subsets defined by conventional flow   cytometry. Emerging technologies have enabled multimodal sequencing of single   cells, such as paired sequencing of the transcriptome and surface proteome by   CITE-seq, but integrating these high dimensional modalities for accurate cell type   annotation remains a challenge in the field. Here, we describe a machine learning   tool called MultiModal Classifier Hierarchy (MMoCHi) for the cell-type annotation of   CITE-seq data. Our classifier involves several steps: 1) we use landmark registration  to remove batch-related staining artifacts in CITE-Seq protein expression, 2) the   user defines a hierarchy of classifications based on cell type similarity and ontology   and provides markers (protein or gene expression) for the identification of ground   truth populations within the dataset by threshold gating, 3) progressing through this  user-defined hierarchy, we train a random forest classifier using all available   modalities (surface proteome and transcriptome data), and 4) we use these forests   to predict cell types across the entire dataset. Applying MMoCHi to CITE-seq data of   immune cells isolated from eight distinct tissue sites of two human organ donors   yields high-purity cell type annotations encompassing the broad array of immune   cell states in the dataset. This includes T and B cell memory subsets, macrophages   and monocytes, and natural killer cells, as well as rare populations of plasmacytoid   dendritic cells, innate T cells, and innate lymphoid cell subsets. We validate the use   of feature importances extracted from the classifier hierarchy to select robust genes  for improved identification of T cell memory subsets by scRNA-seq. Together,   MMoCHi provides a comprehensive system of tools for the batch-correction and cell-  type annotation of CITE-seq data. Moreover, this tool provides flexibility in   classification hierarchy design allowing for cell type annotations to reflect a   researcher’s specific experimental design. This flexibility also renders MMoCHi   readily extendable beyond immune cell annotation, and potentially adaptable to   other sequencing modalities.

overall_design: We performed CITE-seq on immune cell populations from human blood and different human organ donor tissues.

first: Daniel

last: Caron

first: Steven

last: Wells

last: Szabo

first: David

last: Chen

first: Donna

last: Farber


title: Pseudouridine guides germline small RNA transport and epigenetic inheritance.

status: Public on Aug 07 2023

city: Cold Spring Harbor

first: Robert

last: Martienssen

email: martiens@cshl.edu, aschorn@cshl.edu

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Epigenetic modifications that arise during plant and animal development, such as DNA and histone modification, are mostly reset during gamete formation, but some are inherited from the germline including those marking imprinted genes. Small RNAs guide these epigenetic modifications, and some are also inherited by the next generation. In C. elegans, these inherited small RNAs have poly (UG) tails, but how inherited small RNAs are distinguished in other animals and plants is unknown. Pseudouridine (Ψ) is the most abundant RNA modification but has not been explored in small RNAs. Here, we developed novel assays to detect Ψ in short RNA sequences, demonstrating its presence in mouse and Arabidopsis microRNAs and their precursors.  We also detected substantial enrichment in germline small RNAs, namely epigenetically activated siRNAs (easiRNAs) in Arabidopsis pollen, and PIWI-interacting piRNAs in mouse testis. In pollen, pseudouridylated easiRNAs are produced by RNA polymerase IV and localized to sperm cells. We found that PAUSED/HEN5 (PSD), the plant homolog of Exportin-t, interacts genetically with Ψ synthase and is required for transport of easiRNAs into sperm cells from the vegetative nucleus.  We further show that PSD is required for the triploid block: chromosome dosage-dependent seed lethality that is epigenetically inherited from pollen. We propose that Ψ has a conserved role in marking inherited small RNAs in the germline.

overall_design: Mouse testis small RNA sequencing after a) N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide (CMC) treatment and b) pseudouridine immunoprecipitation.

first: Rowan

last: Herridge

first: Cristiane

last: de Santis Alves

first: Andrea

middle: J

last: Schorn


title: Defining embryo dormancy at single-cell resolution reveals cryptic transcriptional dynamics apace with Yap-mediated mechanotransduction

status: Public on Aug 29 2023

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

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

overall_design: Refer to individual Series


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia [hiChIP]

first: Javier

last: Rodriguez Hernaez

summary: Cancer progression is associated with genetic and epigenetic aberrations that affect chromatin 3D organization in the nucleus. Changes in loop extrusion or phase separation alter the relationships between enhancer and promoter elements, defining novel gene expression programs that are selected to promote growth and survival. Here, we provide an integrative approach based on chromatin conformation, accessibility and transcription, further validated by CRISPR interference screenings in order to identify chromatin topologies relevant to different subtypes of T-cell leukemia, namely T-ALL and ETP-ALL. By focusing on highly interconnected elements, we characterized 3D hubs as headquarters of leukemia progression and identity, demonstrating that oncogenes and disease markers are regulated by multiple cis-regulatory regions.

overall_design:
Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) and early T cell precursor leukemia (ETP-ALL) were collected and analyzed for H3K27ac HiChIP. To enrich for blast representation, samples were sorted based on clinical immune-phenotype, for CD2 and/or CD7 surface expression

Please note that the raw data files (SRR13492049,SRR13492050) for GSM5028231 (Jurkat HiChIP; SAMN17391130, GSE165207) sample were downloaded fron SRA and re-analyzed. The resulting processed data file is linked as Series supplementary file.

UPDATE: [11-04-2024] The title and treatment characteristic of Sample GSM7798271 was corrected.

first: Rodriguez-Hernaez

last: Javier

first: Boccalatte

last: Francesco

first: Gambi

last: Giovanni

first: Nadorp

last: Bettina

first: Aifantis

last: Ioannis

first: Tsirigos

last: Aristotelis


title: Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation

status: Public on Sep 19 2023

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering


title: Effect of YTHDF1 on concanavalin A-induced hepatitis

first: yongyou

last: zhang

summary: To investigate the effect of YTHDF1 on concanavalin A (ConA)-induced hepatitis , we performed RNA-seq with the total RNA extracted from the moue liver. Ythdf1-/- or wild type mice were intravenously injected with ConA (8 mg/kg) or saline for 8 hours. Then, the livers were collected, homogenized, and subjected to total RNA extraction.

overall_design: 8 weeks old mice were treated with ConA (8 mg/kg) or saline via tail intravenous injection. Livers were collected at 8 hours post injection, homogenized, and extracted for total RNA. Each group consists of three or four mice

first: Hao

last: Li


title: miRNA expression profile in 3 sporadic young-onset and 2 late-onset Indian colorectal carcinoma patients

status: Public on Jul 26 2023

city: Kolkata

first: Sudarshana

last: Basu

state: West Bengal

address: 3081, Nayabad, New Garia

department: Molecular Biology

institute: Netaji Subhash Chandra Bose Cancer Research Institute

summary: Early-Onset Colorectal Carcinoma (EOCRC) is a growing concern as reports indicate a worldwide increase in the incidence of CRC among young adults (<50 years old). In an effort to understand the different mode of pathogenesis in young-onset CRC, we performed a pilot study wherein we looked at colorectal tumors from both young (< 50 years old) and old patients (>55 years old) and screened them to eliminate tumors positive for Microsatellite Instability (MSI) and showing activation of the Wnt pathway, known canonical factors in CRC pathogenesis. RNA isolated from 3 EOCRC and 2 Late-Onset (LOCRC) tumors and paired normal tissues without MSI, nuclear β-catenin and APC mutations were sent for small RNA seq to identify miRNA alterations between the two subsets. Comparative analysis revealed differential expression of 23 miRNAs specific to EOCRC and 11 miRNAs specific to LOCRC.

overall_design: To investigate differential expression of miRNAs between young-onset and late-onset Indian colorectal carcinoma patients, we chose patients with microsatellite stable tumors (MSS) negative for Wnt pathway activation, as detected by absence of nuclear β-catenin and any APC mutations in the MCR region. These are known canonical factors in CRC pathogenesis and we screened tumors to enable detection of novel oncogenic pathways. Tumours and paired normal tissues of 5 (Patient no. 1, 2, 3, 4 and 5) patients were sent for NGS based miRNA sequencing. The 5 patients which were chosen for miRNA seq consisted of 3 young patients (mean age: 43 years) and 2 old patients (mean age: 63 years). Total twenty paired end fastq files were used for the small RNA-seq analysis via a pipeline FastQC-Fastp-SortMeRNA-miRDeep2-edgeR.

first: Srikanta

last: Goswami


title: Pseudouridine in small RNAs

city: Dunedin

middle: Paul

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

summary: Pseudouridine is an isomer of uridine and is the most common RNA modification in both procaryotes and eucaryotes. It is found in ribosomal, transfer, and other structural RNA as well as in some mRNA and non-coding RNA. We have found abundant pseudouridine in small RNA and their precursors in Arabidopsis.

overall_design: Identification of pseudouridylated small RNAs and their precursors in Arabidopsis thaliana

first: Robert

last: Martienssen

first: Jakub

last: Dolata


title: Single-cell RNA-sequencing of human intestinal organoid cells

status: Public on Sep 13 2023

city: Utrecht

first: Daisong

last: Wang

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We focused on a rare cell population of human intestine, the BEST4+ cells. Using human intestinal organoid as a model, the BEST4+ cells could be differentiated, FACS-enriched and analyzed by scRNA-seq, together with the BEST4- cell lineages such as the enterocytes, goble cells and EECs.

overall_design: Human intestinal organoids were cultured in differentiation medium with/without IFN-gamma. BEST4+/- cells derived from the differentiated orgnaoids were FACS sorted and individally collected in the 384 well plates for SORT-seq based scRNA-seq analysis.


title: RNA-seq analysis of endothelial-specific Myc overexpression mice after bile duct liagtion surgery

status: Public on Jul 18 2023

city: Jinan

first: Jinyuan

last: Liang

address: wenhua road

institute: Shandong university

summary: The precise impact of endothelial cells on modulating the local tissue microenvironment during cholestasis has yet to be determined. Cholestasis, a condition characterized by impaired bile flow within the liver, triggers a noteworthy activation of Myc signaling within the endothelial cells. In this study, we employed RNA-seq analysis to examine the transcriptomic profiles in liver tissue samples obtained from BDL-treated wild-type mice and mice with endothelial cell-specific overexpression of the Myc gene.

overall_design: Liver tissue samples from 4 BDL-treated endothelial Myc-overexpression mice (BDM) and 4 BDL-treated wide-type control mice (BDC), were subjected to RNA-seq analysis.

first: Detian

last: Yuan

first: Shiyang

first: Peng

last: Zhang

first: Xinying


title: Tri-modal Single Cell Approach Reveals Cellular and Molecular Heterogeneity in Naïve T cells Across Human Age

status: Public on Aug 31 2023

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: The naïve T cell compartment undergoes multiple changes across age that associate with altered susceptibility to infection and autoimmunity. In addition to the acquisition of naïve-like memory T cell subsets, recent murine studies describe substantial molecular reprogramming of the naïve compartment in adults compared with adolescents. However, these alterations are not well delineated in human aging. Using a new trimodal single cell technology (TEA-seq), we discovered that the composition as well as the transcriptional and epigenetic programming of the naïve T cell compartment in children (11-13 yrs) is distinct from that of older adults (55-65 yrs). Naive CD4 T cells, previously considered relatively resistant to aging, exhibited far more pronounced molecular reprogramming than the CD8 compartment, in which alterations are preferentially driven by shifts in naive-like memory subsets. These data reveal the complex nature of the naïve T cell compartment that may contribute to differential immune responses across the spectrum of human age.

overall_design:
scRNAseq was performed on 48 samples.  In addition, TEA-seq (a novel method for simulaneous single-cell profiling of transcripts, epitopes, and chromatin accessiblity) was performed on 16 of those samples, as well as on 3 control samples (IMM19_435, IMM19_438, and IMM19_445). As part of TEA-seq testing we prepared CITE-seq, scATAC-seq, single-cell and single-nuclei 10x Multiome ATAC + Gene Expression, and TEA-seq libraries from the same PBMC sample in parallel.
**The submitter declares that the raw data are being deposited in dbGaP due to patient privacy concerns.**

first: Claire

last: Gustafson

first: Zachary

last: Thomson


title: Terminal differentiation and persistence of effector regulatory T cells essential for the prevention of intestinal inflammation [bulk ATAC-seq]

status: Public on Jul 11 2023

city: La Jolla

first: Stanislav

last: Dikiy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

summary: Regulatory T (Treg) cells represent a specialized CD4+ T cell lineage with essential anti-inflammatory functions. Recent studies of the adaptations of Treg cells to non-lymphoid tissues which enable their specialized immunosuppressive and tissue supportive functions raise questions about the underlying mechanisms of these adaptations and whether they represent stable differentiation or reversible activation states. Using novel genetic tools, we characterized the transcriptional programs of distinct colonic effector Treg cell types. We found that attenuated T cell receptor (TCR) signaling and acquisition of substantial TCR independent functionality appears to facilitate the terminal differentiation of a population of colonic effector Treg cells distinguished by stable expression of immunomodulatory cytokine interleukin-10 (IL-10). Functional studies revealed that this subset of effector Treg cells, but not their expression of IL-10, was indispensable for preventing colitis. These findings suggest core features of terminal differentiation of effector Treg cells in non-lymphoid tissues and their function therein.

overall_design: Comparative chromatin acessibility of colonic Treg cells expressing Il10, not expressing Il10 and with a history of Il10 expression (3 paired biological replicates)

first: Andrew

middle: G

last: Levine

first: Yuri

last: Pritykin

first: Chirag

last: Kirshna

first: Ariella

last: Glasner

first: Christina

last: Leslie

first: Alexander

last: Rudensky


title: Terminal differentiation and persistence of effector regulatory T cells essential for the prevention of intestinal inflammation [bulk RNA-seq]

overall_design: Comparative gene expression of colonic Treg cells expressing Il10, not expressing Il10 and with a history of Il10 expression (3 paired biological replicates)


title: Changes in subcutaneous white adipose tissue cellular composition and molecular programs underlie glucose intolerance in persons with HIV

status: Public on Aug 30 2023

city: Nashville

first: Samuel

last: Bailin

address: 1161 21st Avenue South, MCN A-2200

institute: Vanderbilt Universit Medical Center

summary: Subcutaneous adipose tissue (SAT) is a critical regulator of systemic metabolic homeostasis. Persons with HIV (PWH) have an increased risk of metabolic diseases and have significant alterations in SAT immune cells compared with the general population. We generated a comprehensive SAT atlas from 59 PWH with a spectrum of metabolic diseases to characterize cellular compositional and transcriptional changes associated with glucose intolerance and demographic characteristics. In PWH, glucose intolerance was associated with increased lipid-associated macrophages, CD4+ and CD8+ T effector memory cells, and decreased perivascular macrophages. We observed a coordinated intercellular regulatory program enriched for genes related to inflammation and lipid-processing with glucose intolerance that was also present in diabetic HIV-negative persons. Finally, CD4+ tissue resident cells were most strongly associated with altered whole tissue expression of genes related to lipid and glucose metabolism. These data provide a comprehensive assessment of SAT immune cells that may contribute to glucose intolerance.

overall_design: We performed paired single-cell RNA-sequencing and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) of single-cell suspensions generated from subcutaneous white adipose tissue of 20 non-diabetic persons with HIV, 19 prediabetic persons with HIV, 20 diabetic persons with HIV, and 32 HIV-negative persons.

first: Jonathan

last: Kropski

first: Rama

middle: D

last: Gangula

first: Hannah

last: LaToya

first: Joshua

last: Simmons

first: Mona

last: Mahsayekhi

first: Fei

last: Ye

first: Run

last: Fan

first: Simon

last: Mallal

first: Warren

last: Christopher

first: Spyros

last: Kalams

first: Curtis

last: Gabriel

first: Celestine

middle: N

last: Wanjalla

first: John

last: Koethe


title: Terminal differentiation and persistence of effector regulatory T cells essential for the prevention of intestinal inflammation [bulk Trac-deletion RNA-seq]

first: Stanislav

last: Dikiy

overall_design: Comparative gene expression of colonic Treg cells with a history of Il10 expression, losing or retaining cell surface T cell receptor (2 paired biological replicates each for 2 timepoints post-TCR deletion)

first: Andrew

last: Levine

first: Yuri

last: Pritykin

first: Chirag

last: Kirshna

first: Ariella

last: Glasner


title: Pseudouridine in small RNAs

city: Poznan

first: Jakub

middle: Jacek

last: Dolata

address: Uniwersytetu Poznanskiego 6

department: Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

first: Rowan

last: Herridge

first: Robert

last: Martienssen