overall_design: We profiled chromatin accessibility in fibroblast cell lines derived from age- and sex-matched healthy and Bloom Syndrome individuals. During the process of characterizing the differential signals, we noticed that copy number differences at local regions between the samples skew the differential analysis towards the sample with a higher copy number. We explored the impacts of copy number variation on the differential analysis and solutions to segregate the differential signals driven by copy number variation.


title: Distinct Cellular Mechanisms Underlie Chemotherapies and Their Combinations with PD-L1 Checkpoint Inhibitor in Triple-Negative Breast Cancer [TNBC]

status: Public on Feb 12 2025

city: Beijing

first: Yuanyuan

last: Zhang

state: Beijing

address: Panjiayuan nanli #17, Chaoyang District

department: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

country: China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

type: Expression profiling by high throughput sequencing

summary: The combination of immune checkpoint blockade (ICB) and chemotherapy holds promise for treating triple-negative breast cancer (TNBC), yet the underlying mechanisms remain incompletely understood. Here, we integrated previously published and newly generated single-cell RNA sequencing (scRNA-seq) data to investigate the tumor immune microenvironment (TIME) in advanced TNBC patients receiving various therapies, including paclitaxel, nab-paclitaxel, and their combinations with an anti-PD-L1 antibody atezolizumab. Notably, compared to atezolizumab plus paclitaxel, atezolizumab plus nab-paclitaxel primarily rewired TCF7+ stem-like effector memory CD8 T cells (Tsem) and CD4 follicular helper T (Tfh) cells. Nab-paclitaxel, but not paclitaxel, predominantly modulated the myeloid compartment, expanding mast cells and pro-inflammatory macrophage subsets. Our analyses in human TNBC and murine models highlighted the crucial role of mast cells in orchestrating anti-tumor immune responses, likely by recruiting and activating T cells and B cells. In vivo experiments demonstrated that activating mast cells alongside PD-L1 blockade significantly attenuated tumor progression, suggesting mast cells as a promising adjunct for enhancing ICB therapy efficacy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
In this study, we obtained 78 tumor biopsy samples derived from 44 TNBC patients. Within this cohort, 16 patients received nab-paclitaxel plus atezolizumab, 12 received nab-paclitaxel, 9 received paclitaxel plus atezolizumab, and 7 received paclitaxel.

***************************************************************
Submitter states that missing raw data will be uploaded to China Genomic Sequence Archive (GSA), according to the Regulations on the Management of Human Genetic Resources in China.
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first: Hongyan

last: Chen

first: Hongnan

last: Mo

first: Ning

last: Zhao

first: Binghe

last: Xu

first: Zemin

first: Zhihua

last: Liu

first: Fei

last: Ma


title: The myoblast methylome: Multiple types of associations with chromatin and transcription

status: Public on Feb 13 2025

city: Ipswich

first: Sriharsa

last: Pradhan

state: MA

address: 240 County Road

country: USA

institute: New England Biolabs

type: Methylation profiling by high throughput sequencing

summary: Myoblasts are critical progenitor cells for the prenatal formation of skeletal muscle (SkM) as well as in postnatal repair of SkM. This study examined the epigenomics and transcriptomics of human myoblasts  vs. those of diverse other cell and tissue types from both global genomic and single-gene perspectives. Using enzymatic methyl-seq (EM-seq) and whole-genome bisulfite sequencing (WGBS) of myoblast DNA and available WGBS profiles of other cell cultures, we determined myoblast differentially methylated regions (DMRs). We also examined several DMRs in reporter gene assays. Among the unusual findings was the positive association of promoter-adjacent hypermethylation in myoblasts with transcription turn-on for some genes (e.g., SIM2 and TWIST1), but at down-modulated levels. In contrast, some genes, like the brain-specific OLIG2, were silent and embedded in repressed chromatin in myoblasts and many diverse cell populations but displayed myoblast-specific hypermethylated promoters. OLIG2 exhibited binding of the myogenic MYOD transcription factor in its vicinity. One OLIG2-downstream MYOD+ site overlapped enhancer chromatin in myotubes. These findings suggest that OLIG2 silencing only by repressive chromatin is insufficient in myoblasts without the addition of DNA hypermethylation. The numerous hypomethylated DMRs at enhancer chromatin in myoblasts were bound by MYOD much more frequently than by CTCF. Combined with previous studies, our results suggest a more prevalent role for MYOD than for CTCF in organizing transcription-enhancing chromatin interactions at hypomethylated regions. We also found that myoblast-hypomethylated enhancer chromatin enriched in H3K36me3 was much more likely to be associated with genes preferentially expressed in myoblasts than were such regions without H3K36me3 enrichment. Therefore, there may be a special role in gene upregulation for the regional combination of DNA hypomethylation with H3K27ac, H3K4me1, and H3K36me3 enrichment. The unusual relationships between epigenetics and gene expression that we observed need further study in the SkM lineage to better understand fine-tuning of muscle differentiation and diseases.

overall_design: DNA was purified from non-transformed myoblast primary cultures derived from quadriceps biopsies of control individuals (Tsumagari et al., 2013), namely, CM1 (42-year-old female), CM3 (46-year-old male), and CM6 (45-year-old male). Cell cultures had been carefully generated and passaged in collaboration with Rabi Tawil (Tsumagari et al., 2011). Each batch of myoblasts used for DNA methylation analysis was checked for >90% purity by desmin immunostaining because fibroblast-like contaminating cells can easily outgrow myoblasts and give misleading methylome results (Chandra et al. 2015). WGBS was performed on CM3 using standard protocols (Chen F, Zhang G, et al. 2016). Methylation profiling of CM3, CM1, and CM6 was done using enzymatic methyl-seq (EM-seq) (Vaisvila et al. 2021). This process involved enzymatic oxidation of 5mC and 5hmC (by TET2), providing protection from further deamination by APOBEC3A while unmethylated cytosine are deaminated to uracil. Briefly, 0.2 µg of DNA was used to prepare EM-seq libraries in duplicate. The libraries were then cleaned using NEBNext® sample selection beads, pooled, and diluted to 1.5 nM for sequencing on a NovaSeq 6000(Illumina).

first: Chaithanya

last: Ponnaluri

first: Pierre-Olivier

last: Estève

first: Melanie

last: Ehrlich

first: Sagnik

last: Sen


title: FBXW7 Mutations Reprograms Glucose Metabolism by Activating the ETV6-GLUT Axis in Endometrial Cancer

status: Public on Feb 11 2025

city: Shanghai

first: Siqi

last: Fei

address: No. 2005, Songhu Road

institute: Fudan University

summary: Endometrial cancer (EC) is associated with metabolic reprogramming, driven in part by mutations in FBXW7, a key tumor suppressor. In this study, we reveal that FBXW7 regulates glucose metabolism by targeting ETV6 for ubiquitination and proteasomal degradation. Loss of FBXW7 leads to ETV6 stabilization, which in turn upregulates GLUT1 expression and promotes its localization to the plasma membrane. This enhances glucose uptake and reprograms cellular metabolism toward increased aerobic glycolysis and oxidative phosphorylation. Functional studies demonstrate that ETV6 overexpression accelerates EC cell proliferation, colony formation, and tumor growth in vitro and in vivo, effects that are significantly attenuated by pharmacological inhibition or genetic knockdown of GLUT1. Mechanistically, ETV6 directly binds to the GLUT1 promoter via its ETS and PNT domains, driving its transcriptional activation. Furthermore, metabolomics analyses reveal alterations in glycolytic and TCA cycle intermediates, highlighting the broad impact of the FBXW7-ETV6-GLUT1 axis on metabolic pathways. These findings establish ETV6 as a central mediator of FBXW7-deficiency-driven metabolic reprogramming and tumor progression in EC. Targeting GLUT1 provides a potential therapeutic strategy to mitigate ETV6-induced tumor growth and metabolic remodeling in endometrial cancer.

overall_design: RNA seq of  Human Ishikawa Cells in control and experiment ETV6 overexpress group


title: A Novel EBF2 Nonsense Variant Drives Adipose Tissue Fibrosis and Dysfunction in Partial Lipodystrophy Syndrome

status: Public on Feb 17 2025

city: ANN ARBOR

first: Tae-Hwa

last: Chun

state: MI

address: 2800 PLYMOUTH RD, NCRC B10-A186, NCRC B10-A186

department: Internal Medicine

institute: University of Michigan

summary: In vitro disease modeling of an erly B cell factor 2 (EBF2) nonsense variant (EBF2 8:26033143 C>A, c.493G>T, p.E165X) demonstrates that the EBF2 variant impairs adipogenesis causing excess accumulation of extracelluar matrix protein and inflammatory myeloid cells.

overall_design: Human subcutaneous pre-adipocytes were transfected with lentivirus constructs encoding full length EBF2 (575 aa),  truncated EBF2 variant (aa. 1-164), or empty lentivirus expressing GFP. Bulk RNA-sequencing was performed for those cells after adipogenesis induction along with coontrol cells without lentivirus trasnduction (control_no-lentivirus).

first: Maria

last: Foss-Freitas

first: Weisheng

last: Wu

first: Donatella

last: Gilio


title: Regulation of LEAP2 by insulin and glucagon in mice and humans

status: Public on Feb 10 2025

city: Copenhagen

first: Andreas

last: Constantinou

address: Malov

department: Diabetes Pharmacology, Liver & Gut Biology

country: Denmark

institute: Novo Nordisk

summary: Liver-expressed antimicrobial peptide 2 (LEAP2) is an endogenous antagonist and inverse agonist of the growth hormone secretagogue receptor 1a (GHS-R1a), exhibiting opposing effects on cell signaling, feeding, and hormonal secretion compared to ghrelin. However, despite an emerging interest in LEAP2’s physiology and pharmacology, its endocrine regulation remains unclear. Here, we show that plasma LEAP2 levels decrease significantly upon supraphysiological glucagon infusions during pancreatic somatostatin clamps in humans and that a hypercaloric diet and a sedentary lifestyle for two weeks impair this effect. Moreover, in patients with obesity and type 2 diabetes, plasma LEAP2 levels decrease significantly following glucagon infusion. Additionally, we find that postprandial upregulation of LEAP2 in mice is insulin-dependent. In the postprandial state, insulin receptor antagonism offsets the upregulation of hepatic Leap2expression and plasma LEAP2 levels. Finally, we show that insulin and glucagon receptor-expressing hepatocytes are the primary source of hepatic LEAP2 expression. This coincides with a putative enhancer-like signature bound by insulin- and glucagon-regulated transcription factors at the LEAP2 locus in the liver. Collectively, these findings implicate insulin and glucagonin the regulation of LEAP2 and highlight the need for further investigations into the endocrine mechanisms both upstream and downstream of LEAP2.

overall_design: RNA-seq profiling of the insulin response in HepG2-IGF1R-KO cells in response to insulin in normal or insulin resistant media.


title: Transcriptional profiling of striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Pms1 heterozygous and homozygous mice

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: Cerebral cortex and striatum were isolated from 6-month old Pms1+/- and Pms1-/- mice crossed with the Q140 knock-in (KI) mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Pms1+/-, Q140 X Pms1+/-, Pms1-/-, and Q140 X Pms1-/-, 8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the cerebral cortex and striatum tissues of 6 months old wild type, Q140, Pms1+/-, Q140 X Pms1+/-, Pms1-/-, and Q140 X Pms1-/- mice. N = 16 per group (8M/8F)

first: William

last: Yang

last: Wang


title: Airway Organ Tissue Equivalent (OTE) Platform for Modeling Chlorine Gas Toxicology.

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

institute: Wake Forest School of Medicine

summary: The purpose of this study was to assess gene expression changes in airway OTE tissues following chlorine exposure (CE).

overall_design: OTEs were exposed to medical air (MA) or 20 ppm chlorine gas (Cl2) for 30 min. At 0, 6, 12 or 24 hours post-exposure, OTEs were collected and snap-frozen in liquid nitrogen for gene expression studies.

first: Sean

middle: V

last: Murphy

first: Anthony

last: Atala

first: Kimberly

middle: D

last: Reeves

first: Hannah

last: Ainsworth

first: Laura

middle: A

last: Cox

first: Carl

last: Langfeld


title: SUV39H1 inhibition by Chaetocin targets stemness and oncogenic networks and synergizes with ONC201 against Diffuse intrinsic pontine gliomas [RNA-seq]

status: Public on Feb 08 2025

city: Cincinnati

first: Richard

last: Lu

state: Ohio

institute: CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER

summary:
To investigate Chaetocin impact on Diffuse intrinsic pontine gliomas treatment
We then performed gene expression profiling analysis using data obtained from RNA-seq of Chaetocin treatment and SUV39H1 knockdown in SU-DIPG36 cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  control SU-DIPG36 cells, Chaetocin treatment  cells and  SUV39H1 knockdown cells

first: Yunfei

last: Liao

first: Dazhuan

last: Xin


title: Phenotypic complexities of rare heterozygous neurexin-1 deletions

city: New York

first: Yu

last: Fan

state: NY

address: 1425 madison Ave

institute: Icahn school of medicine at mount sinai

summary: Given the large number of genes significantly associated with risk for neuropsychiatric disorders, a critical unanswered question is the extent to which diverse mutations --sometimes impacting the same gene-- will require tailored therapeutic strategies. Here we consider this in the context of rare neuropsychiatric disorder-associated copy number variants (2p16.3) resulting in heterozygous deletions in NRXN1, a pre-synaptic cell adhesion protein that serves as a critical synaptic organizer in the brain. Complex patterns of NRXN1 alternative splicing are fundamental to establishing diverse neurocircuitry, vary between the cell types of the brain, and are differentially impacted by unique (non-recurrent) deletions. We contrast the cell-type-specific impact of patient-specific mutations in NRXN1 using human induced pluripotent stem cells, finding that perturbations in NRXN1 splicing result in divergent cell-type-specific synaptic outcomes. Via distinct loss-of-function (LOF) and gain-of-function (GOF) mechanisms, NRXN1+/- deletions cause decreased synaptic activity in glutamatergic neurons, yet increased synaptic activity in GABAergic neurons. Reciprocal isogenic manipulations causally demonstrate that aberrant splicing drives these changes in synaptic activity. For NRXN1 deletions, and perhaps more broadly, precision medicine will require stratifying patients based on whether their gene mutations act through LOF or GOF mechanisms, in order to achieve individualized restoration of NRXN1 isoform repertoires by increasing wildtype, or ablating mutant isoforms. Given the increasing number of mutations predicted to engender both LOF and GOF mechanisms in brain disorders, our findings add nuance to future considerations of precision medicine.

overall_design: scRNA-seq was performed on 4-6 pooled 6-month-old organoids per donor line, per condition (hCS or hSS) for a total of 48 organoids. A minimum of 10,000 dissociated cells were submitted for sequencing.

first: Michael

middle: B

last: Fernando

first: Yanchun

last: Zhang

first: Alex

last: Tokolyi

first: Aleta

middle: N

first: Sarah

middle: K

last: Kammourh

first: Peter

middle: M

last: Deans

first: Sadaf

last: Ghorbani

first: Ryan

last: Onatzevitch

first: Adriana

last: Pero

first: Christopher

last: Padilla

last: Williams

first: Erin

last: Flaherty

first: Iya

last: Prytkova

first: Lei

last: Cao

first: David

last: Knowles

first: Gang

last: Fang

first: Paul

last: Slesinger

first: Kristen

middle: J

last: Brennand


title: Sleep need driven oscillation of glutamatergic synaptic phenotype

city: Los Angeles

first: Genevieve

last: Konopka

state: CA

address: 650 Charles Young Drive South, 73-214 CHS

department: Neurobiology

institute: UCLA David Geffen School of Medicine

summary: The response to sleep loss, induced by experimental sleep deprivation (SD), provides insight into the function of sleep. Earlier observations have shown an overall increase in synaptic strength and number of cortical, glutamate, AMPA receptor (AMPAR) synapses in response to SD that is recovered by sleep. However, other aspects of glutamatergic transmission, including NMDA receptor mediated neurotransmission and related upstream synaptic regulators of the glutamate synapse function, have not been well examined. Following SD, we report increased AMPA/NMDA ratio in whole cell recordings of frontal cortical (FC) pyramidal neurons of layers 2-3. Additionally, the ratio of silent/active synapse is decreased after SD reflecting decreased silent synapses and plastic potential to convert silent NMDA to active AMPA synapses. All aspects recover with sleep and are associated with differentially expressed genes (DEGs) affecting glutamatergic synaptic phenotype. The DEGs are enriched for a functional group of synaptic shaping cellular components (SSCs) controling glutamate synapse phenotype, overlap with autism risk genes and are primarily observed in a subtype of excitatory pyramidal neurons that project intra-telencephalically (ExIT neurons). Upstream, sleep-related control is suggested by significant enrichment of genes controlled by transcription factor, MEF2c and nuclear HDAC4, a repressor of MEF2c transcriptional activation. Taken together, we propose a functional role of sleep/wake in FC controlling gene expression, regulating an oscillation of glutamate-synaptic phenotypes that facilitates motor learning and training, and if dysfunctional, increases risk for autism.

overall_design: single nuclei RNA-seq on mice with ad-lib sleep and upon sleep deprivation

first: Kaspar

last: Vogt

first: Ashwinikumar

last: Kulkarni

first: Richa

last: Pandey

first: Mantre

last: Dehnad

first: Robert

last: Greene


title: Spatially-structured inflammatory response in the presence of a uniform stimulus: RNAseq screen

status: Public on Feb 07 2025

city: Chicago

first: Elizabeth

middle: R

last: Jerison

state: Illinois

address: 929 E 57th St

department: Physics

institute: University of Chicago

summary: Inflammatory responses occur within the complex spatial context of tissues and organs, and many questions remain about how tissue structure and cellular communication shape their spatiotemporal dynamics. Here, we used single-cell RNA sequencing to screen for genes differentially expressed under LPS (lipopolysaccharide) and vehicle control conditions in epithelial cells in zebrafish larvae. We used this data to choose candidate genes for spatial gene expression analysis.

overall_design: 6 dpf AB zebrafish larvae were immersed in either E3 with 37.5 LPS (P. Aeuruginosa, Sigma), or E3 alone (vehicle control), for 9.5 hours at room temperature. Tail regions from12 larvae per treatment group were pooled and dissociated. The 10X Genomics Chromium 3' platform and reagents (v3.1 kit) was used for cell encapsulation, reverse transcription, and library preparation, according to manufacturer instructions (manual revision D), with 12 cycles of preamplification.


title: Foxp1 developing neocortex

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: Effect of cyclic strain in neurons isolated from dorsal root ganglia

status: Public on Jan 31 2025

city: Pisa

first: Vittoria

last: Raffa

state: Please Select

address: S.S. 12 Abetone e Brennero, 4

department: Department of Biology

country: Italy

institute: Università di Pisa

summary: Organs and cells in our body are continuously exposed to mechanical forces. Neurons, in particular, encounter mechanical stimuli during neurodevelopment, aging, pathological conditions, and routine functions such as homeostatic processes and movement. How do cells, which endure mechanical stress on a daily basis, withstand these forces and remain functional throughout our long lifespans? To maintain their functionality, cells must have evolved self-repair mechanisms that allow them to tolerate stress and repair damage up to a manageable threshold.  This study aims to explore the relationship between damage and repair mechanisms that are crucial for preserving the structural and functional integrity of axons over time. Dorsal Root Ganglia neurons are used as a model system, as they are particularly relevant due to their exposure to daily mechanical movements. An experimental setup has been developed to apply repeated cycles of compression to neurons grown on an elastic substrate. Understanding how neurons respond to mechanical strain and sustain homeostasis will not only deepen our knowledge of the effects of mechanical stress on neurons but also provide valuable insights into restoring cellular functions.

overall_design: Three experimental groups were considered: - control group (CTRL), cells grown on the stimulation device but not subjected to compression cycles; - compressed sample (COMPRESSED), cells grown on the stimulation device, subjected to compression cycles (5% strain, 20 cycles), RNA extraction 6 h post-stimulation; - compressed sample (RECOVERY), cells grown on the stimulation device, subjected to compression cycles (5% strain, 20 cycles), RNA extraction 24 h post-stimulation; Six replicates per condition

first: Coppini

last: Allegra


title: Natural killer cells regulate distinct CD8+ T cell differentiation program in cancer and contribute to resistance against immune checkpoint blockers

status: Public on Feb 01 2025

city: Columbus

first: Sangwoon

last: Chung

address: 2255 Kenny Rd

institute: The Ohio State University

summary: Immune checkpoint blockers (ICBs) targeting the PD-1/PD-L1 axis represent established therapies for many cancers. However, resistance occurs in most patients due to multiple complex immune-suppressive mechanisms in the tumor microenvironment (TME). Natural killer (NK) cells can play effector roles in tumor control, but their impact on T cell dysfunction and ICB efficacy remains controversial. Through genetic and antibody-mediated NK cell depletion, we found that NK cells play negative roles in ICB sensitivity; they further impede CD8+ T cell differentiation toward CD69+ BCL2+ EOMES+ GZMB+ TIM3- GITR- CTLA4- phenotype. Mechanistically, we identified that the retinoic acid receptor alpha (RARα)-dependent differentiation program in CD8+ T cells is hindered due to cytokine competition with NK cells. Finally, we observed that lower frequencies of NK cells correlate with better clinical response to ICBs in cancer patients. These findings suggest a potential avenue for enhancing CD8+ T cell-centered immunotherapy by targeting NK cells.

overall_design: We conducted single-cell sequencing using the 10x Genomics platform to investigate the impact of NK cells on the differentiation program of CD8+ T cells. The MC38 tumor model was utilized, and CD8+ T cells were isolated from tumors of both control and NK cell-depleted mice. Our findings demonstrate that NK cells significantly influence the differentiation trajectory of CD8+ T cells.

first: No-Joon

last: Song

first: Juan

last: Xie

first: Kyeong Joo

last: Jung

first: Yi

last: Wang

first: Joanna

last: Pozniak

first: Niccolò

last: Roda

first: Jean-Christophe

last: Marine

first: Brian

middle: P

last: Riesenberg

first: Hyeongseon

last: Jeon

first: Anjun

last: Ma

first: Nathanael

last: Cox

first: Darren

last: Wethington

first: Kelsi

last: Reynolds

first: Tong

last: Xiao

first: Anqi

last: Li

first: Parker

last: Kronen

first: Nicholas

middle: C

last: Denko

last: Carbone

first: Qin

first: William

middle: E

last: Carson

first: Bethany

last: Mundy-Bosse

first: Christin

last: Burd

first: Jayajit

last: Das

first: Dongjun

first: Zihai


title: SUV39H1 inhibition by Chaetocin targets stemness and oncogenic networks and synergizes with ONC201 against Diffuse intrinsic pontine gliomas [CUT&RUN]

first: Richard

last: Lu

summary: To identify potential direct targets of SUV39H1, we  performed Cut&Run-seq for H3K9me3 and SUV39H1 genomic occupancy

overall_design: Cut&Run for H3K9me3 and Suv39H1 in SU-DIPG13 and SU-DIPG36 cells

first: Dazhuan

last: Xin

first: Yunfei

last: Liao


title: Foxp1 developing neocortex (snRNA-Seq)

first: Genevieve

last: Konopka

summary: The transcription factor Foxp1 is expressed in the neocortex with restricted patterns across development. We used single nuclei-RNA sequencing (snRNA-Seq) to determine the cell-type roles of Foxp1 in control and Foxp1 conditional knock-out animals generated by crossing to Emx1.Cre hemizygous mice. Samples were collected at embyonic day (E)13.5, E16.5, and post-natal day (P)0.5.

first: Ana

last: Ortiz

first: Fatma

last: Ayhan

first: Matthew

last: Harper


title: Non-CG DNA methylation and MeCP2 stabilize repeated tuning of long genes that distinguish closely related neuron types [MERFISH]

city: St. Louis

first: Mati

middle: Tesfaye

last: Nemera

state: Missouri

address: 660 S Euclid Ave

department: Neuroscience

institute: Washington University in St. Louis School of Medicine

summary: The extraordinary diversity of neuron types in the mammalian brain is delineated at the highest resolution by subtle gene expression differences that may require specialized molecular mechanisms to be maintained. Neurons uniquely express the longest genes in the genome and utilize neuron-enriched non-CG DNA methylation (mCA) together with the Rett syndrome protein, MeCP2, to control gene expression, but the function of these unique gene structures and machinery in regulating finely resolved neuron type-specific gene programs has not been explored. Here, we employ epigenomic and spatial transcriptomic analyses to discover a major role for mCA and MeCP2 in maintaining neuron type-specific gene programs that define high resolution cell types. We uncover differential susceptibility to MeCP2 loss in neuronal populations depending on global mCA levels and dissect methylation patterns and intragenic enhancer repression that drive overlapping and distinct gene regulation between neuron types. Strikingly, we show that mCA and MeCP2 regulate genes that are repeatedly tuned to differentiate neuron types at high cellular resolution, including spatially resolved, vision-dependent gene programs in the visual cortex. These repeatedly tuned genes display genomic characteristics, including long length, numerous intragenic enhancers, and enrichment for mCA, that predispose them to regulation by MeCP2. Thus, long gene regulation by the MeCP2 pathway maintains differential gene expression between closely-related neurons to facilitate the exceptional cellular diversity in the brain.

overall_design: We used MERFISH to profile RNA transcripts in MeCP2 KO/+ and WT mouse brains.

first: James

last: Moore

middle: T

first: Rinaldo

last: D'Souza

first: Nicole

last: Hamagami

first: Adam

middle: W

last: Clemens

first: Diana

last: Beard

first: Alaina

last: Urman

first: Victoria

last: Rodriguez Mendoza

first: Yasmin

last: Razia

first: Travis

last: Law

first: John

last: Edwards

first: Harrison

last: Gabel


title: The transcriptomic signature of age and sex is not conserved in human primary myocytes

status: Public on Jan 21 2025

city: Geelong

first: Séverine

last: Lamon

state: VIC

address: 1 Gheringhap St

department: School of Exercise and Nutrition Sciences

country: Australia

institute: Deakin University

summary: Human primary muscle cell (HPMC) lines derived from skeletal muscle biopsies are potentially powerful tools to interrogate the molecular pathways underlying fundamental muscle mechanisms. HPMCs retain their genome in culture, but many endogenous circulating factors are not present in the in vitro environment or at concentrations that do not mirror physiological levels. To address the assumption that HPMCs are valid models of age and sex-specificity in human muscle research, we examined to what extent HPMC lines maintain their source phenotypes in culture. A comparison of the transcriptomic signature of 30 human muscle biopsies (N = 10 young males, N = 10 young females, N = 10 old males) and their corresponding HPMCs indicated a near-complete lack of retention of the genes and pathways that were differentially regulated in vivo when compared to their in vitro equivalent, except for some genes encoded on the Y-chromosome. The diversity of the muscle cell population and the lack of sex- and age-dependent factors in the cellular milieu likely contribute to these observations, which call for caution when using HPMCs as an experimental model of human muscle sex or age. Nuclear single cell sequencing or HMPCs grown in 3D culture as organoids under strain might therefore provide a closer alternative to human muscle tissue.

overall_design: RNASeq profiling of human primary cell lines and tissue samples from the vastus lateralis muscle biopsies of 10 young males (ave age = 23.22), 10 older males (ave age = 67.50), and 10 young females (ave age = 26.90).

first: Megan

last: Soria

first: Ross

last: Williams

first: Annabel

last: Critchlow

first: Andrew

last: Garnham

first: Danielle

last: Hiam

first: Mark

last: Ziemann


title: SUV39H1 inhibition by Chaetocin targets stemness and oncogenic networks and synergizes with ONC201 against Diffuse intrinsic pontine gliomas

first: Richard

last: Lu


title: Histone deacetylase-1 is required for epigenomic stability in Neurospora crassa [HiC]

city: Colorado Springs

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

summary: Polycomb group proteins assemble into chromatin modifying complexes that regulate stem cell identity and multicellular development. The trimethylation of lysine 27 on histone H3 (H3K27me3) is catalyzed by the conserved Polycomb Repressive Complex 2 (PRC2). In Neurospora crassa, the typically-subtelomeric pattern of H3K27me3 depends on other chromatin regulators including the H3K36 methyltransferase ASH1, the chromatin remodeling enzyme IMITATION SWITCH, and components of constitutive heterochromatin including the H3K9 methyltransferase DEFECTIVE IN METHYLATION-5 and the H3K9me3-binding protein HETEROCHROMATIN PROTEIN 1 (HP1). How constitutive heterochromatin impacts PRC2 activity is unclear. HP1 forms multiple protein complexes including the HCHC complex, which removes acetyl groups from histones in constitutive heterochromatin, and contains the proteins Histone Deacetylase 1(HDA-1) and Chromodomain Protein-2 (CDP-2). To identify genes required for Polycomb repression in N. crassa, we performed a genetic screen and identified HDA-1 as necessary for PRC2-targeted gene silencing. In the absence of HDA-1, H3K27me2/3 is lost from the subtelomeres and aberrantly accumulates at constitutive heterochromatin domains normally enriched for H3K9me3; CDP-2 is also important for wildtype H3K27me3 localization. The H3K27me2/3 redistribution in Δhda-1 or Δcdp-2 strains is variable and incomplete, and mutant progeny obtained following a sexual cross displayed wild-type H3K27me3 patterns, consistent with HCHC loss leading to progressive changes in H3K27me3 enrichment. Indeed, a newly constructed ∆hda-1 deletion strain displays a wild-type H3K27me3 pattern that relocalizes to constitutive heterochromatic regions after sequential passages. Thus, HCHC-specific deacetylation prevents aberrant recruitment of PRC2 to constitutive heterochromatin.

overall_design: Chromosome conformation capture coupled with high-throughput sequencing of two independent strains of the filamentous fungus Neurospora crassa deleted of the gene hda-1 (histone deacetylase-1), which is the catalytic subunit of the HCHC histone deacetylase complex

first: Felicia

last: Ebot-Ojong

first: Aileen

last: Ferraro

first: Abigail

last: Deaven

first: Rochelle

last: Yap

first: Farh

last: Kaddar

first: Clayton

last: Hull-Crew

first: Ashley

last: Scadden

first: Zachary

last: Lewis


title: Restoration of LAT signaling through the expression of a novel Adjunctive LAT-Activating CAR (ALA-CART) enhances the antigen-sensitivity and persistence of CAR T cells

status: Public on Feb 04 2025

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

summary: Chimeric antigen receptor (CAR) T cell therapy have demonstrated remarkable success in treating B-cell malignancies that are refractory to standard therapies; however, preclinical and clinical studies have demonstrated that CAR T cell efficacy is greatly reduced against antigen-low tumors. This was exemplified in a clinical trial of CD22-directed CAR T cells where post-CAR relapses were driven by a decrease in the surface expression of the CD22 antigen. To address the poor response of CAR T cells to antigen-low tumor cells, we performed global phosphoproteomics using a SILAC/mass spectrometry approach to examine signal transduction events within CAR T cells in response to high- and low-levels of CD22 antigen. Stimulation with low levels of CD22 antigen resulted in decreased activation of several canonical T cell signaling pathways in CAR T cells, suggesting poor utilization of LAT. To overcome this inefficiency of LAT activation, we designed a bicistronic construct consisting of a clinically active 2nd generation CD22-BBz CAR along with a novel Adjunctive LAT Activating CAR incorporating the intracellular signaling domain of LAT (ALA-CART). ALA-CART cells demonstrated enhanced phosphorylation of LAT and restored downstream signaling in response to low levels of CD22. In xenograft models, ALA-CART cells completely eradicated CD22-low leukemia, significantly extending survival of mice in comparison to the clinically-active, standard CD22-BBz CAR T cells. Compared to the standard CD22-BBz CAR T cells, ALA-CART cells exhibited transcriptional differences in the resting state reflecting a less differentiated state, which corresponded to an enrichment of T stem cell memory cells and enhanced in vivo persistence. Thus, through the identification of CAR signaling deficits, we rationally designed the ALA-CART platform which improves the sensitivity and persistence of CAR T cells to target antigen-low cells, overcoming a mechanism of resistance to standard CAR therapies.

overall_design: To investigate transcriptional differences between the clinically active CD22-BBz CAR and the ALA-CART, we isolated CD4+ (by negative magnetic bead separation) and CD8+ CAR-T cells (by positive magnetic bead separation) of purified CD22-BBz and 22ALA-CART cells. CAR T cells were added to wells of 6-well tissue culture plates that were either uncoated (unstimulated CAR T cells) or wells coated with 3 ug/mL 22Fc-antigen (stimulated CAR T cells). CAR T cells were incubated at 37C for 30 mins and lysed using buffer RLT followed by extraction using RNeasy kit (Qiagen). Comparative gene expression analysis was performed on CD4 and CD8 CAR T cells with and without stimulation.

first: Catherine

last: Pham-Danis

first: M

last: Kohler


title: Pre- and postsynaptic MEF2C promote experience-dependent, input-specific development of Layer 4 to Layer 2/3 excitatory synapses

status: Public on Jan 17 2025

first: Genevieve

last: Konopka

summary: Experience and activity-dependent transcription is a candidate mechanism to mediate development and refinement of specific cortical circuits. Here we provide evidence that the activity-dependent transcription factor Myocyte-Enhancer Factor 2C (MEF2C) is required in both presynaptic layer 4 (L4) and postsynaptic L2/3 somatosensory (S1) cortical neurons for development of their synaptic connection. In contrast, synaptic inputs from local L2/3, contralateral S1, or ipsilateral frontal/motor cortex are unaffected by postsynaptic Mef2c deletion in L2/3 neurons. Postsynaptic MEF2C is required for L4 to L2/3 synapse function during, but not after, an early postnatal, experience-dependent period. Furthermore, homozygous and heterozygous Mef2c deletion in presynaptic L4 neurons weakens L4 to L2/3 excitatory synaptic inputs by decreasing presynaptic release probability. Our results suggested that experience or activity-dependent transcriptional activation of MEF2C promotes development of L4→L2/3 synapses. In support of this idea, expression of transcriptionally active MEF2C (MEF2C-VP16) rescued weak L4 to L2/3 synaptic strength in sensory deprived mice. Consistent with a presynaptic function for MEF2C, we find that MEF2C regulates the activity-dependent expression of many presynaptic assembly genes, including transsynaptic cell adhesion proteins and regulators of neurotransmitter release. This work provides mechanistic insight into the experience-dependent development of specific cortical circuits.

overall_design: Organotypic slice cultures were prepared from P6 pups that were either: CaMKii-α Cre +/-; Mef2c fl/fl or Mef2c fl/fl. These cultures were grown for 8 days in-vitro (DIV) and then treated with either: 1% DMSO and 1% water or 100 μM  Picrotoxin and 100 μM 4-aminopyridine. Then RNA was made and turned into 150 basepair paired end cDNA libraries and sequenced on a NextSeq2000 to give ~80-100 million reads per sample

first: Sean

last: Watson

first: Jennifer

last: Putman

first: Zhe

last: Zhang

first: Kimberly

last: Huber


title: Histone deacetylase-1 is required for epigenomic stability in Neurospora crassa [ChIP-seq]

first: Andrew

last: Klocko

overall_design: Chromatin Immunoprecipitation-sequencing (ChIP-seq) of the trimethylation of lysine 9 on histone H3 (H3K9me3) and di- and trimethylation of lysine 27 on histone H3 (H3K27me2/3) from the filamentous fungus Neurospora crassa


title: Non-CG DNA methylation and MeCP2 stabilize repeated tuning of long genes that distinguish closely related neuron types.

first: Mati

last: Nemera

platform_organism:
Mus musculus
synthetic construct


title: Foxp1 developing neocortex (scATAC-Seq)

summary: The transcription factor Foxp1 is expressed in the neocortex with restricted patterns across development. We used single nuclei-ATAC sequencing (snATAC-Seq) to determine the cell-type roles of Foxp1 in control and Foxp1 conditional knock-out animals generated by crossing to Emx1.Cre hemizygous mice. Samples were collected at embyonic day (E)13.5, E16.5, and post-natal day (P)0.5.

first: Ana

last: Ortiz

first: Fatma

last: Ayhan

first: Matthew

last: Harper


title: Transcriptomic and proteomic characterization of cell and protein biomarkers of checkpoint inhibitor-induced liver injury [scRNA-seq]

status: Public on Jan 22 2025

city: Groton

first: Mark

last: Sheehan

state: CT

address: 274 Eastern Point Rd

department: Drug Safety R&D

institute: Pfizer

summary: Immune checkpoint inhibitors (ICI) targeting CTLA-4 and PD-1 have shown remarkable antitumor efficacy but can also cause immune-related adverse events, including checkpoint inhibitor-induced liver injury (ChILI). This multi-omic study aimed to investigate changes in blood samples from treated cancer patients who developed ChILI. PBMCs were analyzed by transcriptomic and T cell receptor sequencing (bulk and single cell), and extracellular vesicle (EV) enrichment from plasma was analyzed by mass spectroscopy proteomics. Data were analyzed by comparing the ChILI patient group to the control group who did not develop ChILI and by comparing the onset of ChILI to pre-ICI treatment baseline. We identified significant changes in T cell clonality, gene expression, and protein levels in peripheral blood mononuclear cells (PBMCs) or plasma at the time of liver injury. Onset of ChILI was accompanied by an increase in T-cell clonality. Pathway analysis highlighted the involvement of innate and cellular immune responses, mitosis, pyroptosis, and oxidative stress. Single-cell RNA sequencing revealed that these changes were primarily found in select T cell subtypes (including CD8+ effector memory cells), while CD16+ monocytes exhibited enrichment in metabolic pathways. Proteomic analysis of plasma extracellular vesicles showed enrichment in liver-associated proteins among differentially expressed proteins. Interestingly, an increase in PBMC PD-L1 gene expression and plasma PD-L1 protein was also found to be associated with onset of ChILI.

overall_design: 10x Genomics single cell 5' Gene expression and TCR profiling of PBMCs from patients before and after checkpoint inhibitors, including ChILI patients and control patients who did not develop ChILI.

first: Thomas

last: Lanz


title: Spatial hepatocyte plasticity of gluconeogenic gene expression and gluconeogenic activity during the metabolic transitions between fed, fasted and starvation states [targeted scRNA-seq]

status: Public on Jan 23 2025

city: Bronx

first: Jeffrey

last: Pessin

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: Single cell analyses of hepatocytes across the liver lobule demonstrated that gluconeogenic gene expression (Pck1 and G6pc) is relatively low in the fed state and gradually increase first in the periportal hepatocytes during the initial fasting period. As the time of fasting progresses, pericentral hepatocyte gluconeogenic gene expression increases and following entry into the starvation state the pericentral hepatocytes are not significantly different than the periportal hepatocytes. Similarly, pyruvate-dependent gluconeogenic activity is approximately 10-fold higher in the periportal hepatocytes during the initial fasting states but with only 1.5-fold different between the pericentral and periportal hepatocytes in the starvation state. In parallel, starvation induced a reduction of canonical beta-catenin signaling and redistribution of pericentral and periportal glutamine synthetase and glutaminase resulting in an enhanced pericentral glutamine-dependent gluconeogenesis. These data demonstrate that hepatocyte gluconeogenic gene expression and gluconeogenic activity are highly spatially and temporally plastic across the liver lobule and underscore the critical importance of using well-defined feeding and fasting times to define the basis of hepatic insulin resistance and glucose production.

overall_design: Mice were trained for 3 days by removing food at 5PM and feeding at 9:00 the next day (16h fasting overnight and 8h feeding daytime). On the day of experiment, mice were provided food with drinking water that contained 20% of sucrose. The fed (0h) mice were sacrificed at 13:00 equal to 4h of feeding (0h). For fasted mice, the food and sucrose water were taken out at 13:00, then sacrificed at 21:00 for fast 8h (8h), 5:00 the next day for fast16h (16h), 13:00 the next day for fast 24h (24h), and 19:00 the next day for fast 30h (30h).

first: Junichi

last: Okada

first: Li

last: Liu

first: Kosaku

last: Shinoda


title: Histone deacetylase-1 is required for epigenomic stability in Neurospora crassa


title: Non-small Cell Lung Cancer Brain Metastasis Atlas [slide-seq]

first: Somnath

last: Tagore

address: William Black Building, 17th Floor, Lab 1708E

institute: Columbia University

summary: We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), pool matched low pass whole genome sequencing (WGS) and single-cell spatial transcriptomics  of  12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors  (PTs) and 31  treatment-naïve NSCLC brain metastases (BMs) . In total, we recovered 277,206  cell transcriptomes in 43 samples. We performed matched spatial sequencing using SlideSeq2 on 14 snRNA-seq samples.

overall_design:
Single-nuclei RNA sequencing of 277,206 cells  from 12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors and 31 treatment-naïve NSCLC brain metastses (BMs).
*** submitter declares that the raw data will be deposited in dbGap ***

first: Benjamin

last: Izar

first: Lindsay

last: Caprio


title: Non-small Cell Lung Cancer Brain Metastasis Atlas [TCR-seq]

summary: We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq)  of 12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors  (PTs) and 31  treatment-naïve NSCLC brain metastases (BMs) .


title: Histone deacetylase-1 is required for epigenomic stability in Neurospora crassa [CUTnRUN]

status: Public on Jan 16 2025

city: Athens

first: Zachary

last: Lewis

state: GA

address: 120 E. Green St.

department: Microbiology

institute: University of Georiga

summary: Polycomb group (PcG) proteins assemble into chromatin modifying complexes that regulate stem cell identity and multicellular development. The trimethylation of lysine 27 on histone H3 (H3K27me3) is catalyzed by the conserved Polycomb Repressive Complex 2 (PRC2). In Neurospora crassa, the typically-subtelomeric pattern of H3K27me3 depends on other chromatin regulators including the H3K36 methyltransferase ASH1, the chromatin remodeling enzyme IMITATION SWITCH, and components of constitutive heterochromatin including the H3K9 methyltransferase DEFECTIVE IN METHYLATION-5 (DIM-5) and the H3K9me3-binding protein HETEROCHROMATIN PROTEIN 1 (HP1). How constitutive heterochromatin impacts PRC2 activity is unclear. We performed a genetic screen to identify histone deacetylase genes required to repress PRC2-methylated genes in N. crassa. We found that HISTONE DEACETYLASE-1 (HDA-1) is required for transcriptional repression in PcG-repressed domains and for normal patterns of H3K27me3. In the absence of HDA-1, H3K27me3 is lost from typical PRC2-methylated domains and instead is enriched at a subset of constitutive heterochromatin domains normally marked for H3K9me3. In addition to altered H3K27me3 patterns, HDA-1-deficient mutants displayed aberrant patterns of H3K9me3, H3K36me3, and lysine acetylation (Kac). Mutants lacking the HP1/HDA-1-interacting protein CHROMO DOMAIN PROTEIN-2 (CDP-2) displayed a similar but non-identical phenotype, and we observed variable patterns of aberrant H3K7me3 enrichment in genetically identical ∆hda-1 strains, raising the possibility that loss of HDA-1 activity leads to progressive changes in H3K27me3 enrichment. Indeed, a newly constructed ∆hda-1 deletion strain displayed a near-wild type H3K27me3 chromatin modification profile that decayed over multiple strain passages corresponding to hundreds of nuclear divisions. Together, our data indicate that HDA-1 is a critical regulator of epigenome stability in N. crassa.

overall_design: Zachary Lewis

first: Aileen R.

last: Ferraro

first: Farh

last: Kaddar

first: Clayton

last: Hull-Crew

first: Ashley W.

last: Scadden

first: Andrew D.

first: Zachary A.

first: Felicia

last: Ebot-Ojong


last: Klocko


title: RNA sequencing(RNA-Seq)in liver tissues from different exercise interventions in NAFLD mice

city: Wuhan

first: Mingliang Wei

last: Mingliang Wei

state: Hubei

address: 299 Bayi Road, Wuchang District

institute: Wuhan University

overall_design: C57BL/6 male mice (GemPharmatech Co., Ltd) aged 6 weeks were randomly divided into normal diet control (NC) group (n=13) and HFD group (D12492, Research Diets, n=29) after one week of adaptive feeding. After eight weeks, HFD group mice were randomly divided into the following three groups (n=8): HFD, HAE (HFD + AE group), and HRE (HFD + RE group) and received at least 12 weeks of exercise training.

first: Chaorui

last: Hu

first: Chuanfei

last: Zeng

first: Huan

last: Li

first: Mingliang

last: Wei

first: Shiqian

first: Lianyun

first: Yong

last: Xiao

first: Du

last: Cheng

first: Min

last: Wu

first: Mingkai

last: Chen


title: Non-small Cell Lung Cancer Brain Metastasis Atlas

first: Somnath

last: Tagore


title: Neuronal activation triggers rapid biphasic FMRP-mediated translational control linking synaptic and nuclear regulation [FMRP-CLIP]

status: Public on Jan 15 2025

first: Ruth

last: Singer

address: 1230 York Avenue, TSH 314

institute: The Rockefeller University

summary: A central question in protein synthesis–dependent synaptic plasticity is how translation of neuronal mRNAs is dynamically regulated in time and space. Here, we develop Opto-CLIP, integrating optogenetic stimulation with cell-type-specific crosslinking immunoprecipitation (CLIP) of FMRP in CA1 neurons to define activity-dependent RNA regulation. Following patterned neuronal activation, we identify dynamic changes in FMRP-mediated translational control at minute-scale resolution. Within five minutes, FMRP is released from synaptic transcripts, accompanied by increased ribosome association. By 30 minutes, FMRP dissociates from transcripts encoding nuclear and RNA regulatory factors, also accompanied by increased ribosome association. At this stage, despite a marked reduction in protein levels, FMRP selectively reassociates with synaptic transcripts, coincident with reduced ribosome association. These coordinated shifts define temporally structured waves of translational control linking synaptic and nuclear programs. Our findings reveal a biphasic program of FMRP-mediated translational control that couples local synaptic responses to delayed nuclear regulation, providing a mechanistic framework linking activity-dependent RNA regulation, its disruption in Fragile X syndrome, and homeostatic plasticity.

overall_design: FMRP CLIP analyses of control and optogenetically activated CA1 excitatory neurons of the mouse hippocampus

first: Robert

last: Darnell


title: Neuronal activation triggers rapid biphasic FMRP-mediated translational control linking synaptic and nuclear regulation [RiboTag]

overall_design: RiboTag analyses of control and optogenetically activated CA1 excitatory neurons of the mouse hippocampus


title: SINEUP RNA rescues molecular phenotypes associated with CHD8 suppression in Autism Spectrum Disorder model systems

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

institute: University of Trento

summary: Paired-end of RNA-seq of SINEUP silencing of CHD8 in hiNPCs cells

overall_design: total RNA-seq of control (shGFP) and SINEUP-silenced CHD8

first: Marta

last: Biagioli

first: Francesca

last: Di Leva

first: Miguel

last: Pellegrini


title: Non-small Cell Lung Cancer Brain Metastasis Atlas [lpWGS]

summary: We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS)  of 12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors  (PTs) and 31  treatment-naïve NSCLC brain metastases (BMs) . In total, we recovered 277,206  cell transcriptomes in 43 samples.

overall_design:
Pool matched lp-WGS was performed in addtion to single-nuclei RNA sequencing of 277,206 cells  from 12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors and 31 treatment-naïve NSCLC brain metastases (BMs).Together, this data served to improve the identification of the malignant and non-malignant cell compartments.
*** submitter declares that the raw data will be deposited in dbGap ***

first: Benjamin

last: Izar

first: Lindsay

last: Caprio


title: Non-small Cell Lung Cancer Brain Metastasis Atlas [single nuclei RNAseq]


title: Effect of HERV-R env Knockout on Tumorigenic Characteristics of Colorectal Cancer Cells

status: Public on Jan 08 2025

city: Busan

first: Min-Hye

last: Kim

address: 262, Gamcheon-ro, Seo-gu

country: South Korea

institute: Kosin University College of Medicine

summary: To investigate the cancer properties of HERV-R knockout in the colon cancer cell line DLD1, we knocked out HERV-R from Crispr-cas9 in DLD1. We performed RNA-seq to profile gene expression in DLD1, DLD1R (HERV-R KO) cells, respectively.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DLD1 cells and its KO derivatives (DLD1R).

first: Eun-Ji

last: Ko

first: HyoJin

last: An

first: Heui-Soo

first: Sun-Hee

last: Leem

first: Hee-Jae

last: Cha


title: Proteolethargy is a pathogenic mechanism in chronic disease

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The pathogenic mechanisms of many diseases are well understood at the molecular level, but there are prevalent syndromes associated with pathogenic signaling, such as diabetes and chronic inflammation, where our understanding is more limited. Here we report that pathogenic signaling suppresses the mobility of a spectrum of proteins that play essential roles in cellular functions known to be dysregulated in these chronic diseases. The reduced protein mobility, which we call proteolethargy, was linked to cysteine residues in the affected proteins and signaling-related increases in excess reactive oxygen species. Diverse pathogenic stimuli, including hyperglycemia, dyslipidemia and inflammation, produce similar reduced protein mobility phenotypes. We propose that proteolethargy is an overlooked cellular mechanism that may account for various pathogenic features of diverse chronic diseases.

overall_design:
To investigate the role of pathogenic signaling on transcriptional regulation and heterochromatic repression, we treated HepG2 cells for 3 days with 3 nM insulin (insulin resistant samples) or 0.1 nM insulin (insulin sensitive samples) as a control. Cells were washed with EMEM to remove insulin and cultured in EMEM for 4 hours. RNA was then purified using TRIzol™ reagent (Thermo Fisher Scientific, 15596026) following the manufacturer’s instructions. RNA-seq libraries were prepared using KAPAHyperRiboErase (Roche, KK8561) and were sequenced on Illumina NovaSeq 6000, generating at least 200 million paired-ended 150-bp reads per sample.

We next performed differential gene expression analysis using data obtained from RNA-seq of 3 replicates each for resistant samples and sensitive samples. Reads were mapped to the human genome GRCh38 using STAR aligner (v2.7.1a), allowing up to 100 multiple alignments and up to 200 loci anchors (--outFilterMultimapNmax 100 --winAnchorMultimapNmax 200). Differential expression analysis of genes and transposable elements was performed on BAM files using TEtranscripts (v2.2.3). Read counts per gene and transposable element family were quantified from BAM files with TEcount in TEtranscripts (v2.2.3) using multi-sample mode and the provided GRCm38 repeat annotation. Count data were normalized using the rlog function in DESeq2 (v1.42.1).

first: Alessandra

last: Dall’Agnese

first: Ming

last: Zheng

first: Shannon

last: Moreno

first: Jesse

last: Platt

first: An

last: Hoang

first: Deepti

last: Kannan

first: Giuseppe

first: Kalon

last: Overholt

first: Hailey

last: Erb

first: Olivia

last: Corradin

first: Arup

last: Chakraborty

first: Tong

middle: I

last: Lee


title: Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina [mm10_ATAC-seq]

city: La Jolla

first: Ying

last: Yuan

address: Palmilla Dr.

department: MATS

institute: UCSD

summary: Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap, we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture in human retina, macula, and retinal pigment epithelium (RPE). We identified 420,824 unique candidate regulatory elements and characterized their chromatin state in 23 sub-classes of retinal cells. Comparative analysis of chromatin landscapes between human and mouse retina cells revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the rapid advancements in deep-learning techniques, we developed sequence-based predictors to interpret non-coding risk variants of retina diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases, and provides a resource for studying the gene regulatory programs of the human retina, leading to mechanistic insights into a wide-spectrum of eye diseases.

overall_design: The eye globes were collected from eight unrelated mouse donors with the collaboration of San Diego Eye Bank.

first: Yuan

last: Ying

first: Biswas

last: Pooja

first: Dang

last: Kelsey

first: Lin

last: Lin

first: Lancione

last: Ryan

first: Wang

last: Allen

first: Preissl

last: Sebastian


title: Genome-wide rearrangement of protein translation levels for cell and organelle proliferation in a simple unicellular alga

status: Public on Jan 14 2025

city: Tokyo

first: Yoshitaka

last: Matsuo

address: 4-6-1, Shirokanedai, Minato-Ku

department: IMSUT

country: Japan

institute: The University of Tokyo,

summary: Cell proliferation is a fundamental characteristic of organisms, driven by the holistic functions of multiple proteins encoded in the genome. However, the individual contributions of thousands of genes and the millions of protein molecules they express to cell proliferation are still not fully understood, even in simple eukaryotes. Here, we present proteome maps of cells during proliferation in the unicellular alga Cyanidioschyzon merolae, based on the sequencing of ribosome-protected messenger RNA (mRNA) fragments. Ribosome footprint profiling of genes encoded by nuclear, mitochondrial, and chloroplast DNAs has revealed qualitative and quantitative changes in mRNA transcription and protein translation within each gene during cell division. Comparisons of ribosome footprints from non-dividing and dividing cells allowed the identification of proteins involved in cell proliferation. Given that in vivo experiments on two selected candidate proteins identified a division-phase-specific mitochondrial nucleoid protein and a mitochondrial division protein, these results offer key insights into the comprehensive protein functions that facilitate cell and organelle division.

overall_design: 2 replicates in 2 different states in same strain

first: Yuko

last: Mogi

first: Yuiki

last: Kondo

first: Tetsuya

last: Higashiyama

first: Toshifui

last: Inada

first: Yamato

last: Yoshida


title: The transcriptional landscape of the developing chick trigeminal ganglion

status: Public on Jan 01 2025

city: Washington

first: Chunling

last: Yi

state: DC

address: 3700 O St NW

department: Oncology

institute: Georgetown University

summary: The trigeminal ganglion is a critical structure in the peripheral nervous system, responsible for transmitting sensations of touch, pain, and temperature from craniofacial regions to the brain. Trigeminal ganglion development depends upon intrinsic cellular programming as well as extrinsic signals exchanged by diverse cell populations. With its complex anatomy and dual cellular origin from cranial placodes and neural crest cells, the trigeminal ganglion offers a rich context for examining diverse biological processes, including cell migration, fate determination, adhesion, and axon guidance. Avian models have, so far, enabled key insights into craniofacial and peripheral nervous system development. Yet, the molecular mechanisms driving trigeminal ganglion formation and subsequent nerve growth remain elusive. In this study, we performed RNA-sequencing at multiple stages of chick trigeminal ganglion development and generated a novel transcriptomic dataset that has been curated to illustrate temporally dynamic gene expression patterns. This publicly available resource identifies major pathways involved in trigeminal gangliogenesis, particularly with respect to the condensation and maturation of placode-derived neurons, thus inviting new lines of research into the essential processes governing trigeminal ganglion development.

overall_design: RNA-seq profiling of pooled trigeminal ganglia from chicken embryos at multiple developmental stages (HH13/14, HH15/16, and HH17/18) with 3 biological replicates per stage.

first: Carrie

last: Leonard

first: Alec

last: McIntosh

first: Johena

last: Sanyal

first: Lisa

last: Taneyhill


title: Nuclei isolation from frozen heart tissues through an easy-to-operating, prompt, and inexpensive method for single-nucleus Multiome-seq

city: Duarte

first: Zhao

last: Wang

address: 1500 E Duarte Rd

department: Diabetes and Cancer Metabolism

institute: City of Hope

summary: Existing protocols are difficult to obtain high-quality sequencing data for isolating nuclei from long-term cryopreserved frozen tissues, especially such as hearts that contain rich fibrous connective tissue for single-nucleus multiome sequencing (snMultiome-seq, including snRNA-seq and snATAC-seq for the same nucleus). Here, we optimize some current methods for isolating nuclei from frozen tissues and describe an easy-to-operating, prompt, and inexpensive method for obtaining high-quality single-nucleus sequencing data, which is named as Douncer-Filter-Gradient-Centrifugation (DFGC). This protocol takes about 1.5h to complete, including mincing (1min), douncing (3min), filtering (20min) and density gradient centrifugating (40min), depending on how many samples are done at the same time, and does not require special reagents and instruments, so it is versatile and economical for most laboratories. We selected two commonly used isolating nuclei methods, microBeads- and FACS-, as controls and all analysis processes are carried out in accordance with unified standardization, including nucleus morphology, library construction, library quality inspection, data parameters, clustering, cell-type identification, and gene expression distribution. This protocol provides a step-by-step guide to nuclei isolating from frozen heart tissues to generate high-quality single nucleus gene expression and chromatin transposase accessibility sequencing data for the same nucleus.

overall_design: We isolated nuclei from the frozen heart tissues of C57BL/6J mice with three different protocols to examine the quality differences.

first: Yin

first: Di

last: Ren

first: June-Wha

last: Rhee

middle: V


title: Single-cell transcriptomic characterization of immune cells from hepatic tumors of wild type and ATF6 transgenic mice

status: Public on Dec 28 2024

city: München

first: Robert

middle: Stefan

last: Piecyk

state: Bayern

address: Marchioninistr. 15

department: Klinik und Poliklinik für Strahlentherapie und Radioonkologie

country: Germany

institute: LMU Klinikum

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We isolated CD45+ cells from livers tumors (induced by HDTVi) of hepatocyte-specific nATF6 overexprerssion mice receiving anti-IgG/PD1 treatment for scRNAseq to decrible the the immune cell population.

overall_design: In total 6 ATF6 transgenic mice were induced, 3 were treated with anti-IgG and 3 were treated with anti-PD1.

first: Kristian

last: Unger

first: Mathias

last: Heikenwälder

first: Xin

last: Li

first: Menjie

last: Qiu


title: Corticosteroid resistance is predetermined by early immune response dynamics at acute Graft-versus-Host disease onset

city: Paris

first: David

last: Michonneau

address: 1 avenue Claude Vellefaux

department: Hematology and transplantation

country: France

institute: Assistance Publique des Hôpitaux de Paris

summary: Transcriptomic analysis from patient's samples  after hematopoietic stem cell transplantation with or without acute GVHD

overall_design: PBMC samples of patients treated with haematopoietic stem cell transplant, presenting with or without aGVHD

first: Sophie

last: Le Grand


title: CUT&RUN of  3 months old wild type and hepatocyte-specific ATF6 overexpression mice

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We generated hepatocyte specific n-ATF6 overexpression transgenic mice via Cre-mediated recombination.

overall_design: At 3 months age, livers from the transgenic mice and their wild type controls were harvested for CUT&Run.

middle: S

first: Borja

last: Gomez Ramos

first: Moritz

last: Mall


title: Fibronectin and E-cadherin drive collective invasion in drug-resistant ovarian cancer cells

status: Public on Jan 07 2025

city: Bangalore

first: Ramray

last: Bhat

state: Karnataka

address: CV Raman Rd

department: Developmental Biology & Genetics

country: India

institute: Indian Institute of Science

summary: Rapid progression in epithelial ovarian cancer (EOC) is characterized by resistance to platinum-based therapy. We asked if progression kinetics is caused by coevolution of invasiveness with drug resistance. Isogenic carboplatin-resistant counterparts of high grade serous human cancer cells invaded better through, and on, ECM and within murine peritonea. The resistant cell transcriptome was ontologically enriched for signatures of migration, erstwhile reported resistance signatures in patients and mediators of transition between epithelial, mesenchymal, and amoeboid states, which was confirmed through higher expression of fibronectin and E-cadherin. Lower matrix adhesion, weak focal adhesion, and higher translatory dynamics of deformable cell collectives that could clear surrounding mesothelia indicated that resistant cancer cells displayed a unique collective amoeboid-like migration. E-cadherin knockdown partially restored sensitivity to carboplatin and decreased collective integrity, but did not affect migration. In contrast, silencing fibronectin decreased migration but did not affect resistance and integrity. Therefore, unique migrative abilities coevolve with EOC drug-resistance through the upregulation of distinct molecular trait drivers.

overall_design: RNA-seq profiling of wildtype 'OVCAR-3' cells and its isogenic carboplatin resistant variant 'res OVCAR-3' cells at 24 hrs

first: Shyamili

last: Goutham

first: Nivedhya

last: Venas

first: Sabarinathan

last: Radhakrishnan


title: MUTE overexpression in mature Kalanchoë laxiflora leaves

status: Public on Dec 29 2024

city: BERN

first: Michael

last: Raissig

address: Altenbergrain 21

department: Institute of Plant Sciences

country: Switzerland

institute: University of Bern

summary: Overexpression of KlaxMUTE1 induced asymmetric, subsidiary-cell-like divisions. To determine the downstream target genes induced, an RNA-sequencing experiment of mature wild-type and mature leaves that overexpress KlaxMUTE1 and show many ectopic asymmetric cell divisions was performed.

overall_design: mature leaf tissue of wild-type and KlaxMUTE1 overexpression lines; 4 and 3 biological replicates, respectively

first: Heike

last: Lindner

last: Cheng


title: CDK4/6 inhibition mitigates chemotherapy-induced expansion of TP53-mutant clonal hematopoiesis

status: Public on Jan 09 2025

city: SAINT LOUIS

first: Irenaeus

last: Chan

address: 660 S. Euclid Ave

institute: Washington University in Saint Louis

summary: Therapy-related myeloid neoplasms (tMN) represent a fatal consequence of exposure to cytotoxic therapy administered in the treatment of cancer. Individuals with pre-existing TP53 clonal hematopoiesis (CH) are at high risk for development of tMN but currently avoidance of therapy is the only strategy to reduce tMN risk. Here, we show in four randomized clinical trials of the CDK4/6 inhibitor trilaciclib given in conjunction with a variety of chemotherapeutic regimens and across diverse cancer patient populations that trilaciclib mitigates expansion of chemotherapy-related CH clones with mutations in DNA damage response genes (including TP53, PPM1D, and CHEK2 mutations). This finding was also observed in a syngeneic murine model of TP53 mutant CH demonstrating that trilaciclib blocks platinum-induced TP53 competitive repopulation through promoting hematopoietic stem and progenitor quiescence and decreasing TP53 mutant stemness advantage. This represents the first demonstration of a pharmacologic strategy to block chemotherapy-induced expansion of pre-leukemic TP53-mutant clones.

overall_design: Following 4 weeks of treatment with either vehicle, carboplatin, trilaciclib, or a combination of carboplatin with trilaciclib, bone marrow cells from competitive transplanted Vav-cre Tp53 WT or Vav-cre Tp53 R172H/WT mice were washed twice with cold PBS before labeling with unique TotalSeqA-compatible HashTags. Subsequently, samples were incubated with mouse Fc receptor-blocking agent and labeled with DAPI for live cell sorting by flow cytometry. After sorting equal numbers of cells were pooled and submitted for scRNA-sequencing

first: Pu

last: Zhang

first: Xiangyu

last: Pan

first: Cynthia

last: Castro

first: Nina

last: Fox

first: Giulia

last: Petrone

first: J Scott

last: Beeler

first: Duc

last: Tran

first: Catrina

last: Fronick

first: Omar

last: Abdel-Wahab

first: Kelly

last: Bolton


title: Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina [10x multiome]

first: Ying

last: Yuan

summary: Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap,  we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture  in human retina, macula, and retinal pigment epithelium (RPE). We identified 420,824 unique candidate regulatory elements and characterized their chromatin state in 23 sub-classes of retinal cells. Comparative analysis of chromatin landscapes between human and mouse retina cells revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the rapid advancements in deep-learning techniques, we developed sequence-based predictors to interpret non-coding risk variants of retina diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases, and provides a resource for studying the gene regulatory programs of the human retina, leading to mechanistic insights into a wide-spectrum of eye diseases.

overall_design: The eye globes were collected from three unrelated human donors (aged 21, 27 and 43 years) (Table-X) with the collaboration of San Diego Eye Bank. The sample processing time starting from eye enucleation to dissection was restricted within 2 hours to identify the macula, a visible yellowish/whiteish indent that is slightly lateral to the optic disk inside the globe. Prior dissection, the eye globe with proper label was collected in a sterile moist chamber. At first the cornea was removed by cutting 2-3 mm around the limbus using a surgical blade. Pull off the iris and lens. This will leave you with the eye cup, which contains the posterior pole. After removing enough vitreous and aqueous fluid the temporal region can be located by two main blood vessels that curl around the macula. Using a sterile 3mm skin biopsy punch, the macula was collected. Sections were made for the other regions, temporal, nasal, superior and inferior. For all these regions, the retina and RPE tissue were separated and stored immediately in Liquid Nitrogen.

first: Yuan

last: Ying

first: Biswas

last: Pooja

first: Yang

last: Qian

first: Wang

last: Allen


title: Liver transcriptomic profile of  wild type and hepatocyte-specific ATF6 knockout mice feeding CD-HFD

first: Robert

last: Piecyk

summary: RNA were isolated and treated with RNAse-free DNAse, and sequenced with Novaseq 6K PE 100 S4 split.

overall_design: In total 11 samples were included, 6 from wild type mice and 5 from ATF6 knockout mice.

first: Xin

last: Li

first: Kristian

last: Unger

first: Mathias

last: Heikenwälder


title: ATAC-seq of 3 months old wild type and hepatocyte-specific ATF6 overexpression mice

summary: Hepatocellular carcinoma (HCC) is the fastest growing cause of cancer-related mortality with limited therapies. While endoplasmic reticulum (ER)-stress and the unfolded protein response (UPR) are implicated in HCC, the involvement of the UPR-transducer activating transcription factor 6 alpha (ATF6α) remains unclear. We generated hepatocyte specific n-ATF6 overexpression transgenic mice via Cre-mediated recombination. At 3 months age, livers from the transgenic mice and their wild type controls were harvested for ATAC-sequencing.

overall_design: In total 9 mice were included, 4 from wild type mice and 5 from ATF6 transgenic mice.

first: Borja

last: Gomez Ramos

first: Moritz

last: Mall


title: Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations [8 cancer cell lines]

status: Public on Dec 26 2024

city: San Francisco

first: Hani

last: Goodarzi

department: Department of Biochemistry and Biophysics

institute: UCSF

summary: Heterogeneity between patients poses a significant challenge in cancer drug development. Although success of a drug candidate in the clinic depends on efficacy across large numbers of diverse patients, only a few in vivo preclinical models are used for assaying a preclinical drug candidate due to the lack of scalability of traditional xenograft models. To address this limitation, we developed GENEVA, a scalable platform that enables the measurement of molecular and phenotypic responses to drug perturbations at single-cell resolution, both in 3D and in vivo. GENEVA models the genetic diversity of cancer by combining multiple patient-derived cell lines and cancer cell lines into pooled 3D cultures and xenograft models, allowing us to study drug responses across a wide range of genetic backgrounds within a single experiment. This platform integrates high-resolution transcriptomics with multiplexed single-cell profiling, providing a unique ability to uncover the interplay between cancer genotypes and drug responses. In this study, we apply GENEVA to investigate KRAS G12C inhibitors and demonstrate that mitochondrial activation is a key driver of cell death following KRAS inhibition. Additionally, we identify epithelial to mesenchymal transition (EMT) as a prominent resistance mechanism to KRAS G12C inhibition using in vivo GENEVA mice. These findings highlight the utility of GENEVA in identifying novel therapeutic targets and optimizing combination therapies, while underscoring its potential to bridge the gap between preclinical cancer models and patient outcomes by modeling the complexity of tumor heterogeneity in a scalable and robust assay.

overall_design: A total of 8 cancer cell lines with varying genetic backgrounds, including BRAF(V600E) and KRAS G12C mutations, were pooled together into a single experimental setup. These pooled cells were cultured in 3D conditions and then split into 4 treatment groups:   Vehicle control (DMSO),   ARS-1620 (0.4 µM, 1.6 µM, 25 µM)  After six days of treatment, cells were harvested and subjected to scRNA-seq

first: Johnny

middle: X

last: Yu

first: Jung

last: Suh

first: Katerina

middle: D

last: Popova

first: Kristle

last: Garcia

first: Tanvi

last: Joshi

first: Bruce

last: Culbertson

first: Jessica

middle: B

last: Spinelli

first: Vishvak

last: Subramanyam

first: Kevin

last: Lou

first: Kevan

last: Shokat

first: Jonathan

last: Weissman


title: Loss of CLN3 in HEK cells

status: Public on Dec 23 2024

city: Hershey

first: Nuno

last: Raimundo

state: PA

address: 500 University Dr, College Of Medicine, Room C4769

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

summary: To understand the consequences of CLN3 loss, we performed RNAseq in HEK cells with CRISPR-Cas9-mediated KO of CLN3 (CLN3-KO) or parental HEK WT cells.

overall_design: three parental HEK WT, three CLN3-KO


title: Expression data from SAMP8 and SAMR1 mice brains in TFQA treatments

city: Tsukuba City

first: Hongyu

last: Lin

state: Ibaraki

address: Tennodai 1-1-1

department: Life and Earth Sciences

institute: University of Tsukuba

summary:
TFQA treatment in SAMP8 mice showed the significant performance on improving learning and memory compared with no treatment SAMP8 mice brains.  TFQA treatments in SAMP8 mice also had significant activation of neurotrophin signaling pathway, by increasing BDNF.
We used microarrays to detail the global programme of gene expression underlying treatment and identified distinct classes of regulated genes during this process.

overall_design: SAMP8 and SAMR1 mice brains were selected  for RNA extraction on Affymetrix microarrays. We selected 6 months old adult male SAMP8 and SAMR1 mice. After 37 days administration of TFQA,  mice were dissected and brains were isolated.


title: Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina [snm3c-seq]

first: Ying

last: Yuan

first: Yuan

last: Ying

first: Zemke

first: Biswas

last: Pooja

first: Dong

last: Keyi

first: Lau

last: Pik Ki

first: Bartosik

last: Weronika


title: Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations [11 cancer cell lines]

first: Hani

last: Goodarzi

state: CA

overall_design:
A total of 11 cancer cell lines with varying genetic backgrounds, including BRAF(V600E) and KRAS G12C mutations, were pooled together into a single experimental setup. These pooled cells were cultured in 3D conditions and then split into three treatment groups:
Vehicle control (DMSO),
Vemurafenib (0.8 µM) targeting BRAF(V600E) mutants,
ARS-1620 (1 µM) targeting KRAS G12C mutants.
After six days of treatment, cells were harvested and subjected to scRNA-seq

first: Johnny

last: Yu

first: Jung

middle: M

last: Suh

first: Katerina

last: Popova

first: Kristle


title: Single-cell transcriptomics of human organoid-derived enteroendocrine cell populations from the small intestine.

status: Public on Dec 16 2024

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Enteroendocrine cells (EECs) are the source of a variety of gut hormones that control local intestinal functions such as gallbladder contraction, pancreatic enzyme secretion and intestinal motility, as well as peripheral nutrient metabolism and appetite. This study aimed to map human EECs isolated from organoids derived from duodenum and ileum using single-cell RNA sequencing.

overall_design: Organoids derived from human duodenum and ileum were genetically modified using CRISPR-Cas9 to express the fluorescent protein Venus driven by the chromogranin-A promoter. Fluorescent cells from CHGA-Venus organoids were purified by flow cytometry and analysed by 10X single-cell RNA sequencing.

first: Christopher

middle: A

last: Smith


title: Regulation of GLIS3 in neonatal kidney development

status: Public on Dec 18 2024

city: Research Triangle Park

first: Anton

last: Jetten

state: NC

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS, NIH

summary: Loss of transcription factor GLIS3 function in humans and mice leads to the development of neonatal polycystic kidney disease (PKD). To investigate how loss of GLIS3 function in kidney affects postnatal kidney development and PKD, we analyzed the gene expression profiles of kidneys from WT and Glis3-null mice at P7, P14, and P28 by RNA-Seq analysis using Glis3 global KO model Glis3-mCherry.

overall_design: Total kidney RNAs were isolated from WT and Glis3-null mice and gene expression profiles were analyzed by RNA-Seq.

first: Yun-Gil

last: Roh

first: Chitrangda

last: Srivastava

first: Hong

last: Kang

first: Justin

last: Collier

first: Sara

last: Grimm


title: Multiplexed mosaic tumor models reveal natural phenotypic variations in drug response within and between populations

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

overall_design: Refer to individual Series


title: Evolutionary pressures shape undifferentiated pleomorphic sarcoma development and radiotherapy response.

status: Public on Dec 13 2024

city: Stanford

first: Ajay

last: Subramanian

address: 450 Serra Mall

department: Radiation Oncology

institute: Stanford University School of Medicine

summary: Although radiotherapy plays a crucial role in treating many cancers, the effect of radiation on tumor evolution remains unclear. We integrated temporal genomic profiling of 120 spatially distinct tumor regions from 20 patients with undifferentiated pleomorphic sarcomas (UPS), longitudinal circulating tumor DNA (ctDNA) analysis, and evolutionary biology computational pipelines to study UPS evolution during tumorigenesis and in response to radiotherapy. Most unirradiated UPS displayed initial linear evolution followed by subsequent branching evolution with distinct mutational processes during early and late development. Using metrics of genetic divergence between regions, we demonstrated evidence of strong selection pressures during UPS development that further increased during radiotherapy. We observed changes in subclone abundance following radiotherapy with subclone contraction tied to alterations in calcium signaling and demonstrated that inhibiting calcium transporters can radiosensitize sarcoma cells. Finally, ctDNA analysis accurately measured subclone abundance and enabled non-invasive monitoring of subclonal changes. These results demonstrate that radiation exerts selective pressures on UPS and suggest that targeting radioresistant subclonal populations could improve outcomes after radiotherapy.

overall_design: Bulk RNA-sequencing was performed on a total of 13 pre-treatment and 25 post-treatment soft tissue sarcoma specimens from 12 patients treated with chemoradiation therapy.

first: Everett

middle: J

last: Moding

first: Marius

last: Fried

first: Matthias

last: Gaida


title: Molecular effects of arsenic and smokeless tobacco aqueous extract in cultured cells  [RNA-seq]

status: Public on Dec 04 2024

city: LYON

first: Samrat

last: Das

address: 25 avenue Tony Garnier

institute: International Agency for Research on Cancer (IARC)

summary: Chronic arsenic exposure can lead to various health issues including cancer. There has been a growing concern about co-exposure to various prevalent lifestyle habits and their role in the enhancement of arsenic toxicity. Smokeless tobacco (SLT) products are extensively consumed in many South Asian countries, where their use frequently co-occurs with exposure to arsenic from contaminated groundwater. To decipher the oral epithelial cell responses to arsenic and SLT alone and in co-exposure, we performed multi-omics analyses of DNA methylome, transcriptomic reprogramming and genotoxic effects in controlled experimental settings. Chronic exposure studies revealed hypomethylation of genes involved in inflammation response and apoptosis, further corroborated by the upregulation of genes involved in these processes due to arsenic and the combined treatment in acute exposure setting. Next, to validate the omics results at the phenotypic level, we observed a dose dependent decrease in cell viability, induction of DNA damage, cell cycle changes, and an increase in apoptotic cells, with the most pronounced effects observed under arsenic and SLT co-exposure conditions. The observed DNA damage was likely the result of apoptosis induction, as chronic exposure experiments based on whole-exome sequencing did not reveal increased mutagenicity following the arsenic and/or SLT exposure. Our integrative omics study provides insights into both chronic and acute responses to arsenic and SLT co-exposure, with both types of responses converging on some of the same mechanisms. We identified large-scale epigenomic and transcriptomic reprograming associated with arsenic and SLT co-exposure, alongside genotoxic effects presumably manifesting as consequences of apoptosis induction. The findings point to a role of arsenic and SLT in altering key molecular responses, especially in the context of the co-exposure, and call for further studies in humans in the areas of exposure, to validate the observed mechanisms.

overall_design: hTERT Normal oral keratinocytes cells were grown in T25 flasks (seeding density ~ 3 - 5 × 105 cells). Upon reaching a confluency of around 70%, the cells were treated with media containing the test substances and were grouped into various time points based on exposure period (2 hrs, 4 hrs and 8 hrs). Two experimental control groups were included, the baseline untreated control (0 hr), and time-matched untreated control (harvested at 8 hrs). Each timepoint condition consisted of four experimental replicates. After exposure, the media containing the test substances were removed from the flasks and the cellular RNA was extracted using standard methods (TRIzol™ Reagent, Cat. No. 15596026, Invitrogen). Estimation of yield was done by Qubit analysis (Qubit 3.0 Fluorometer, Life Technologies, Invitrogen™, Thermo Scientific Fisher) . RNA integrity was analysed on High Sensitivity RNA ScreenTape (Cat. No. 5067- 5579, Agilent), using the 4200 TapeStation automated electrophoresis instrument (Agilent). All samples exhibited RNA Integrity Number (RIN) above 8.4. 500 ng RNA per sample was used to prepare libraries (QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina (FWD)), Cat. No. 015, Lexogen).


title: Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer [ATAC-seq]

status: Public on Dec 14 2024

city: Boston

first: Seong Won

last: Kim

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Heterozygous truncating variants in the sarcomere protein titin (TTN) are the most common genetic cause of heart failure. To understand mechanisms that regulate abundant cardiomyocyte TTN expression we characterized highly conserved intron 1 sequences that exhibited dynamic changes in chromatin accessibility during differentiation of human cardiomyocytes from induced pluripotent stem cells (hiPSC-CMs). Homozygous deletion of these sequences in mice caused embryonic lethality, while heterozygous mice demonstrated allele-specific reduction in Ttn expression. A 296 bp fragment of this element, denoted E1, was sufficient to drive the expression of a reporter gene in hiPSC-CMs. Deletion of E1 downregulated TTN expression, impaired sarcomerogenesis, and decreased contractility in hiPSC-CMs. Site-directed mutagenesis of predicted NKX2-5- and MEF2-binding sites within E1 abolished its transcriptional activity. Embryonic mice expressing E1 reporter gene constructs validated in vivo cardiac-specific activity of E1 and the requirement for NKX2-5 and MEF2 binding sequences. Moreover, isogenic hiPSC-CMs containing a rare E1 variant in the predicted MEF2 binding motif that was identified in a patient with unexplained DCM showed reduced TTN expression. Together, these discoveries define an essential, functional enhancer that regulates TTN expression. Manipulation of this element may advance therapeutic strategies to treat DCM caused by TTN haploinsufficiency.

overall_design: We performed ATACseq in WT hiPSCs during differentiation into cardiomyoyctes. hiPSCs were differentiated to cardiomyocytes using the standard protocols. Multiple biological replicates per time point were collected and later merged for peak calling.

first: Lauren

middle: K

last: Wasson

first: Seongwon

first: Yuri

first: Steven

last: R DePalma

first: Joshua

last: Gorham

first: Christine

last: Seidman

first: Jonathan

middle: G


title: Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer.

status: Public on Dec 10 2024


title: Next Generation Sequencing Facilitates Quantitative Analysis of undamage chondrocyte and damage chondrocyte whole Transcriptomes

status: Public on Nov 06 2024

city: guangzhou

first: dianbo

last: long

state: guangdong

address: Zhongshan second road

institute: First Affiliated Hospital of Sun Yat-sen University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare undamage chondrocyte and damage chondrocyte whole transcriptomes

overall_design: Whole Transcriptomes profiles of undamage chondrocyte and damage chondrocyte were generated by deep sequencing

first: Dianbo

first: Guping

last: Mao

first: Guangxin

last: Huang

first: Zengfa

last: Deng

first: Yan

first: Aishan

last: He

first: Ziji

last: Zhang


title: Molecular effects of arsenic and smokeless tobacco aqueous extract in cultured cells

first: Samrat

type: Methylation profiling by genome tiling array

overall_design: htert-immortalized normal oral keratinocytes (NOK) cells underwent the respective, controlled treatment protocols. Briefly, each week the cells were exposed for 24 hr, and following treatment, the exposure medium was replaced with normal media and cells were left for recovery. Exposures were repeated in for a period of 5 weeks. Following the repeated exposure protocol, genomic DNA was extracted from the cells using standard protocol.  For each sample, 500ng DNA were bisulfite converted to enable quantitative assessment of methylation level over 850K CpG sites. Following this treatment, methylation profiles were obtained with Infinium® Methylation EPIC bead arrays (Illumina), using recommended protocols for amplification, labelling, hybridisation, and scanning. For each treatment condition triplicate wells were analysed. Samples: Samples: Parental (4 biological replicates), NT (Non treated time matched control, 3 biological replicates), SA (Sodium arsenite treated: 10µM, 3 biological replicates), SLT (smokeless tobacco aqueous extract treated: 3000 µg/mL, 3 biological replicates), SA+SLT [co-exposed: (SA: 7µm)+(SLT: 1000 µg/mL), 3 biological replicates].


title: Effect of the Mbov_0496 mutation on gene expression of Mycoplasma bovis under normal and high potassium conditions

status: Public on Dec 01 2024

city: Wuhan

first: Jiongxi

last: Chen

address: No.1, Shizishan Street, Hongshan District

department: College of Animal Science & Technology

institute: Huazhong Agriclutural University

summary: Cyclic di-AMP is an essential and ubiquitous second messenger that regulates bacterial potassium (K+) concentrations to maintain osmotic equilibrium. And its specific K+ regulation mechanism in Mycoplasma has rarely been investigated. We used the ruminant pathogen Mycoplasma bovis (M. bovis) to investigate this mechanism. We verified that MbovP496 is a c-di-AMP synthetase and its mutant T5.415 showed growth inhibition under high K+ condition. To deliver why the mutant strain T5.415 can regulate M. bovis growth, we held a RNA-seq analysis to reveal that the differentially expressed genes between WT and T5.415 under normal condition and high K+ condition. The K+ transport pathways and metabolism related pathways were enriched. In conclusion, we found that the mutation of c-di-AMP synthetase, MbovP496 can broadly influence not only the metal ions transport pathway, but also has an effect on metabolism pathways,which could significantly contribute to understanding the regulation of growth by c-di-AMP synthetase in mycoplasmas.

overall_design: RNA-seq profiling of wild-type Mycoplasma bovis and the MbovP496 mutant T5.415 under normal PPLO culture conditions and PPLO medium supplemented with 50 mM K+


title: Transcriptional Stress as a Cause of DNA Double-Stranded Breaks

city: Houston

first: Priyatansh

last: Gurha

state: Texas

address: 6770 Bertner Ave

department: School of Medicine

institute: UTHealth

summary:
ABSTRACT
Aims: Double-stranded breaks (DSBs) cause genomic instability, a hallmark of aging, and activate the DNA damage response (DDR) and the cytosolic DNA-sensing proteins (CDSP) pathways. The activated pathways induce cell cycle arrest, inflammation, senescence, cell death, fibrosis, and organ dysfunction. The purpose of the study was to identify and characterize genome-wide DSBs at the nucleotide resolution in adult cardiac myocytes.
Methods and Results: We identified the genome-wide DSBs in the genomes of ~ 6 million adult cardiac myocytes (1 million per sample) in the 3 wild-type and 3 myocyte-specific LMNA-deficient mice (Myh6-Cre:LmnaF/F) mice by END-Sequencing. We identified 6,774 differential DSBs between the wild-type and Myh6-Cre:LmnaF/F cardiac myocytes, which, except for 8, were exclusive to the Myh6-Cre:LmnaF/F genotype. The differential DSBs were enriched in the gene regions, transcription initiation sites, cardiac transcription factor motifs, and at the G quadruplex forming structures, suggesting the involvement of the transcriptional stress. Because LMNA regulates transcription, we performed a CUT&RUN assay with an anti-LMNA antibody (N=5) to test the role of transcriptional stress in an increased prevalence of DSBs. We identified an average of 818 genome-wide lamin-associated domains (LADs), which encompassed 30% of the mouse genome. LADs were associated with a 16-fold reduction in the transcript levels of protein-coding genes located at the LAD regions (N=3,975) as opposed to genes located at the non-LAD regions (N=~ 17,778). Consistent with increased transcription at the non-LAD regions DSBs were ~ 6-fold more prevalent in the non-LAD than LAD regions. Likewise, the loss of LAD was associated with a 2.3-fold higher prevalence of differential DSBs in the Myh6-Cre:LmnaF/F cardiac myocyte genomes, which were predominantly localized to the transcription start sites.
Conclusions: To our knowledge, this is the first identification of the DSBs, a hallmark of aging, at the nucleotide resolution in the cardiovascular system. The findings implicate transcriptional stress in the pathogenesis of DSB and the protective role of LMNA against DSBs likely through transcriptional suppression. Given the ubiquitous nature of transcriptional stress, DSBs are expected to be pervasive and pathogenic through activation of the DDR and CDSP pathways not only in cardiovascular diseases but also in other conditions, including aging.

overall_design: End-seq was performed from CM isolated from 3 WT and 3 Myh6-Cre:LmnaF/F mice.

first: Ali

last: Marian

first: Benjamin

last: Cathcart


title: A Blood-based Transcriptomic Signature Stratifies Severe Crohn's disease and Defines Potentially Targetable Therapeutic Pathways

status: Public on Nov 04 2024

city: Los Angeles

first: Rivkah

last: Gonsky

state: California

address: 8700 Beverly Blvd. Davis Building, Room D4062

department: Gastroenterology/IBIRI

institute: Cedars-Sinai

summary: Surgical resection in severe Crohn's disease is a common consequence of therapeutic failure. We identified 2 severe CD subtypes: one similar to non-IBD subjects, the other exhibited a mucosal-like gene signature, altered T-cell subsets, severity features and decreased pro-inflammatory expression post-surgery. These findings may identify targets for CD subtype-specific therapeutic and biomarker development.

overall_design: CD3+ T-cells were purified from paired blood and mucosa from 100 CD and 17 non-inflammatory bowel disease (IBD) subjects requiring surgery. Longitudinal samples (n=49) were collected 4-13 months postoperatively. Expression profiles were generated by RNA-Seq. Transcriptional Risk Scores (TRS), T-cell subset deconvolution, gene pathway and kinase analyses were performed.

first: Evan

last: Adams

first: Alka

last: Potdar

first: Gregory

last: Botwin

first: Eva

last: Biener-Ramanujan

first: Dermot

last: McGovern

last: Braun

first: Phillip

last: Fleshner

first: Stephan

middle: R

last: Targan