title: Extensive functional divergence of the RosR transcription factor across haloarchaea [ChIP-Seq]

status: Public on Nov 20 2024

city: Durham

first: Amy

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

summary: For microbial cells, an appropriate response to changing environmental conditions is critical for viability. Transcription regulatory proteins, or transcription factors (TFs) sense environmental signals to change gene expression. However, it remains unclear how TFs and their corresponding gene regulatory networks are selected for over evolutionary time scales. The function of TFs and how they evolve are particularly understudied in archaeal organisms. Here we identified, characterized, and compared the function of the RosR transcription factor across three related species of hypersaline adapted model archaea. RosR was previously characterized as a global regulator of gene expression during oxidative stress in the species Halobacterium salinarum (HsRosR). Here we use functional genomics and quantitative phenotyping to demonstrate that, despite strong conservation of HsRosR across species, its function diverges substantially. Surprisingly, RosR in Haloferax volcanii and Haloferax mediterranei regulates genes whose products function in motility and the outer membrane, leading to significant defects in motility when rosR is deleted. Given weak conservation and degeneration in the RosR cis-regulatory sequence across species, we hypothesize that the RosR regulatory network is easily rewired during evolution across related species of archaea.

sample_organism:
Haloferax volcanii DS2
Haloferax mediterranei ATCC 33500

overall_design: To determine the genome-wide location of binding of the RosR transcription factor, we conducted chromatin immunoprecipitation coupled to DNA sequencing (ChIP-seq) in rich medium, mid-exponential phase for each of the Hfx. volcanii and Hfx. mediterranei species of hypersaline archaeal cells.

first: Joey

last: Prinz

first: Mar

last: Martinez Pastor


title: Extensive functional divergence of the RosR transcription factor across haloarchaea

middle: K

country: USA

type: Expression profiling by high throughput sequencing

platform_organism:
Haloferax volcanii DS2
Haloferax mediterranei ATCC 33500

overall_design: To determine the function of the RosR transcription factor across the species Haloferax volcanii (HVO), Haloferax mediterranei (HFX), we measured RNA expression by RNA-seq transcriptomics in rosR knockout strains of each species compared to its corresponding parent strain (ura3 , HBT; pyrE in HVO and HFX)


title: HuR coordinates systemic aging through platelet infiltration

status: Public on Nov 16 2024

city: Beijing

first: liu

last: cihang

address: Xueyuan Road

country: China

institute: Peking University Health Science Center

summary: Aging involves morphological and functional changes across different organs, but how these changes are linked among the different organs remains to be elucidated. Here, we uncover a central role of platelets in sys temic aging. In aged mice, the levels of platelet secreted pro inflammatory factors (PSPF) increased greatly in the serum and platelets, leading to a diffuse increase of platelet infiltration in brain, liver, lung, kidney, and aortic root. The RNA binding protein HuR/ELAVL1, a major regulator of R NA metabolism, promoted the production of PSPF in platelets. Platelet specific deletion of HuR reduced the expression of PSPF in platelets, alleviated platelet infiltration in brain, liver, lung, kidney, and aortic root, and delayed systemic aging. Our findings highlight a role of platelets in coordinating aging traits across organs.

overall_design: To investigate the function of platelet HuR in systemic aging, we generated a conditional platelet-specific HuR knockout (cKO) mouse. We collected three 25 month-old wild type(WT) and cKO mice liver, lung and brain for single-nucleus RNA sequencing. We then performed gene expression profiling analysis using data obtained from sn-RNA-seq of 3 WT and cKO mice. Comparative gene expression profiling analysis of different cell type from different tissue of sn-RNA-seq data for cKO mice and its WT littermates.

first: Cihang

last: Liu

first: Ying

last: Wang

first: Tianjiao

last: Xia

first: Jing

last: Lin


title: Identification of Rbm25-binding RNAs in bone-marrow-derived macrophages by RIP-seq

status: Public on Nov 06 2024

city: Shanghai

first: Xingguang

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

summary: To identify the potential mRNAs that bound by Rbm25, which might be the direct target of Rbm25 for alternative splicing in murine macrophages.

overall_design: RIP-seq assays were performed using antibody against Rbm25 in M-CSF-differentiated BMDMs, following the instructions of Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore).

first: Yunkai

last: Zhang


title: Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophages

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: CRISPR-Cas9 Whole-Genome Screen Identify Critical Genes Regulating Cholesterol Metabolism in Macrophages

status: Public on Nov 01 2024

city: Brookings

first: Natalie

last: Thiex

state: SD

address: 1066 Campanile Ave, Box 2022A ookings

department: Biology and Microbiology

institute: South Dakota State University

summary: We designed CRISPR-Cas9 whole genome screens to identify and rank critical genes for cholesterol metabolism in modified LDL treated BMDMs

overall_design: Identify and rank critical genes for cholesterol metabolism in bone marrow-derived macrophages (BMDM) by CRISPR/Cas9 whole genome screen. The screens assayed cellular neutral lipid amounts following exposure of BMDM to  low-density lipoprotein. Here, we have screens with change in neutral lipid content following 1) 24-h exposure to AcLDL or OxLDL (24h LDL) 2) 24-h exposure followed by 36-48 h post AcLDL or OxLDL removal culture (post-LDL 48h)

first: Kevin

last: Wanniarachchi

first: Rifat

last: Sultana

first: Jared

last: Wollman

first: Lu

last: Huang

first: Xijin

last: Ge


title: Gene expression analysis of mouse adipose tissue macrophages

status: Public on Oct 29 2024

city: Debrecen

first: Tamás

last: Röszer

address: Nagyerdei krt. 98.Gyermekklinika

department: Pediatrics

country: Hungary

institute: University of Debrecen

summary: We collected adipose tissue macrophages from C57Black/6 mice on postnatal day 6 (P6) and postnatal day 56 (P56) by enzyntic digestion of the inguinal fat depots and megnetic cell sorting of F4/80 antigen positive macrophages. Total RNA was isolated and used for next generation RNA sequencing.

overall_design: Samples are labeled as P6 (infant) and P56 (adult) ATMs (adipose tissue macrophages).

first: Röszer

last: Tamás


title: Transcriptional landscape of human adipose tissue in infancy and childhood

summary: Incidence of obesity is increasingly prevalent among children: global pediatric obesity incidence raised by 30% globally in the last two decades and increased tenfold in the last four decades. Being obese as a child increases the likelihood of being obese as an adult, and suffer from obesity-related health complications. Adipose tissue development in the first year of life may determine adiposity in early childhood. Our aim is to understand mechanisms that control healthy adipose tissue development from infancy to childhood. We collected adipose tissue specimens during elective surgery from the inguinal region of human infants and children, with normal BMI and without known metabolic or endocrine diseases. Samples were proceesed for extraction of total RNA, using phenol:chlorophorm extraction. Next generation RNA sequencing were performed.

overall_design: Samples are labeled as patient groups ("infants", "children"). Our aim was to identigy differentially expressed genes (DEGs) in the adipose tissue of the the human infant and child, to understand molecular mechanisms and cellular processes that affect adipose tissue development.


title: Global transcriptome of Arabidopsis plants (Col-0, Rld2 and Shahdara genotypes) inoculated by the fungal pathogen Sclerotinia sclerotiorum following temperate, mediterranean and continental acclimation

status: Public on Oct 24 2024

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

summary: The short-term, reversible process that allows plants to cope with immediate environmental fluctuations is often referred to as acclimation. Plant acclimation help maintain the balance of natural systems, supporting biodiversity and the services that ecosystems provide, such as carbon sequestration and water regulation. With climate change modifying the distribution area of plants and causing more frequent and severe weather events, knowledge of how plants acclimate can inform strategies to manage ecosystems and agriculture. Analyses of plant immune responses under abiotic constraints generally focus on pathogen inoculation under prolonged and stable abiotic conditions. Daily fluctuations of the environment may alter plant metabolism, growth and flowering as well as gene regulation and invasive growth of fungal pathogens. Yet, how plant immunity acclimates to daily temperature fluctuations remains largely unexplored. To study the molecular bases of quantitative disease resistance acclimation, we performed a global transcriptome analysis of Arabidopsis thaliana accessions Col-0, Rld-2 and Sha grown in temperate, continental and Mediterranean climates, followed or not by Sclerotinia sclerotiorum inoculation.

overall_design: Periphery of S. sclerotiorum disease lesions collected 24 hours post-inoculation on detached leaves of A. thaliana Col-0, Rld2 and Shahdara. Plants were previously acclimated under three different day/night temperature regimes. Mock inoculated plants acclimated at the same time serve as controls. Samples were collected in three independent replicates of the experiment.

first: Justine

last: Sucher

first: Marie

last: Didelon


title: The control of H. pylori-mediated gastric cancer development and progression through YAP/TAZ signal regulation

status: Public on Oct 28 2024

city: Seoul

first: BYEONGMIN

last: YU

address: Yonsei University college of medicine

country: South Korea

institute: Department of Internal Medicine, Yonsei University College of Medicine

summary: Helicobacter pylori(H. pylori), a gastrointestinal pathogen, is known to increase the risk of gastric cancer by activating chronic pro-inflammatory signaling pathways in epithelial cells. Cytotoxin-related protein A (CagA) is known to play an important role in gastric cancer development. CagA has been reported to induce tumors by inducing overexpression of YAP/TAZ, a component of Hippo signaling, and dysregulation of the pathway, thereby promoting cell proliferation and resistance to apoptosis. However, the role of H.pylori-mediated YAP/TAZ has not yet been fully investigated. Our study aimed to investigate the role of YAP/TAZ in H.pylori-mediated Hippo pathway dysregulation in gastric carcinogenesis using H.pylori-infected gastric cancer cell lines, knockout mice, and patient-derived organoids. CagA-mediated YAP overexpression in gastric epithelial cells induced intestinal epithelial metaplasia and induced intracellular rearrangement of the binding protein ZO1, thereby conferring cell motility.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from gastric cancer epithelial cell line AGS with/ without Helicobacter pylori (60190, ΔCagA) infection.

first: ByeongMin

last: Yu

first: YongChan

last: Lee


title: ZFPL1 drives hepatocellular carcinoma via palmitoylation-dependent interaction with CLDN3 at Cys106

status: Public on Oct 19 2024

city: Shenyang

first: Wensu

last: Liu

address: 77 Puhe Road, Shenbei District

institute: China Medical University

summary: Massive studies have been applied in exploring the factors driving pathogenesis, progression and metastasis of hepatocellular carcinoma. However these studies were inefficient in disclosing the fundamental mechanism which promotes hepatocellular carcinoma. Zinc and zinc-finger proteins have been important in extensive biological processes for human. Supervised machine learning using bootstrapping algorithm on GEO and TCGA transcriptome data for hepatocellular carcinoma identified zinc-finger like protein ZFPL1 as potential hepatocellular carcinoma driver. Further studies validated ZFPL1 significantly promoted progression and metastasis of hepatocellular carcinoma. We performed RNA-seq on si-ZFPL1 xenograft tissue and identified CLDN3 as potential target gene for ZFPL1. Further experiments confirmed interaction between ZFPL1 and WNT signaling pathway markers. Conclusively, these studies indicated the effect and mechanism of ZFPL1 on promoting progression and metastasis of hepatocellular carcinoma and might gap the bridge between zinc-finger like proteins and hepatocellular carcinoma.

overall_design:
We used Trizol Reagent (Invitrogen Life Technologies) to extract total RNA in siNC as control group (n=3) and siZFPL1 group (n=3). The sequencing library was prepared using the TruSeq RNA sample preparation kit (Illumina, USA) and sequenced at the Hiseq platform (Illumina) of Shanghai Personal Biotechnology Co. LTD. (Shanghai, China). After screening for CutAdapt-based 3'end adapter sequences or reads with average quality score lower than Q20, the high-quality sequences were compared with the reference genome (Assembly GRCm38). The processed data were then normalized and derepeated. Finally fold change and p-value for Students’ t-test were calculated for control and siZFPL1 groups.

UPDATE:
[Jul-29-2026] In the titles and treatments of GSM8511870 to GSM8511873, "control" was replaced with "siNC".

first: Zhuo

last: Wang

first: Xiaobei

last: Zhou

first: Zhanyou


title: Identification of new therapeutic candidates for Congenital Central Hypoventilation Syndrome

status: Public on Oct 10 2024

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

summary: Congenital central hypoventilation syndrome (CCHS), a rare genetic disease caused by heterozygous PHOX2B mutations, is characterized by life-threatening breathing deficiencies. PHOX2B is a transcription factor required for the specification of the autonomous nervous system that contains respiratory centers. To date, the only treatment offered to patients is mechanical ventilatory support. Therefore, identifying molecules with potential alleviating effects is of prime importance. A transcriptomic dataset from cells transiently expressing both wild type and variant PHOX2B allowed to run the CMap online tool and to identify, using in vitro models, drug compounds capable of relocating PHOX2B mutated proteins in the nucleus and restoring proper regulation of PHOX2B target gene expression. Subsequently, we tested the most efficient molecule ex vivo on hindbrain preparations isolating the principal components of the central respiratory command. Our results provide evidence that the HDAC inhibitor Vorinostat, also known as SAHA, is a promising molecule for the treatment of CCHS

overall_design: To identify drugs of interest for CCHS, SK-N-BE cells were plated in triplicate, transfected with constructs expressing  wild-type or mutant PHOX2B proteins, and treated with vehicle (DMSO) or 17-AAG.

first: Chiara

last: Africano

first: Tiziana

last: Bachetti

first: Gabriel

last: Pitollat

first: Genny

last: Del Zotto

first: Francesca

last: Giacopelli

first: Nicolas

last: Lenfant

first: Amélia

last: Madani

first: Nathan

last: Beckouche

first: Muriel

last: Thoby-Brisson

first: Isabella

last: Ceccherini


title: Analysis of gene expression in Mel Z cells grown on plastic (MP).

status: Public on Oct 08 2024

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

summary: RNA-Seq procedure was used for analysis of expression in melanoma cells. Cells were separately lysed with Trizol reagent (Invitrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with  BioAnalyser and  RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 14.8 millions of reads were generated for each sample.

overall_design: Analysis of gene expression in Mel Z cells grown on plastic (MP), Matrigel (MM), and on Matrigel in the presence of inhibitor(MMI).

middle: A

first: Yuri

middle: V

last: Kravatsky

first: Amalia

last: Vartanian


title: Encoding of odors by mammalian olfactory receptors

status: Public on Oct 06 2024

first: Aashutosh

last: Vihani

address: 264 CARL Building

summary: Deorphanization of mouse olfactory receptors using pS6-IP-Seq.

overall_design: Phosphorylated S6 ribosomal subunit capture and associated mRNA profiling (pS6-IP-Seq) on whole olfactory mucosa.

first: Hiroaki

last: Matsunami


title: Uncovering the Dynamics of Immune Cell Populations in the First Week of Life: The Interplay of Neutrophils and Breastfeeding

status: Public on Oct 01 2024

city: Boston

first: Ofer

last: Levy

state: MA

address: 300 Longwood Avenue

department: Infectious Disease

institute: Boston Children's Hospital

summary: The first few days of life are characterized by rapid external and internal changes that require rapid host adaptations. Despite growing evidence of the impact of this period on an individual’s lifelong health trajectory, this period remains largely uncharted. To decipher key factors associated with changes in peripheral blood cell composition we conducted a stringently standardized, high-throughput immune phenotyping investigation on 796 newborns across diverse settings (The Gambia, West Africa and Papua New Guinea, Australasia) in the framework of a Human Immunology Project Consortium study. Samples were collected twice from each newborn during the first week of life and analyzed via high throughput flow cytometry with an unbiased automated gating algorithm to capture cell compositional changes at an unprecedented level of detail. We found that immune cell composition in peripheral blood changes along patterns highly conserved across populations and environments. Changes with age/day of life were most pronounced in the innate myeloid compartment. While there was minimal impact of sex, season of birth, mother’s age or origin (i.e., environmental and genetic background), breastfeeding and vaccination were strongly associated with increase in cell counts of peripheral blood neutrophils and monocytes. Our results may suggest a possible association of initiation of breastfeeding with changes in immune ontogeny, and thus possibly host immune-mediated protection from infection. These data begin to outline a specific window of opportunity for interventions that can deliberately direct immune ontogeny.

overall_design: longitudinal neonatal cohort study

first: Tobias

last: Kollmann

first: Sebastiano

last: Montante

first: Joann

last: Arce

first: Rym

last: Ben-Othman

first: EPIC

last: Consortium


title: Transcriptomic profiling of blood mTreg and mTeff from healthy control (HC) and multiple sclerosis (MS)

status: Public on Sep 30 2024

city: New Haven

first: Tomokazu

middle: S

last: Sumida

state: CT

address: 300 George St,, 3rd floor room349

department: Neurology

institute: Neurology, Yale School of Medicine


title: Transcriptomic and epigenetic profiling of blood mTreg and mTeff from healthy control (HC) and multiple sclerosis (MS) [ATAC-Seq]

summary: Autoimmune diseases, among the most common disorders of young adults, are mediated by genetic and environmental factors. While CD4+Foxp3+ regulatory T cells (Tregs) play a central role in preventing autoimmunity, the molecular mechanism underlying their dysfunction is unknown. Here, we performed comprehensive transcriptional and epigenetic profiling of Tregs in multiple sclerosis (MS) to identify central transcriptional programs regulating human autoimmunity.

overall_design: CD4+CD25hiCD127loCD45RO+ memory Tregs and CD4+CD25low/negCD127hiCD45RO+ memory Tconvs are sorted by FACS and subjected to ATAC-seq

first: David

last: Hafler


title: Saturation genome editing-based functional evaluation and clinical 2 classification of BRCA2 single nucleotide variants

city: Rochester

first: Fergus

last: Couch

address: 200 1st St SW

institute: MAYO CLINIC ROCHESTER

summary: Germline BRCA2 loss-of function (LOF) variants identified by clinical genetic testing predispose to breast, ovarian, prostate and pancreatic cancer. However, variants of uncertain significance (VUS) (n>5000) limit the clinical use of testing results. Thus, there is an urgent need for functional characterization and clinical classification of all BRCA2 variants. Here we report on comprehensive saturation genome editing-based functional characterization of 99% of all possible single nucleotide variants (SNVs) in the BRCA2 DNA Binding Domain hotspot for pathogenic missense variants that is encoded by exons 15 to 26. The assay was based on deep sequence analysis of HAP1 haploid cells endogenously targeted using a CRISPR/cas9 knockin approach. A total of 6959 SNVs were characterized for effects on cell survival. The assay was validated relative to nonsense and synonymous variants, ClinVar pathogenic/likely pathogenic and benign/likely benign variants and homology directed repair cell based DNA repair assay results, all of which showed >94% sensitivity and specificity. Variants were assigned posterior probabilities of pathogenicity using a VarCall two component Bayesian mixture model and were further grouped according to ACMG strength of evidence under the PS3/BS3 rule resulting in Benign Strong (n=5430), Benign Moderate (n=190), Benign Supporting (n=61), VUS (122), Pathogenic Strong (n=1021), Pathogenic Moderate (n=88), and Pathogenic Supporting (n=47). Breast cancer case-control association studies showed that pooled SNVs encoding functionally pathogenic missense variants were associated with increased risks of breast (odds ratio (OR)3.81, 95%CI: 2.88-5.07) and ovarian cancer (OR 5.93, 95%CI: 4.12-8.52). The functional data were also combined with other sources of information in the ClinGen BRCA1/2 VCEP ACMG/AMP-classification model. A total of 785 SNVs, including 261 missense SNVs, were classified as pathogenic or likely pathogenic, while 5566 SNVs, including 3786 missense SNVs, were classified as benign or likely benign. These classified variants can now be used for risk assessment and clinical care of variant carriers.

overall_design:
Saturation genome editing was used to introduce variants and the variant count on day 5 and day 14 were measured. The log2 ratio between D5 and D14 was used to measure the variant effects
Multiplexed Assays for Variant Effects (MAVE)

first: Huaizhi

last: Huang

first: Chunling

last: Hu

first: Jie

first: Steven

middle: N

last: Hart

first: Rohan

middle: D

last: Gnanaolivu

first: Mohamed

last: Abozaid

first: Tara

last: Rao

first: Yohannes

last: Tecleab

first: Nicholas

last: Boddicker

first: Wenan

last: Chen

first: Marcy

middle: E

last: Richardson

middle: J


title: Transcriptomic profiling of blood mTreg and mTeff from healthy control (HC) and multiple sclerosis (MS) [RNA-Seq]

overall_design:
CD4+CD25hiCD127loCD45RO+ memory Tregs and CD4+CD25low/negCD127hiCD45RO+ memory Teffectors are sorted by FACS and subjected to mRNA-seq

>>>Submitter states that raw data will be submitted to dbGaP due to patient privacy concerns<<<


title: Saturation genome Editing of BRCA2 variants from C-terminal DNA binding domain

status: Public on Sep 27 2024

city: Frederick

first: Shyam

last: Sharan

state: MD

address: 1050 Boyles Street

department: Mouse Cancer Genetics Program

institute: National Cancer Institute

summary: Accurate interpretation of genetic variation is a critical step towards realizing the potential of precision medicine. Sequencing-based genetic tests have uncovered a vast array ofBRCA2sequence variants. Due to limited clinical, familial and/or epidemiological data, thousands of variants are considered to be variants of uncertain significance (VUS). Here we have utilized CRISPR-Cas9-based saturation genome editing (SGE) in a humanized-mouse embryonic stem cell line. We have categorized nearly all possible missense single nucleotide variants (SNVs) encompassing the C-terminal DNA binding domain ofBRCA2.We have generated the function scores for 6270 SNVs, covering 95.5% of possible SNVs in exons 15-26 spanning residues 2479-3216, including 1069 unique missense VUS, with 81% functional and 14% found to be nonfunctional. Our classification aligns strongly with pathogenicity data from ClinVar, orthogonal functional assays and computational meta predictors. Our statistical classifier exhibits 92.2% sensitivity and 96% specificity in distinguishing clinically benign and pathogenic variants recorded in ClinVar. Furthermore, we offer proactive evidence for 617 SNVs being non-functional and 3396 SNVs being functional demonstrated by impact on cell growth and response to DNA-damaging drugs like cisplatin and olaparib. This classification serves as a valuable resource for interpreting unidentified variants in the population and for physicians and genetic counselors assessingBRCA2VUSs in patients.

overall_design: Saturation genome editing (SGE) of BRCA2

first: Sounak

last: Sahu


title: Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2 [Spatial Transcriptomics]

status: Public on Sep 25 2024

city: Aurora

first: Christina

last: Como

state: CO

institute: University of Colorado

summary: During development, the meninges act as a regulator of neocortical development by secreting ligands that act on neural cells to regulate neurogenesis and neuronal migration.  Meninges-derived retinoic acid (RA) promotes neocortical progenitor cell cycle exit however the underlying mechanism is unknown. Here, we use Foxc1-mutant embryos that lack meninges-derived ligands, spatial transcriptomics, and profiling of retinoic-acid receptor-a (RARa) DNA binding to identify the neurogenic transcriptional mechanisms of RA signaling in cortical neural progenitors. We determined that meningeal-derived RA controls neurogenesis by suppressing self-renewal pathways Notch signaling and the transcription factor Sox2. We show that RARα binds in the Sox2ot promoter, a long non-coding RNA that regulates Sox2 expression, and RA promotes Sox2ot expression in neocortical progenitors. Our findings elucidate a previously unknown mechanism of howmeningeal RA coordinates neocortical development and insight into how defects in meningeal develop can cause neurodevelopmental disorders.

overall_design: Spatial transcriptomics data from E14 mouse coronal sections including 2 controls and 2 Foxc1 Mutants

first: Julie

last: Siegenthaler


title: Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2


title: Gene expression profile of B lymphocytes from GPR40 KO and WT mice

status: Public on Sep 23 2024

city: Huzhou

first: Yunliang

last: Yao

state: Zhejiang

address: 759 East Second Ring Road

department: Medical School

institute: Huzhou Normal University

summary: GPR40 deficiency in B cells was shown to result in enhanced B cell activation and proliferation, antibody production, germinal center formation, and class switch recombination. We used whole transcriptome sequencing to analyze B cells isolated from the spleens of both GPR40-WT and GPR40-BKO mice.

overall_design: B lymphocytes from  GPR40-WT and GPR40-BKO mice were separated by B cell isolation kit and analyzed using RNAseq.

first: Anqi

last: Li


title: Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2 [CUT&Run]

overall_design: CUT&RUN DNA sequencing for Myctag-Rar alpha in E14 Prom1+ magnetically separated cortical cells


title: Low-input bulk RNA sequencing of Drosophila nephrocytes

status: Public on Sep 13 2024

city: Baltimore

first: Hangnoh

last: Lee

address: 670 W Baltimore St

institute: University of Maryland School of Medicine

summary: To validate the applicability of pre-amplified low-input RNA sequencing method in Drosophila melanogaster cell types, we used Drosophila nephrocytes as an example case.

overall_design: We dissected Drosophila nephrocytes from adult animals to obtain 100 to 200 nephrocytes. We isolated total RNA using a low-input cDNA pre-amplification kit and then performed RNA sequencing on an Illumina-based platform.

first: Jin-Gu

first: Yunpo

last: Zhao

first: Jianli

last: Duan

first: Zhe

last: Han


title: Navigating Illumina Methylation Data: Biology vs. Technical Artefacts

status: Public on Dec 19 2024

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University and Ulm University Medical Center

summary:
Illumina-based BeadChip arrays have revolutionized genome-wide DNA methylation profiling, pushing it into diagnostics. However, comprehensive quality assessment remains a challenge within a wide range of available tissue materials and sample preparation methods. This study tackles two critical issues: differentiating between biological effects and technical artefacts in suboptimal quality samples and the impact of the first sample on the Illumina-like normalization algorithm.
We introduce three quality control scores based on global DNA methylation distribution (DB-Score), bin distance from copy number variation analysis (BIN-Score), and consistently methylated CpGs (CM-Score), that rely on biological features rather than internal array controls. These scores were explored and benchmarked across independent study cohorts. Additionally, we reveal deviations in beta values caused by different sample rankings with the Illumina-like normalization algorithm, verified these with whole-genome methylation sequencing data and showed effects on differential DNA methylation analysis.
Our findings underscore the necessity of consistently utilizing a pre-defined normalization sample within the ranking process to boost the reproducibility of the Illumina-like normalization algorithm. In conclusion, our study delivers valuable insights, practical recommendations, and R functions designed to enhance the reproducibility and quality assurance of DNA methylation analysis, particularly for challenging sample types.

overall_design: Six paired samples from patients with Burkitt lymphoma, once formalin-fixed paraffin-embedded (FFPE) tissue and once cryo preserved material, as well as 5 non-neoplastic samples were collected from the ICGC MMML-Seq consortium. In addition, 1 sample from the peripheral blood of healthy donors were used as normalization sample.

first: Ole

last: Ammerpohl


title: Inhibition of SUMOylation Induces Adaptive Anti-Tumor Immunity Against Pancreatic Cancer through Multiple Effects on the Tumor Microenvironment

status: Public on Sep 02 2024

city: New York

first: Hyojae

middle: James

state: NY

address: 101 6th Ave

institute: New York Genome Center

summary: Improvement of pancreatic ductal adenocarcinoma (PDAC) patients’ outcomes require exploration of novel therapeutic mechanisms. Thus far, most studies of PDAC therapies, including those inhibiting small ubiquitin-like modifications (SUMOylation), have focused on PDAC epithelial cell biology. The mechanisms by which SUMOylation impacts PDAC in the context of its tumor microenvironment (TME) are poorly understood. We used clinically relevant orthotopic PDAC mouse models to investigate the effect of SUMOylation inhibition using a specific, clinical stage compound, TAK-981. TAK-981 monotherapy improved survival in immunocompetent mice. However, in contrast to its inhibition of PDAC cell proliferation in vitro, the survival benefit of TAK-981 in vivo is dependent on the presence of T cells.  Induction of adaptive anti-tumor immunity is the dominant anti-tumor effect of SUMOylation inhibition in vivo.  To elucidate the mechanism of adaptive immunity, we performed comparative single cell transcriptomics analyses of murine and human PDAC tumors, including cancer cells, T cells, tumor associated macrophages (TAM) and cancer associated fibroblasts (CAF), in combination with immunofluorescence, immunohistochemistry, western blots and qPCR. Mechanistically, SUMOylation regulates T cell activation and differentiation.  In addition, TAK-981 changed gene expression in TAM, CAF and cancer cells that are likely to enhance the anti-tumor T cell response. These findings provide rationale for combination strategies to augment adaptive immune responses to PDAC that are necessary for durable disease control in PDAC patients.

overall_design: KPC46 tumors were harvested from mice that are either treated with vehicle (Cremophor) or TAK-981. The processed tumors were then analyzed using scRNA-seq

first: Suna

last: Erdem

first: Jayanth

last: Narayanan

first: Neranjan

last: Tharuka

first: Jorge

last: De La Torre Medina

first: Tianchen

last: Ren

first: Yixuan

last: Kuang

first: Tharindumala

last: Abeywardana

first: Kevin

first: Allison

last: Berger

first: Andrew

middle: M

last: Lowy

first: Rebekah

middle: R

last: White

first: Yuan


title: Cell and state-specific eQTL analysis in human endometrial mesenchymal cells uncovers candidate susceptibility genes for reproductive diseases and traits

status: Public on Sep 01 2024

city: Herston

first: Sally

last: Mortlock

state: Queensland

address: AWaGHR Centre, School of Public Health, The University of Queensland

department: School of Public Health

country: Australia

institute: University of Queensland

summary: The functional consequence of genetic variants and how they contribute to disease remains elusive. Studying genetic variants in disease-relevant cells captures variations in effects in cell types and states. The endometrium is a heterogenic tissue with critical reproduction roles considered complex genetic traits. We assessed the association between genetic variants and gene expression in purified endometrial mesenchymal cells using both bulk and single-cell RNA-sequencing data from patients with endometria-driven reproductive disorders. We compared these to those identified in whole endometrium and to reproductive disease-associated genetic loci. We identified cis-eQTLs for 947 unique eGenes in isolated endometrial mesenchymal cells of which 50% had not previously been identified in whole endometrium. Single-cell RNA-sequencing data stratifying by differentiation state we found a further 25 and 26 unique eGenes in stem and mature mesenchymal cells respectively. Comparison with reproductive disease-associated variants identified overlaps with COG6 and AC012313.10 with age of menarche and HELB with age of menopause. Summary Mendelian Randomisation (SMR) identified potential causal effects of RPS2 on age of menarche and KANSLI on age at first birth, as well as a mesenchymal stem cell state-specific influence of GATD3A on uterine fibroid formation. Identifying functional consequences of genetic variants critical to disease can be enhanced with disease-relevant, purified cells. We provide evidence for critical roles for COG6 and HELB in age-related traits of reproduction and a causal role for GATD3A on uterine fibroid formation during early cell development supporting that genetic influences on early stem cell state and subsequent differentiation can contribute to disease pathology.

overall_design: Endometrial stromal cells were isolated from endometrial biopsies and cultured. RNA was extracted from the cultured primary cells and RNA-sequencing perofrmed.

first: Brett

last: McKinnon

first: Samuel

last: Lukowski

first: Joanna

last: Crawford

first: Michael

last: Mueller

first: Grant

last: Montgomery


title: TGFβ primes alveolar-like macrophages to induce type I IFN following TLR2 activation.

status: Public on Sep 11 2024

city: Lansing

first: Kayla

last: Conner

state: Michigan

address: 4125 Beaumont Rd

institute: Michigan State University

summary: Alveolar macrophages (AMs) are key mediators of lung function and are potential targets for therapies during respiratory infections. TGFb is an important regulator of AM differentiation and maintenance but, how TGFb directly modulates the innate immune responses of AMs remains unclear. This shortcoming prevents effective targeting of AMs to improve lung function in health and disease. Here we leveraged an optimized ex vivo AM model system, fetal-liver derived alveolar-like macrophages (FLAMs), to dissect the role of TGFb in AMs. Using transcriptional analysis, we first globally defined how TGFb regulates gene expression of resting FLAMs. We found that TGFb maintains the baseline metabolic state of AMs by driving lipid metabolism through oxidative phosphorylation and restricting inflammation. To better understand inflammatory regulation in FLAMs, we next directly tested how TGFb alters the response to TLR2 agonists. While both TGFb (+) and TGFb (-) FLAMs robustly responded to TLR2 agonists, we found an unexpected activation of type I interferon (IFN) responses in FLAMs and primary AMs in a TGFb-dependent manner. Surprisingly, mitochondrial antiviral signaling protein and the interferon regulator factors 3 and 7 were required for IFN production by TLR2 agonists. Together, these data suggest that TGFb modulates AM metabolic networks and innate immune signaling cascades to control inflammatory pathways in AMs.

overall_design: FLAMs with and without TGFβ were plated in 6-well plates at 1 x 106 cells/well and treated with Pam3 as described for 18 hours. We used the Direct-zol RNA Extraction Kit (Zymo Research, Cat no. R2072) to extract RNA according to the manufacturer’s protocol. Quality was assessed by the MSU Genomics Core using an Agilent 4200 TapeStation System. The Illumina Stranded mRNA Library Prep kit (Illumina, Cat no. 20040534) with IDT for Illumina RNA Unique Dual Index adapters was used for library preparation following the manufacturer’s recommendations but using half-volume reactions. Qubit™ dsDNA HS (ThermoFischer Scientific, Cat no. Q32851) and Agilent 4200 TapeStation HS DNA1000 assays (Agilent, Cat no. 5067-5584) were used to measure quality and quantity of the generated libraries. The libraries were pooled in equimolar amounts, and the Invitrogen Collibri Quantification qPCR kit (Invitrogen, Cat no. A38524100) was used to quantify the pooled library. The pool was loaded onto 2 lanes of a NovaSeq S4 flow cell, and sequencing was performed in a 2x150 bp paired end format using a NovaSeq 6000 v1.5 100-cycle reagent kit (Illumina, Cat no. 20028316). Base calling was performed with Illumina Real Time Analysis (RTA; Version 3.4.4), and the output of RTA was demultiplexed and converted to the FastQ format with Illumina Bcl2fastq (Version 2.20.0). RNAseq analysis was completed using the MSU High Performance Computing Center (HPCC). FastQC (Version 0.11.7) was used to assess read quality. Bowtie2 (Version 2.4.1) with default settings was used to map reads with the GRCm39 mouse reference genome. Aligned reads counts were assessed using FeatureCounts from the Subread package (Version 2.0.0). Differential gene expression analysis was conducted using the DESeq2 package (Version 1.36.0) in R (Version 4.2.1).

first: Sean

last: Thomas

first: Laurisa

last: Ankley

first: Alexander

middle: W

last: Rapp

first: Abigail

middle: P

last: McGee

first: Francois

last: LeSage

first: Christopher

last: Tanner

first: Taryn

last: Vielma

first: Eleanor

middle: C

last: Scheeres

first: Joshua

last: Obar

last: Olive


title: Comparative Analysis of Host Responses Between Sepsis and COVID-19: A Prospective Observational Study of Whole Blood Transcriptome

status: Public on Aug 28 2024

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Comparative Analysis of Host Responses Between Sepsis and COVID-19: A Prospective Observational Study of Whole Blood Transcriptome (miRNA-Seq)

summary: This prospective observational study conducted at Osaka University Graduate School of Medicine aimed to compare host responses in sepsis and COVID-19 patients by analyzing mRNA and miRNA profiles. They included 22 sepsis patients, 35 COVID-19 patients, and 15 healthy subjects. Sepsis was diagnosed using Sepsis-3 criteria, while COVID-19 was confirmed through SARS-CoV-2 RT-PCR testing and chest CT scans for pneumonia assessment.                    For RNA sequencing, 14,500 mRNAs, 1121 miRNAs, and 2556 miRNA-targeted mRNAs were available for analysis in sepsis patients. Numbers of genes showing upregulated:downregulated gene expression (false discovery rate <0.05, |log2 fold change| >1.5) were 256:2887 for mRNA, 53:5 for miRNA, and 49:2507 for miRNA-targeted mRNA. Similarly, in COVID-19 patients, 14,500 mRNAs, 1121 miRNAs, and 327 miRNA-targeted mRNAs were analyzed, with numbers of genes exhibiting upregulated:downregulated gene expression of 672:1147 for mRNA, 3:4 for miRNA, and 165:162 for miRNA-targeted mRNA.  Sepsis patients had a greater number of upregulated and downregulated genes and pathways compared to COVID-19 patients, indicating a dynamic change in gene expression and pathway activation in sepsis.

overall_design: We performed the single miRNA-seq analysis using whole blood from 22 sepsis patients and 35 COVID-19 patients admitted to our department, as well as 15 healthy subjects.

first: A

last: Muratsu

first: D

last: Okuzaki

first: H

last: Matsumoto


title: A mouse model of human coronavirus HCoV-NL63 infection: comparison with rhinovirus-A1B

status: Public on Aug 25 2024

city: Ann Arbor

first: Marc

last: Hershenson

address: 1150 E. Medical Center Drive

institute: University of Michigan

summary: We establish a mouse model of HCoV-NL63 and compare outcomes with a model of rhinovirus (RV)-A1B.  Transgenic mice expressing human ACE2 were infected intranasally with sham LLC-MK2 cell lysate,  100,000 TCID50 units HCoV-NL63, or 1,000,000 PFU RV-A1B.  Lungs were assessed for host gene expression by next generation sequencing.  RNAseq showed increases in IFN-α, IFN-β, IFN-λ and many IFN-stimulated genes (ISGs) in NL63-infected mice.  In addition to ISGs, RV-A1B induced expression of IFN-γ, IL-1β, NLRP3, TLR2 and C-X-C chemokines. We established a mouse model of HCoV-NL63 replicative infection characterized by expression of ISGs but fewer pro-inflammatory genes compared to RV-A1B.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for B6.Cg-Tg(K18-ACE2)2Prlmn/J mice treated with RVA1B or HCoV-NL63.

first: J

last: Bentley

first: Jordan

last: Kreger

first: Haley

last: Breckenridge

first: Shilpi

last: Singh

first: Yiran

last: Li

first: Susan

last: Baker

first: Carey

last: Lumeng

middle: B


title: Senescent fibroblasts in the tumor stroma rewire lung cancer metabolism and plasticity

status: Public on Aug 27 2024

city: San Francisco

first: Tien

last: Peng

state: California

address: 513 Parnassus Avenue

department: medicine

institute: UCSF

summary: Our study identified a druggable component of the tumor stroma that fulfills the metabolic requirement of tumor cells to acquire a more aggressive phenotype.

overall_design: The p16INK4a+ and p16INK4a- lung fibroblasts and tdTomato+ LUAD cells of KPTI mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence of eGFP signal and analyzed using scRNAseq. tdTomato+ tumor cells were isolated by FACS after digestion of tumor organoids. KPTI mouse lung sections and human LUAD sections were analyzed by Xenium for spatial transcriptomics data.

first: Jinyoung

last: Lee


title: Comparative Analysis of Host Responses Between Sepsis and COVID-19: A Prospective Observational Study of Whole Blood Transcriptome (RNA-Seq)

overall_design: We performed the single RNA-seq analysis using whole blood from 22 sepsis patients and 35 COVID-19 patients admitted to our department, as well as 15 healthy subjects.


title: Therapy of allergic rhinitis using ribavirin spray to clear nasal commensal viruses

status: Public on Aug 21 2024

city: Shanghai City

first: Yue

last: Dong

address: 800 Xiangyin Road

institute: Naval Medical University

summary: To elucidate the potential role of commensal viruses in the etiology of AR, we performed a metagenomic analysis of nasal lavage fluid (NLF) to identify commensal viruses in the nose of mice colonizing in the specific pathogen-free (SPF) circumstances (Vehicle group). To evaluate the potential role of these commensal viruses, we reduced them in the nose of mice by administrating intranasal drops of broad-spectrum antiviral drug ribavirin daily, starting at 4-week-old and lasting for three weeks (Ribavirin group).

overall_design: Nasal lavage fluid (NLF) was obtained from mice that were administered intranasal drops of either vehicle (n=7) or ribavirin (n=7) daily, starting at 4 weeks old and lasting for three weeks. The NLF samples were then subjected to metatranscriptomic sequencing to assess the abundance of viruses.

first: Ye

last: Zhou

first: Jin

last: Hou


summary: For analyzing the exploratory nasal commensal viruses, we performed the metatranscriptomic analysis of the nose swabs from the enrolled AR patients both before and after treatments, as well as sequenced the nose swabs from a set of healthy volunteers without AR history.Simultaneously, to assess the expression of interferon-stimulated genes in patients with allergic rhinitis, we analyzed the gene expression of host reads.

overall_design: We had designed and conducted a randomized, double-blind, parallel-controlled phase 2 clinical trial. Eligible patients diagnosed with AR based on the typical symptoms and either a positive skin prick test (SPT) or allergen-specific IgE level ≥ 0.35 kU/L following the Chinese Guidelines for the Diagnosis and Treatment of Allergic Rhinitis criteria were enrolled. Each patient received detailed information on the study procedures, the treatments, the potential risks and benefits, and the fundamental rights in the clinical trial. To evaluate the efficacy and safety of ribavirin spray for AR treatment, ribavirin (12 mg daily) or placebo was given twice a day, one spray per nostril for 4 weeks.  We obtained nasal swab samples from enrolled patients with allergic rhinitis for metatranscriptomic sequencing, with sampling time points before medication and four weeks after commencing treatment. Simultaneously, to assess whether there is a significant difference in the abundance of nasal commensal viruses between healthy individuals and patients with allergic rhinitis, we collected nasal swabs from healthy individuals without allergic rhinitis as controls for metatranscriptomic sequencing. All patients provided written informed consent.The clinical trial was registered at Chinese Clinical Trial Registry (ChiCTR2400082642).


title: Inhibition of circulating glycocholic acid-regulated signaling potentiates immune checkpoint therapy in colorectal cancer

status: Public on Aug 17 2024

city: Shanghai

first: Senlin

last: Zhao

address: 270 Dong An Road

department: Colorectal Surgery

institute: Cancer Hospital, Fudan University

summary: Serum bile acids (BAs) are an important risk factor for the initiation and progression of cancer, but their roles in colorectal cancer (CRC) remain largely unknown. The present study showed that glycocholic acid (GCA), a primary BA, was highly accumulated in the serum of patients with CRC. In a mouse model of CRC, GCA diet promoted programmed death-ligand 1 (PD-L1) expression in tumors, which attenuated CD8+ T cell-mediated antitumor responses in the tumor microenvironment (TME), and promoted the occurrence and development of CRC. Increased PD-L1 expression was caused by the reduction in activity of the BA receptor farnesoid X receptor (FXR). Mechanistically, FXR acted as transcriptional repressor for the transcription factor SRY-box transcription factor 14 (SOX14), and suppressed the palmitoylation and stabilization of PD-L1 by inhibiting the SOX14-mediated expression of zinc finger DHHC-type palmitoyl transferase 9 (DHHC9). Notably, genetically silencing SOX14 and DHHC9 in cancer cells or administering an FXR agonist synergized with anti-PD-1 therapy, leading to reduced tumor growth in GCA-fed mice. Together, the present findings reveal a previously unrecognized mechanism of BA in remodeling the TME to mediate CRC resistance to immunotherapy, which may have clinical implications for developing immunotherapy strategies for patients with CRC.

overall_design: To explore the function of GCA , we cocultred MC38 cells with or without GCA for 24h. We then performed gene expression profiling analysis using data obtained from RNA-seq of these treatments. Comparative gene expression profiling analysis of RNA-seq data for MC38 cells treated with or without GCA(CON and GCA).

first: Jing

last: Zhang

first: Yushuai

last: Mi

first: Zijuan

last: Hu

first: Xinyang

last: Zhong

last: Xu

first: Sanjun

last: Cai

first: Xinxiang

first: Ping

last: Wei

first: WanJun

last: Chen

first: Dawei


title: Transcriptome expression study with chronological aging in human hippocampus

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

country: Spain

institute: Biodonostia Institute

summary: In our study, we performed a transcriptomic analysis from hippocampal samples from human individuals of different ages. We identified a set of genes that were differentially expressed in aged samples. Moreover, we revealed a subset of genes whose expression correlated with chronological aging. Analysis in a validation cohort confirmed some genes having negative correlation with age. Additional immunohistochemistry in another validation cohort confirmed transcriptomic results. In summary, these results identify putative biomarkers and regulators of brain aging.

overall_design: Brain hippocampal samples from human individuals from different ages ranging from 27 to 88 years-old.

first: Ander

last: Saenz-Antoñanzas

first: Manuel

last: Moreno-Valladares

first: Ainhoa

last: Alberro

first: Marian

last: de Pancorbo

first: David

last: Otaegui

last: Matheu


title: Transcriptomic dissection of an appendicularian larva at single cell resolution

status: Public on Aug 16 2024

city: Bergen

first: Simon

last: Henriet

address: Thormøhlensgate 55

country: Norway

institute: University of Bergen

summary: Oikopleura dioica is a larvacean urochordate that has arisen as an emerging model due to its specific characteristics. Through single cell analysis, we have mapped the different cell populations that are present during its development, and instruct the formation of lineage-specific structures.

overall_design: O. dioica individuals (embryos and larvae) were dissociated at 10 time-points. Cells were isolated and analyzed using scRNA-seq recommendations from 10xGenomics

first: Anthony

last: Leon

last: Lagman

first: Daniel

last: Chourrout


title: Gene expression profile at single cell level of PBMC from HFD/STZ-induced type 2 diabetic mice

status: Public on Aug 15 2024

first: Yunliang

last: Yao

summary: T2DM patients are believed to have long-term chronic inflammation. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity  of immune cell in peripheral blood mononuclear cells （PBMC）from  HFD/STZ-induced type 2 diabetic mice

overall_design: PBMCs of  from  T2D modeld or healthy control mice were separated by Ficoll gradient centrifugation and analyzed using scRNAseq.

first: Yang

last: Liu


title: Localization of HIRA in PML bodies is tightly linked SASP expression

status: Public on Aug 13 2024

city: La Jolla

first: Peter

middle: D.

last: Adams

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Cellular senescence, a stable proliferation arrest caused by a range of cellular stresses, is a bona fide cause of cell and tissue aging. As well as proliferation arrest, cell senescence is associated with a potent pro-inflammatory phenotype, the senescence-associated secretory phenotype (SASP). Given that SASP is regulated at various levels, gaining a comprehensive understanding of its regulation is crucial. This understanding can pave the way for potential therapeutic approaches aimed at modulating SASP, which could promote healthy aging and alleviate the burden of senescence-associated diseases and degeneration. We show here that both the Promyelocytic Leukemia (PML) protein and HIRA histone chaperone are required for SASP expression in senescent cells. PML protein is the key organizer of PML nuclear bodies, nuclear features up to 1mM in diameter, containing many proteins and previously implicated in diverse cellular processes, including control of cell senescence and cellular intrinsic anti-viral immunity. HIRA is a histone chaperone best known for its ability to incorporate histone variant H3.3 into nuclear chromatin in a DNA replication-independent manner, including in non-proliferating senescent cells. HIRA localizes to PML nuclear bodies in senescent cells. We show that both HIRA and PML are required for activation of NF-kB and SASP. We found that HIRA regulates cytoplasmic NF-kB signaling in senescent cells through CCF-cGAS-STING-TBK1 pathway and interaction with autophagy cargo receptor Sequestosome-1 (p62/SQSTM1).

overall_design: mRNA profiling in senescent fibroblasts after ectopic expression of a mutant form of HIRA known as delHIRA(520-1017)

first: Nirmalya

last: Dasgupta

first: Xue

last: Lei

first: Christina

last: Shi


title: Modulation of Integrin α9β1 in Macrophages Reduces Periodontal Inflammation and Supports Alveolar Bone Preservation in Periodontitis [scRNA-seq]

status: Public on Aug 14 2024

city: Guangdong

first: Shihan

last: Xu

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Road/Street, Yuexiu District, Guangzhou City

institute: Sun Yat-sen University

summary: Establish an experimental periodontitis model using Itga9-Lyz2-cKO mice and Itga9-Lyz2-cHet mice, and collect gingival tissues for single-cell analysis.

overall_design: An experimental periodontitis model was established in transgenic mice by performing silk suture ligation and applying Porphyromonas gingivalis to the maxillary second molar. After 14 days, gingival tissues were harvested for single-cell sequencing.

first: Zeyu

last: Bai

first: Shiwen

last: Yang

first: Weiyu

last: Li

first: Wenjun

last: Zhu

first: Jiayan

first: Juan

last: Xia


title: Modulation of Integrin α9β1 in Macrophages Reduces Periodontal Inflammation and Supports Alveolar Bone Preservation in Periodontitis [RNA-seq]

summary: Bone marrow-derived macrophages (BMMs) from Itga9-Lyz2-cKO and Itga9-Lyz2-cHet mice  were stimulated with Porphyromonas gingivalis (Pg) for 2 hours, then subjected to mRNA sequencing.

overall_design: Induce bone marrow mononuclear cells from 8-week-old male Itga9-Lyz2-cKO and Itga9-Lyz2-cHet mice to BMMs by 50 ng/mL macrophage colony-stimulating factor (M-CSF).After stimulation with Pg (MOI = 1:20) for 2 hours, total RNA was extracted using Trizol and subjected to sequencing.


title: Treg insufficiency in autoimmune diabetes is driven by selective loss of Neuropilin-1 on intra-islet regulatory T cells

status: Public on Aug 10 2024

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: Assembly building, 5051 Centre Ave

department: Department of Immunology

institute: University of Pittsburgh

summary: Strategies targeting Treg insufficiency are vital for treating autoimmune diseases like T1D. Our findings highlight the critical role of Neuropilin 1 (Nrp1) in stabilizing Tregs within pancreatic islets. Boosting Nrp1 levels delays diabetes onset by enhancing Treg function. This underscores Nrp1 as a potential target for bolstering Treg activity and combating autoimmune diseases.

overall_design: Our experimental design aimed to explore the influence of Neuropilin 1 (Nrp1) expression on regulatory T cell (Treg) function within NOD mouse islets, a model of autoimmune diabetes. We first identified Tregs lacking Nrp1 expression and observed diminished function. Augmenting Nrp1 levels delayed disease onset, suggesting its importance in Treg function and stability. Comparing Nrp1-induced Tregs to wild-type counterparts, we conducted single-cell RNA sequencing (scRNAseq) experiments to elucidate transcriptional changes. Our findings revealed improved Treg activity in response to Nrp1 expression within the islets, indicating potential therapeutic implications for autoimmune diseases.

first: Stephanie

last: Grebinoski

first: Dario

last: Vignali


title: Obesity-driven phosphatidylethanolamine dysregulation impairs neuroimmune crosstalk and accelerates Alzheimer's pathogenesis

status: Public on Nov 08 2024

city: Houston

first: Li

address: 6565 Fannin Street

department: Department of System Medicine and Bioengineering (SMAB)

institute: METHODIST HOSPITAL RESEARCH INSTITUTE

summary: The paradox of Alzheimer’s disease (AD) and cancer refers to the asynchronism of the two diseases. Understanding the correlation between cancer and AD could enhance research efficiency by consolidating efforts, lead to broader therapeutic impacts through drugs targeting shared mechanisms. Obesity is believed to synchronize this dichotomy by coordinating the onset and progression of both AD and cancer, although the precise mechanism remains unclear. In this study, leveraging integrated multi-modality data, including lipidomics, proteomics, bulk and single-cell RNA transcriptomics, drug repositioning and subcellular visualization, we identified that an overabundance of phosphatidylethanolamine (PEhigh) flux from white adipose tissue in obese individuals underlies this agonist role, driving lipid droplet accumulation and disrupting lipid homeostasis. PEhigh flux escalates both cancer and AD by potentiating immune evasion in tumor models and facilitating amyloidosis and tauopathies in AD models, while restoring PE homeostasis in the brain alleviates cognitive impairment. Mechanistically, our validation demonstrates that PEhigh flux induces autophagic, immunological, and membrane remodeling processes, driving T-cell and microglia dysfunction, spatiotemporal disruption of intracellular signaling, and destabilization of critical membrane structures. The potentially convergent mechanisms and divergent details of PE across AD and cancer highlight its multifaceted implications and the druggability of the associated signaling pathways.

overall_design: Each 7~10-week 5XFAD mouse was intravenously administered with 100 µL phosphate-buffered saline (PBS) or 6.55 X 10^9 exosome-enriched EVs with PE-low or PE-high. Phosphatidylethanolamine (PE).

first: Jianting

last: Sheng

first: Stephen

last: Wong


title: Histone chaperone HIRA and PML are required for SASP expression but not for proliferation arrest

first: Peter

overall_design: mRNA profiling in senescent fibroblasts after knocking-down HIRA and PML


title: LAG3 and PD1 synergize on CD8+ T cells to drive T cell exhaustion and hinder autocrine IFN gamma-dependent anti-tumor immunity

status: Public on Aug 07 2024

summary: Combined nivolumab (anti-PD1) and relatlimab (anti-LAG3) have shown enhanced effectiveness in melanoma patients. However, how these two receptors work together to hinder anti-tumor immunity remains unclear. Our study demonstrates that PD1/LAG3-deficient CD8+ T cells with more effectively clearing tumors  and survive longer in melanoma mouse models. These PD1/LAG3-deficient CD8+ T cells have unique transcriptional profiles, broad TCR clonality, and enriched effector-like and interferon-responsive genes, leading to increased IFN gamma release indicating functionality. PD1 and LAG3 together drive T cell exhaustion, with a significant impact on TOX modulation. Mechanistically, autocrine IFN gamma signaling is crucial for enhancing anti-tumor immunity in PD1/LAG3-deficient CD8+ T cells, providing insights into the enhanced efficacy of combined PD1 and LAG3 targeting.

overall_design: We employed single-cell RNA sequencing to profile CD8 cells from polyclonal/pMEL mice, both with and without single or double deficiencies of PD1 or LAG3. This comprehensive approach aimed to gain a deeper understanding of the enhanced efficacy observed in the melanoma model.

first: Lawrence

last: Andrews


title: Microglial heterogeneity in the ischemic stroke mouse brain of both sexes

status: Public on Jul 01 2024

city: Durham

first: Wei

state: United States

address: 300 Duke Street

institute: Duke University

summary: The objective of the current study was to dissect the effect of permanent stroke on the diversity of microglia, the resident immune cells within the brain parenchyma.

overall_design: To characterize microglial diversity after permanent stroke in Tmem119-2A-CreERT2;Ai6 mice in which microglia were labeled with ZsGreen, we sorted ZsGreen positive cells on day 3 after stroke for scRNA-seq analysis. Four samples were analayzed: female_sham, female_stroke, male_sham, and male_stroke,  (F_Sham, F_Stroke, M_Sham, M_Stroke). Each sample were pooled from 4 mice.

first: Angela

last: del Aguila

first: Vaibhav

last: Jain


title: Activation-induced cytidine deaminase induces DNA demethylation and expression of Ninjurin-2 gene

status: Public on Jun 30 2024

city: Kurume City

first: Toshiyuki

last: Okada

address: 67 Asahi-machi

department: Department of Immunology,

institute: Kurume University School of Medicine

summary: This study investigated the epigenetic role of AID induced by inflammation. AID, which binds to the promoter region of NINJ2, induces DNA demethylation. Thus, these findings suggest physiological roles of AID expression in colonic epithelial cells.

overall_design: DLD-1 cell line was transfected with a pEGFP-N1 empty vector (control#2) or an AID-Myc/his tag vector (AID-OP#1) to identified AID-induced genes.

first: Toshyuki

first: Yusuke

last: Toyoda

first: Atsushi

last: Mizoguchi

first: Shigeaki

last: Saitoh


title: Next Generation Sequencing Facilitates Quantitative Analysis of GSL1 function

status: Public on Jun 28 2024

city: Atlanta

first: Liwei

last: Lang

state: GA

address: 1701 Uppergate Drive

institute: Emory University

summary: The aim of this study is to investigate the influence of GLS1 on the transcriptome profile of human head and neck squamous cell carcinoma (HNSCC)

overall_design: Investigation of mRNA profiles in human head and neck squamous cell carcinoma with or without GLS1 knockdown

first: Yong

last: Teng


title: Immunologic drivers of immune checkpoint inhibitor therapy myocarditis, fatality and anti-tumor response in cancer patients

status: Public on Jun 22 2024

city: Charlestown

first: Neal

middle: Patrick

last: Smith

address: 149 13th Street

institute: Massachusetts General Hospital

summary: Immune checkpoint inhibitors (ICIs) can offer remarkable benefits to patients with cancer, but these agents can cause morbid and potentially fatal immune-related adverse events (irAEs), the most lethal of which is ICI-related myocarditis (irMyocarditis). The pathogenesis of irMyocarditis and its relationship to anti-tumor immunity remain poorly understood. We sought to define how immune cell trafficking between heart, tumor and blood contributes to irMyocarditis pathogenesis and fatality by leveraging single-cell (sc)RNA-seq coupled with T cell receptor (TCR) sequencing, microscopy, and proteomics analysis of 28 irMyocarditis patients and 23 controls. Our analysis of ~284,360 cells from the heart and blood specimens identified enrichment of cytotoxic T-cell subsets, inflammatory macrophage subsets, conventional dendritic cells (cDCs), and fibroblasts in the heart that accompany the upregulation of potentially targetable, pro-inflammatory transcriptional programs. Expanded TCR clones enriched in irMyocarditis are largely distinct from those in paired tumors, suggesting distinct mechanisms between anti-tumor immune response and irMyocarditis. We also identified circulating biomarkers of fatality, including decreased circulating CD4+ T cells, decreased cDCs, and the presence of cardiac-expanded TCRs in a circulating, cycling CD8+ T cell population. Collectively, these findings highlight critical biology driving disease pathogenesis and nominate putative biomarkers and tailored therapeutic interventions for patients with irMyocarditis.

overall_design:
Heart samples were taken through endomyocardial biopsies or autopsy from patients receiving an ICI for cancer. Additionally, patients had PBMCs collected at multiple timepoints through their course of treatment. Samples were then used for scRNA-seq.

UPDATE:
[Jul-07-2027] The 'group' for GSM7133702 was corrected from "irMyocarditis" to "control".

>>>Submitter states: The raw data will be submitted via dbGaP as it needs to be under controlled access.<<<

first: Isabela

last: Kernin

first: Steven

last: Blum

first: Daniel

last: Zlotoff

first: Alexandra-Chloe

last: Villani


title: Wnt/Wingless signaling promotes lipid mobilization through signal-induced transcriptional repression

status: Public on Jun 18 2024

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

summary: The Wnt/Wingless signaling pathway plays critical roles in metazoan development and energy metabolism, but its involvement in lipid mobilization has remained unclear. Here, we report that canonical Wnt/Wg signaling reduces lipid accumulation in both larval and adult adipocytes, as well as cultured S2R+ cells, in Drosophila. This reduction occurs through promoting lipolysis while concurrently repressing lipogenesis and fatty acid β-oxidation. Leveraging RNA-sequencing and CUT&RUN assays, we have identified a set of Wnt target genes responsible for intracellular lipid homeostasis. Notably, active Wnt signaling directly represses the transcription of these genes, resulting in decreased triglyceride accumulation in lipid droplets, increased lipolysis, and reduced fatty acid β-oxidation. These changes lead to elevated free fatty acids and reduced triglyceride accumulation in adipocytes with active Wnt signaling. Conversely, downregulation of Wnt signaling in the fat body promotes triglyceride accumulation in both larval and adult stages. The attenuation of Wnt signaling also increases the expression of specific lipid metabolism-related genes in larval adipocytes, wing discs, and adult intestines. Collectively, our findings suggest that Wnt signaling-induced transcriptional repression plays an important role in regulating lipid homeostasis by enhancing lipolysis while simultaneously suppressing lipogenesis and fatty acid β-oxidation processes.

overall_design: To gain insights into the molecular mechanism underlying Wnt signaling-stimulated lipid catabolism and reduced lipogenesis, we conducted bulk RNA sequencing (RNA-seq) analyses on dissected larval fat body with specific depletions of Axn or slmb, and BTZ treated animals. To investigate potential direct targets of Wnt signaling, we performed CUT&Run on EGFP tagged Pan.

first: Mengmeng

last: Liu

first: Rajitha-Udakara-Sampath

last: Hemba-Waduge

first: Xiao

last: Li

first: Xiahe

last: Huang

first: Tzu-Hao

first: Xianlin

last: Han

first: Yingchun

last: Wang

first: Jun-Yuan


title: Iterative deep learning-design of human enhancers exploits condensed sequence grammar to achieve cell type-specificity [scRNA-Seq]

status: Public on Jun 14 2024

city: Seattle

first: Christopher

last: Yin

state: WA

address: 3946 W Stevens Wy NE

department: Electrical & Computer Engineering

institute: University of Washington

summary: An important and largely unsolved problem in synthetic biology is how to target gene expression to specific cell types. Here, we apply iterative deep learning to design synthetic enhancers with strong differential activity between two human cell lines. We initially train models on published datasets of enhancer activity and chromatin accessibility and use them to guide the design of synthetic enhancers that maximize predicted specificity. We experimentally validate these sequences, use the measurements to re-optimize the predictor, and design a second generation of enhancers with improved specificity. Our design methods embed relevant transcription factor binding site (TFBS) motifs with higher frequencies than comparable endogenous enhancers while using a more selective motif vocabulary, and we show that enhancer activity is correlated with transcription factor expression at the single cell level. Finally, we characterize causal features of top enhancers via perturbation experiments and show enhancers as short as 50bp can maintain specificity.

overall_design: We transfected a library of synthetic enhancers (R1-MPRA) into two different human cell lines, HepG2 and K562. We quantified enhancer strength at the single cell level and correlate enhancer activity with transcriptome analysis.

first: Yin

last: Christopher

first: Castillo-Hair

last: Sebastian

first: Byeon

last: Gun Woo

first: Bromley

last: Peter

first: Meuleman

last: Wouter

first: Seelig

last: Georg


title: Iterative deep learning-design of human enhancers exploits condensed sequence grammar to achieve cell type-specificity [RNA-Seq]

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: We designed 3 plasmid libraries (R1-MPRA, R1-DHS, R2) of synthetic candidate enhancer sequences placed upstream of a minimal promoter (minP) and unique barcode sequence, and transfected them into two different human cell lines, HepG2 and K562. We quantified enhancer strength by sequencing the mRNA of transfected cells as well as the DNA of the plasmid libraries, and calculated a ratio of RNA barcode counts to DNA barcode counts. Two biological replicates of each cell line measurement were obtained.


title: A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer promoter communication

status: Public on Jun 13 2024

city: Montpellier

first: Bernd

last: Schuettengruber

address: 141, rue de la cardonille

institute: Institute de Génétique Humaine

summary: 3D genome folding plays a fundamental role for the regulation of developmental genes by facilitating or constraining chromatin interactions between cis-regulatory elements (CREs). Polycomb response elements (PREs) are a specific kind of CREs involved in the memory of transcriptional states in Drosophila melanogaster. PREs act as nucleation sites for Polycomb group (PcG) proteins, which deposit the repressive histone mark H3K27me3, leading to the formation of a class of topologically associating domain (TADs) called Polycomb domains. PREs can establish looping contacts that stabilize gene repression of key developmental genes during development. However, the mechanism by which PRE loops fine tune gene expression is unknown. Using CRISPR/Cas9 genome engineering, we specifically perturbed PRE contacts or enhancer function and used complementary approaches including 4C-seq, Hi-C, and Hi-M to analyze how chromatin architecture perturbation affects gene expression. Our results suggest that the PRE loop at the dac gene locus acts as a constitutive 3D chromatin scaffold during Drosophila development that forms independently of gene expression states and has a versatile function: it restricts enhancer promoter communication and contributes to enhancer specificity.

overall_design:
Hi-C experiments of wilt type imaginal leg discs and pupae or imaginal leg discs carrying a gypsy insertion and/or enhancer deletion
4C-seq experiments of wilt type embryos, imaginal leg discs or pupae or embryos, imaginal leg discs or pupae carrying a gypsy insertion and/or enhancer deletion
Cut&Run experiments of wilt type imaginal leg discs or imaginal leg discs carrying a gypsy insertion and/or enhancer deletion

first: Sandrine

last: Denaud

first: Marion

last: Bardou

first: Giorgio-Lucio

last: Papadopoulos

first: Stefan

last: Grob

first: Marco

last: Di Stefano

first: Gonzalo

last: Sabaris

first: Marcelo

last: Nollmann

first: Giacomo

last: Cavalli


title: The role of adipocyte lipolysis during dermal fibrosis

status: Public on Jun 01 2024

city: New Haven

first: Elizabeth

middle: Ann

last: Caves

state: Connecticut

address: 260 Whitney Ave

department: Molecular, Cellular and Developmental Biology

institute: Yale University

summary: Lipolysis is an early event during derma; fibrosis progression. We wanted to see how the loss of lipolysis impacted cell dynamics within the

overall_design: The mouse model, AdiCreER; mT/mG; Atglfl/fl, are able to conditionally knock out adipocyte lipolysis. Male mice between 6-8 weeks are shaved and receive 1 dose of topical tamoxifen on the back skin 2 days prior to injections. Mice were then injected subcutaneously for 5 days with either PBS or Bleomycin Sulfate. Back skin was collected and dissociated and submitted for scRNA-sequencing.

first: Valerie

last: Horsley


title: Transcriptome analysis of circulating circRNA expression profiles from patients with coronary artery disease and healthy controls

city: Hangzhou

first: Zhicheng

last: Pan

address: 79 Qingchun Road

department: Department of Cardiology

institute: The First Affiliated Hospital, Zhejiang University School of medicine

summary: Transcriptome analysis of Peripheral Blood Mononuclear Cells (PBMC) samples from nine participants, including three in the Ctrl group, three in the (stable angina) SA group, and three in the acute coronary syndrome (ACS) group, was performed.

overall_design: We included 9 participants into our study: 3 healthy controls without coronary artery stenosis confirmed by coronary angiography, 3 patients diagnosed with stable angina, 3 patients diagnosed with acute coronary syndrome. PBMCs were isolated from whole blood samples of these patients. Total RNA was extracted from the PBMC samples. The integrity of the extracted RNA was assessed. For library construction, 1 μg of the total RNA was utilized. To remove rRNA, the RiboZero Magnetic Gold Kit was employed. Subsequently, the KAPA Stranded RNA-Seq Library Prep Kit was used to construct the RNA-sequencing library. Sequencing was performed on an Illumina HiSeq 4000 system using the HiSeq 3000/4000 SBS kit (Illumina).


title: Impaired Taurine Transport Contributes to Bronchopulmonary Dysplasia: A Systems Biology Analysis

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
Background: Metabolic dysregulation has been implicated in bronchopulmonary dysplasia development. Taurine is an essential amino acid for neonates and is critically involved in glucose and fatty acid metabolism. Neonatal tissue obtains taurine mainly through the taurine transporter. The biological role of taurine in neonatal lung development has never been explored. As glucose metabolism mechanistically modulates angiogenesis and angiogenesis is the central player for neonatal lung development, we hypothesize that taurine depletion contributes to bronchopulmonary dysplasia development.   Results: Although most genes and proteins for oxidative phosphorylation were enriched in hyperoxia pup lungs, the complex-1 activity decreased. The decrease in taurine-dependent complex-1 core subunits, ND5 and ND6, in hyperoxia lungs reasonably explained the discrepancy. Metabolomics analysis demonstrated decreased lung taurine with increased blood taurine of hyperoxia pups, compatible with the decreased taurine transporter expression. Decreased glycosylation and increased degradation explained the decreased taurine transporter expression. The results of the complementary study using tunicamycin and tauroursodeoxycholic acid studies supported that endoplasmic reticulum stress contributes to decreased taurine transporter expression in hyperoxia lungs. The effect of taurine treatment on reducing endoplasmic reticulum stress, increasing ND5 and ND6 expression, angiogenesis, and, most importantly, the alveolar formation is beneficial to hyperoxia rat pups.
Conclusion: Hyperoxia exposure causes endoplasmic reticulum stress, increases taurine transporter degradation, and leads to taurine depletion in the neonatal lungs with subsequent metabolic dysregulation, resulting in poor alveolar formation of the neonatal lungs. We provide evidence of the never-being-reported protective role of taurine in neonatal lung development. The fact that taurine attenuates the severity of bronchopulmonary dysplasia by reducing hyperoxia-induced endoplasmic reticulum stress and mitochondrial dysfunction indicates its therapeutic potential for treating bronchopulmonary dysplasia.

overall_design: Sprague-Dawley rat pups exposed to >90% oxygen (hyperoxia) were used as the bronchopulmonary dysplasia phenotype between postnatal days one and ten. Some rat pups received tunicamycin or tauroursodeoxycholic acid to study the effect of endoplasmic reticulum stress. Taurine was used as rescue therapy. Plasma and lungs were obtained at postnatal day ten for multiomics analyses.  The dam and pups were cared for in either >90% oxygen chamber (HOX) or room air (NOX) from postnatal day 1 to day 10 (P1-P10). An oxygen sensor continuously monitored oxygen concentrations (Reming Bioinstruments Co., Redfield, NY). Pups were then recovered in room air between P11-P21. Pups were caged with nursing dams while the dams were alternated between oxygen environments to diminish oxygen toxicity. Lungs obtained at P21 from both NOX and HOX groups were used for transcriptomic studies using Affymetrix chips, histology, and immunoblots.

first: Xigang

last: Jing

first: Yekai

last: Wang

first: Mark

last: Roethle

first: Shuang

last: Jia

first: Michelle

last: Teng

first: Ganesh

last: Konduri

first: Kirkwood

middle: A

last: Pritchard Jr.

first: Billy

last: Day

first: Yan

last: Jin

first: Stephen

last: Naylor

first: Haiwaei

last: Gu

first: Jainhai

last: Du

first: Ru-Jeng


title: SLAM-seq profiling of IMR-90 SV40-T Cells expressing wild-type and mutant H2B

status: Public on Mar 02 2026

first: Peter

last: Adams

summary: Nucleosomes are the minimal repeating units of chromatin. Their dynamic assembly and disassembly underpins chromatin organization and genome regulation. However, how intrinsic nucleosome stability contributes to higher-level yet fundamental cellular and organismal properties—such as preservation of cell identity, lineage specification, stress resilience and healthy aging—remains unclear. To address this, we tested the impact of intrinsic nucleosome instability across multiple cell, tissue and organismal models by introducing histone mutants that weaken histone–histone interactions. Despite no overt effects on global chromatin accessibility, DNA damage, steady-state proliferation or cell viability, nucleosome instability impaired lineage-specific gene expression programs, altered lineage specification and activated intrinsic inflammatory and stress pathways in a manner reminiscent of aging in mouse tissues and human cells. Consistently, in Caenorhabditis elegans and Drosophila melanogaster, nucleosome instability accelerated the onset of age-associated transcriptional alterations and functional decline in Caenorhabditis elegans and Drosophila melanogaster, and . At the cellular level, nucleosome instability also heightened cellular sensitivity vulnerability to exogenous perturbations—including environmental, epigenetic and mitotic stress—in human cells and Saccharomyces cerevisiaeyeast.  These cross-species findings identify nucleosome stability as an evolutionarily conserved epigenetic safeguard that preserves cell identity and stress resilience, sustaining organismal function and longevity.

overall_design: IMR-90 SV40-T cells expressing WT or mutant H2B were labeled with 100 µM 4sU for 6 hours. RNA was extracted and alkylated with iodoacetamide (IAA). Libraries were prepared using Lexogen QuantSeq kits and sequenced on NovaSeq 6000. Reads were trimmed with Trimmomatic, aligned to GRCh38 and analyzed using SLAM-DUNK for mutation calling and quantification. DESeq2 was used to identify transcriptionally regulated transcripts based on T>C conversion rates.

first: Hiroshi

last: Tanaka

first: Xue

last: Lei


title: HER2-driven mammary tumorigenesis enhances bioenergetics despite reductions in mitochondrial content

status: Public on Feb 28 2026

city: Hamilton

first: Dongdong

state: Ontario

address: 1200 Main Street West

department: Department of Medicine

country: Canada

institute: McMaster University

summary: It is now recognized that mitochondria play a crucial role in tumorigenesis; however, it has become clear that tumor metabolism varies significantly between cancer types. The failure of recent clinical trials aimed at directly targeting tumor respiration through oxidative phosphorylation inhibitors underscores the critical need for further studies providing an in-depth evaluation of mitochondrial bioenergetics. Accordingly, we comprehensively assessed the bulk tumor and mitochondrial metabolic phenotype in murine HER2-driven mammary cancer tumors and benign mammary tissue. Transcriptomic and proteomic profiling revealed a broad downregulation of mitochondrial genes/proteins in tumors, including OXPHOS subunits comprising Complexes I-IV. Despite reductions in tumor mitochondrial proteins, mitochondrial respiration was several-fold higher compared to benign mammary tissue, which persisted regardless of normalization method (wet weight, total protein content, and when corrected for mitochondrial content). This upregulated respiratory capacity could not be explained by OXPHOS uncoupling, suggesting HER2 signaling regulates intrinsic mitochondrial bioenergetics. In further support, lapatinib, an EGFR/HER2 tyrosine kinase inhibitor, attenuated mitochondrial respiration in NF639 murine mammary tumor epithelial cells. Together, this data highlights that the typical correlation between mitochondrial content and respiratory capacity may not apply to all tumor types and implicates HER2-linked activation of mitochondrial respiration supporting tumorigenesis in this model.

overall_design: Murine MMTV-Neu-NDL-YD5 HER2-driven tumors and benign mammary tissue were compared (no treatment).

first: Sara

last: Frangos

first: Henver

last: Brunetta


title: Bulk mRNA-seq analysis of mouse skeletal muscle, heart and liver expressing wild-type and mutant H2B

overall_design: Mouse skeletal muscle, heart and liver were transduced with AAV9 vector expressing wild-type or mutant H2B. After four weeks, tissues were collected. Total RNA was isolated, sequenced and analyzed to identify gene expression changes.


title: Epigenetic Memory of Intestinal Epithelial Cells in Inflammatory Bowel Disease [RNA-seq]

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

summary: The pathogenesis of Inflammatory Bowel Disease (IBD) is a multifactorial process characterized by inflammation and damage to the intestinal barrier, which is made up of intestinal epithelial cells (IECs). Since IBD is a remitting and relapsing disease, we postulated that epigenetic memory exists in IECs following an inflammatory encounter. The objective of this study was to uncover the mechanisms of a retained altered IEC epigenetic landscape in the context of IBD. We have generated adult stem cell organoids (containing all epithelial cell lineages) from patients with Ulcerative Colitis (UC); two organoid lines per patient were propagated: 1) from a site of active inflammation and from the same patient, and 2) a never inflamed region. We performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and bulk RNA-seq on each organoid line. Established bioinformatic pipelines were used to determine significantly different chromatin accessibility and differentially expressed genes. Functional significance of the open chromatin regions was assessed by pathway and motif analysis. Treatment with TNF-alpha (10 and 100ng/ml) for 24 hours on the organoids was performed to determine re-activation of pro-inflammatory genes. This study shows for the first time that epithelial cells derived from organoids of IBD patients retain an epigenetic memory of the prior inflammatory state.

first: Brooke

last: Druliner

first: Feda

last: Hamdan


title: Kidney gene expression dynamics during torpor-arousal cycles in hibernating 13-lined ground squirrels

city: Aurora

first: Austin

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: RNA-seq libraries were prepared from replicate samples (n=5-6) from six physiolocial groups to capture key changes in circannual hibernation.

overall_design: RNA-seq libraries were prepared from replicate samples (n=5-6) in the kidney from six physiological groups to capture key changes in circannual hibernation.

first: Sandra

middle: L

last: Martin


title: Mis-splicing derived neoantigens and cognate T cell receptors in splicing factor mutant leukemias

status: Public on May 22 2024

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

summary: Mutations in RNA splicing factors are prevalent across cancers and generate recurrently mis-spliced mRNA isoforms. Here we identified a series of bona fide neoantigens translated from highly stereotyped splicing alterations promoted by neomorphic, leukemia-associated somatic mutations in the splicing machinery. We utilized feature-barcoded peptide-MHC dextramers to isolate neoantigen-specific T cell receptors (TCR) from both healthy donors and patients with leukemia. While circulating neoantigen-specific CD8+ T cells were identified in patients with active disease, they were dysfunctional with reduced inflammatory response gene signatures. In contrast, donor CD8+ T cells with tumor-reactive TCRs were present following curative allogeneic hematopoietic cell transplant. T cells engineered with TCRs recognizing an SRSF2 mutant-induced neoantigen in CLK3 resulted in specific recognition and cytotoxicity of SRSF2 mutant leukemia. These data identify RNA mis-splicing derived neoantigens and neoantigen-specific TCRs across patients and provide proof-of-concept to genetically redirect T cells to public mis-splicing derived neoantigens in myeloid leukemias.

overall_design: We isolated bulk T cells from patient PBMCs via negative selection and stained the T cells with a dextramer pool. We sorted live, CD3+, CD8+ dextramer+ cells and performed RNA-, TCR-, and dextramer feature barcode sequencing (Fig. S5A). For certain samples where dextramer+ cell numbers were limiting, live CD3+ CD8+ dextramer- cells were also sorted, stained with cell hashing antibodies, and doped into the dextramer+ populations. Using this approach, we single-cell profiled CD8+ T-cells from nine samples across five distinct HLA-A*02:01+ SRSF2 mutant myeloid leukemia patients (Fig. 5A, Fig.S5B, and Table S3) yielding 75,343 high-quality T cells.

first: Won

last: Kim

first: Edie

last: Cross

first: Emma

last: de Neef

first: Inaki

last: Etxeberria

first: Erich

last: Sabio

first: Eric

last: Wang

first: Sydney

middle: X

last: Lu

first: Andrea

last: Belleville

first: Nina

last: Fox

first: Cynthia

last: Castro

first: Pu

last: Zhang

first: Takeshi

last: Fujino

first: Jennifer

last: Lewis

first: Beatrice

first: Robert

middle: F

last: Stanley

first: Susan

last: Dewolf

first: Ronan

last: Chaligne

first: Priya

last: Koppikar

first: Jeffrey

last: Molldrem

first: Matthew

last: Gigoux

first: Taha

last: Merghoub

first: Anthony

last: Daniyan

first: Benjamin

last: Greenbaum

first: Christopher

last: Klebanoff

middle: K

last: Bradley

first: Omar

last: Abdel-Wahab


title: Single cell RNA sequencing data of brain myeloid cells after experimental stroke

city: Edinburgh

first: Barry

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

summary: Acute stroke triggers extensive changes to myeloid immune cell populations in the brain that may be targets for limiting brain damage and enhancing repair. Immunomodulatory approaches will be most effective with precise manipulation of discrete myeloid cell phenotypes in time and space. Here, we investigate how stroke alters mononuclear myeloid cell composition and phenotypes at single-cell resolution and key spatial patterns. Our results show that multiple reactive microglial states and monocyte-derived populations contribute to an extensive myeloid cell repertoire in post-stroke brains. We identify important overlaps and distinctions among different cell types/states that involve ontogeny- and spatial-related properties. Notably, brain connectivity with infarcted tissue underpins the pattern of local and remote altered cell accumulation and reactivity. Our discoveries suggest a global but anatomically governed brain myeloid cell response to stroke that comprises diverse phenotypes arising through intrinsic cell ontogeny factors interacting with exposure to spatially organized brain damage and neuro-axonal cues.

overall_design: Distal middle cerebral artery occlusion was performed on three C57BL/6 mice using electrocoagulation. Mononuclear phagocytes (CD45+CD3-CD19-Ly6G-) were isolated from ipsilateral and contralateral brain regions using FACs at day three. Samples obtained from each mouse were individually barcoded with hash-tag oligonucletide-conjugated CD45 antibodies and then multiplexed for 10x Chromium single cell RNA sequencing with feature barcoding technology.

first: Anirudh

last: Patir

first: Jack

last: Barrington


title: Single nucleus RNA sequencing analysis of vagal sensory neurons

status: Public on May 10 2024

city: bronx

first: Young-Hwan

last: Jo

state: NY

address: 1300 Morris Park ave, Forchheimer 505B

institute: Albert Einstein college of Medicine

summary: We report that molecularly distinct populations of vagal sensory neurons would play a role in causing differences in metabolic homeostasis between the sexes.

overall_design: Examination of the molecular identity of vagal sensory neurons in female and male mice


title: Analysis of gene expression in Mel Z cells grown on MM, MP, and with MMI

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

institute: Engelhardt Institute of Molecular Biology

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

overall_design: Refer to individual Series


title: Analysis of gene expression in Mel Z cells grown on Matrigel (MM).

summary: RNA-Seq procedure was used for analysis of expression in melanoma cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with  BioAnalyser and  RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 14.8 millions of reads were generated for each sample.

overall_design: Analysis of gene expression in Mel Z cells grown on plastic (MP), Matrigel (MM), and on Matrigel in the presence of inhibitor(MMI).

first: Yuri

middle: V

last: Kravatsky

first: Amalia

last: Vartanian


title: Mucosal immune response against equine herpesvirus type 1

status: Public on May 08 2024

city: Ithaca

first: Bettina

last: Wagner

address: 240 Farrier Drive

department: Population Medicine and Diagnostic Sciences

institute: Cornell University

summary:
To investigate pre-existing mucosal immunity in equine herpesvirus type 1 (EHV-1) immune and non-immune horses during experimental viral challenge.
RNAseq was performed on nasal mucosal swab samples from immune and non-immune horses from  pre (d-2), early (d1pi and d3pi), mid (d8pi and d10pi), and late (d18pi) infection.

overall_design: Comparative gene expression analysis of immune and non-immune horses throughout viral challenge.

first: Camille

last: Holmes

first: Susanna

last: Babasyan

first: Naya

last: Eady

first: Christiane

last: Schnabel


title: ReDD: RNA editing detection by direct RNA sequencing and deep learning

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

summary: Many previous studies, including the Next Generation Sequencing (NGS)-based ones, have shown the critical roles of RNA editing in biomedicine. Direct RNA sequencing emerges as another powerful technique to advance the understanding of RNA editing by new paradigms, especially in single-molecule and long-range characterization. The urgent gap is the accurate and robust identification of RNA editing at the single-molecule and single-nucleotide resolution from direct RNA sequencing. This is challenging due to the inherent nature of the context-dependence on the raw signals, which requires enormous training data with considerable diversity. Here we propose two coupled measures to address them: 1) an abductive deep learning strategy implemented as the software ReDD fully utilizes the widely accessible NGS-based RNA editing data as indirect labels of direct RNA sequencing to achieve the detection at the single-molecule level; 2) a cloud-based platform Argo-ReDD serves as a central database for assembling large and diverse data from the community to continuously train the abductive deep learning model, which also meets the community demand of a user-friendly way to perform RNA editing analyses, such as co-occurrence analysis, quantitative analysis and gene isoform-resolved analysis, based on the specific information from direct RNA sequencing.

overall_design:
We generated definitive endoderm and pharyngeal endoderm, and primordial germ cell-like cells from human ESC, using the in vitro differentiation systems we have recently developed. We also generated HEK293T ADAR1(E912A/E912A) cells using the E912A mutation method we have previously developed.We further transfected the E912A cells with the ADAR2 gRNAs of "TGTAGAAACACTTATCACCT" and "ACCATCTTTACCTGGCAGTT", and selected single clone cells to create the HEK293T double mutant cells with ADAR1(E912A/E912A) and ADAR2(-/-).
We generate long-read RNA-seq data using Oxford Nanopore Technologies (ONT) direct RNA sequencing (dRNA-ONT) protocols with one replicate and short-read RNA-seq data using Illumina with three replicates.
We detects the A-to-I RNA editing sites in HEK293T, H1 and H9 cells by ReDD, our in-house software on the direct RNA sequencing data.

first: Yunhao

last: Wang

first: Roberta

last: Sala

first: Andrea

last: Cipriano

first: Vittorio

last: Sebastiano

first: Shi-Bin

last: Hu

first: Jin

last: Li

first: Kin