title: Plasma microRNAs as prognostic biomarkers for development of severe epilepsy after experimental traumatic brain injury - EpiBioS4Rx Project 1 study

status: Public on Dec 12 2024

city: Kuopio

first: Mette

last: Heiskanen

address: Neulaniementie 2, P.O.B. 1627

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

summary: Purpose: Post-traumatic epilepsy (PTE) is an epilepsy that develops after traumatic brain injury (TBI), and it comprises 10-20% of structural epilepsies and 5% of all epilepsies. The lack of prognostic biomarkers for PTE hinders the development of anti-epileptogenic treatments. In this preclinical multicenter study, plasma samples collected from a rat model of PTE were analyzed by small RNA sequencing to reveal the post-TBI expression profile of circulating microRNAs and to identify potential miRNA biomarkers for PTE development. Methods: The animal experiments were conducted at 3 different study sites: University of Eastern Finland (Finland), Monash University (Australia), and University of California, Los Angeles (USA). Severe TBI was induced in adult male Sprague-Dawley rats by the lateral fluid-percussion injury (LFPI) method. Rats that developed PTE were identified by video-EEG monitoring during the 7th post-injury month (TBI rats with epilepsy, TBIE; TBI rats without epilepsy, TBIN). Small RNA sequencing was conducted with plasma samples collected 48 hours after TBI or sham operation (craniotomy). Following the primary quantification, DESeq2 (v. 1.42.0) was used to identify differentially expressed miRNAs between the experiment groups. Results were further validated in a larger sample cohort by droplet digital PCR (ddPCR). Results: Small RNA sequencing detected a total of 754 miRNAs that were expressed in at least one sample. DESeq2 detected 23 differentially expressed (DE) miRNAs between the TBI and sham groups, 12 between the TBIE and sham groups, and 5 between the TBIN and sham groups. In contrast, no DE miRNAs were detected between the TBIE and TBIN groups. From the list of 23 DE miRNAs between the TBI and sham groups, 3 upregulated miRNAs (rno-miR-183-5p, rno-miR-323-3p, and miR-434-3p) were selected for further ddPCR validation. The list of miRNAs for validation was further complemented by 4 miRNAs (rno-miR-9a-3p, rno-miR-124-3p, rno-miR-132-3p, and rno-miR-212-3p), which were not differentially expressed in the DESeq2 analysis, but which we have previously detected to be acutely upregulated in TBI rat plasma. The validation was conducted with samples from the entire EpiBioS4Rx cohort [26 baseline samples, 45 sham, 164 TBI (32 TBIE, 132 TBIN)]. DdPCR analysis revealed that all 7 investigated miRNAs were upregulated in the TBI rats compared with the sham controls. No differences were detected between the rats with (TBIE) or without epilepsy (TBIN). In contrast, TBIE rats that had seizure clusters (severe PTE) had lower levels of plasma miR-212-3p compared with other TBI rats. Furthermore, elastic net regularized logistic regression (glmnet) analysis identified miR-212-3p and miR-132-3p as the optimal set to differentiate TBIE rats with seizure clusters from other TBI rats. Conclusions: The profile of circulating plasma microRNAs differed between TBI rats and sham controls. MiR-212-3p alone or in combination with miR-132-3p showed potential as prognostic biomarkers for development of severe PTE.

overall_design: Small RNA sequencing of rat plasma samples collected 48 h after lateral fluid-percussion injury (TBI, n=19) or sham operation (n=10). The plasma samples were collected at three different study sites: UEF, Monash, and UCLA. The TBI group contains 9 rats with epilepsy (TBIE) and 10 rats without epilepsy (TBIN), which was defined by a 4-week continuous video-EEG monitoring during the 7th month after injury.

first: Xavier

last: Ndode-Ekane

first: Idrish

last: Ali

first: Cesar

last: Santana-Gomez

first: Noora

last: Puhakka

first: Shalini

last: Das Gupta

first: Pedro

last: Andrade

first: Riikka

last: Immonen

first: Pablo

last: Casillas-Espinosa

first: Eppu

last: Manninen

first: Gregory

last: Smith

first: Rhys

last: Brady

first: Juliana

last: Silva

first: Emma

last: Braine

first: Matt

last: Hudson

first: Glenn

last: Yamakawa

first: Nigel

last: Jones

first: Sandy

last: Shultz

first: Neil

middle: G

last: Harris

first: David

middle: K

last: Wright

first: Olli

last: Gröhn

first: Richard

last: Staba

first: Terence

last: O'Brien

first: Asla

last: Pitkänen


title: Genomic and transcriptomic data analyses highlight KPNB1 and MYL4 as novel risk genes for congenital heart disease

status: Public on Nov 08 2024

city: Helsinki

first: Martin

last: Broberg

address: Viikinkaari 5D

department: Biosciences

institute: University of Helsinki

type: Expression profiling by high throughput sequencing

summary: Congenital heart defects (CHD) are structural defects of the heart affecting approximately 1% of newborns. CHDs exhibit a complex inheritance pattern. While genetic factors are known to play an important role in the development of CHD, relatively few variants have been discovered so far and very few genome-wide association studies (GWAS) have been conducted. We performed a GWAS of general CHD and five CHD subgroups in FinnGen followed by functional fine-mapping through eQTL analysis in the GTEx database, and target validation in human induced pluripotent stem cell -derived cardiomyocytes (hiPS-CM) from CHD patients. We discovered that the MYL4-KPNB1 locus (rs11570508, beta = 0.24, P = 1.2x10-11) was associated with the general CHD group. An additional four variants were significantly associated with the different CHD subgroups. Two of these, rs1342740627 associated with left ventricular outflow tract obstruction defects and rs1293973611 associated with septal defects, were Finnish population enriched. The variant rs11570508 associated with the expression of MYL4 (normalized expression score (NES) = 0.1, P = 0.0017, in the atrial appendage of the heart) and KPNB1 (NES = -0.037, P = 0.039, in the left ventricle of the heart). Furthermore, lower expression levels of both genes were observed in human induced pluripotent stem cell -derived cardiomyocytes (hiPSC-CM) from CHD patients compared to healthy controls. Together, the results demonstrate KPNB1 and MYL4 as in a potential genetic risk loci associated with the development of CHD.

overall_design: hIPSC lines from 4 patients and 2 pooled controls were sequenced and compared for gene expression.

first: Minna

last: Ampuja

first: Samuel

first: Tiina

last: Ojala

first: Otto

last: Rahkonen

first: Riikka

last: Kivelä

first: James

last: Priest

first: Hanna

middle: M

last: Ollila

first: Emmi

last: Helle


title: Transcriptional landscape of direct reprogramming toward the hematopoietic lineage

status: Public on Dec 09 2024

city: Ann Arbor

first: Lindsey

middle: A

last: Muir

state: MI

address: 1600 Huron Parkway B520

country: USA

institute: University of Michigan

summary: Direct reprogramming of human fibroblasts into hematopoietic stem cells (HSCs) offers a promising strategy for generating autologous cells to treat blood and immune disorders. Current protocols are limited by low efficiency and insufficient tools for evaluating reprogramming outcomes. Although functional assays are the standard for confirming cell identity, they require fully reprogrammed cells, limiting their utility during protocol development. To address this, we assembled a single-cell transcriptomic reference atlas of hematopoietic reprogramming and tested an algorithmically-predicted transcription factor recipe—GATA2, GFI1B, FOS, REL, and STAT5A—for HSC induction. Long-read single-cell RNA sequencing of CD34+ reprogrammed cells revealed progressive loss of fibroblast identity alongside induction of early hematopoietic and endothelial programs, with reference-atlas benchmarking placing reprogrammed cells in an intermediate transcriptomic state between fibroblasts, endothelial cells, and HSCs. Isoform-level analysis further revealed transcriptional remodeling not captured by gene-level analyses. This experimental-computational framework offers a generalizable strategy for characterizing partially reprogrammed states and guiding optimization of reprogramming protocols.

overall_design: Direct reprogramming of human fibroblasts into hematopoietic stem cells (HSCs) was investigated using a defined set of five transcription factors (TFs): GATA2, GFI1B, FOS, STAT5A, and REL. TFs were selected using a data-guided control algorithm that identified combinations minimizing transcriptional differences between fibroblasts and HSCs. TFs were delivered via lentiviral vectors encoding doxycycline-inducible expression cassettes, and expression was induced with doxycycline for 48 hours. Cells used in control and reprogramming conditions were maintained between passages 2 and 4 at initiation, and all samples were collected before passage 10. Single-cell RNA sequencing was performed using the 10x Genomics Chromium platform, followed by long-read sequencing using Oxford Nanopore Technologies (ONT) platforms. Four libraries were generated: (1) human neonatal foreskin fibroblasts (ATCC CRL-2522), (2) cells reprogrammed with the 5TF cocktail collected on day 48 of reprogramming, (3) primary human bone marrow (ATCC PCS-800-012TM, Lot 80516705), and (4) 5TF-induced cells collected on days 0, 7, 14, and 21 of reprogramming.

first: Jillian

last: Cwycyshyn

first: Cooper

last: Stansbury

first: Sarah

last: Golts

first: Hyunsu

last: Lee

first: Joshua

last: Pickard

first: Walter

last: Meixner

first: Indika

last: Rajapakse


title: Leucegene: AML sequencing (GRCh38 reference)

status: Public on Apr 23 2025

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

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

overall_design: Refer to individual Series


title: The competition between splicing and 3′ processing shapes the human transcriptome

status: Public on Oct 28 2024

city: Irvine

first: Yongsheng

last: Shi

state: California

address: 811 Health Sciences Road, Medical Sciences B Room 262

department: Microbiology & Molecular Genetics

institute: UC Irvine

summary: Eukaryotic pre-mRNA processing steps, including splicing and 3′ processing, are tightly coordinated, but the underlying mechanisms remain poorly understood. Previous studies proposed that the splicing factor U1 snRNP inhibits 3′ processing at intronic polyadenylation (IPA) sites through a splicing-independent mechanism, called telescripting. However, we found that global or gene-specific perturbation of splicing by targeting multiple splicing factors, including U1 snRNP, U2 snRNP, U2AF, and SF3b led to activation of 3′ processing at IPA sites. Inhibiting different splicing factors activated overlapping and distinct IPA sites and such specificity was determined, at least in part, by alterations in RNA polymerase II elongation and termination. Conversely, we showed that blocking pre-mRNA 3′ processing promoted splicing globally. These results strongly suggest that splicing and 3′ processing are competing processes that shape the transcriptome. Finally, as splicing inhibition-induced shifts to IPA site usage can lead to gene inactivation, including tumor suppressor genes, the use of general splicing inhibitors to treat human diseases may pose a significant risk.

overall_design:
Examination of 30 samples by PAS-seq, a type of 3′ end mRNA-sequencing. There are 3 biological replicates of 50uM control AMO treatment, 3 biological replicates of 50uM U2 AMO treatment, 3 biological replicates of control shRNA treatment, 3 biological replicates of U2AF1 shRNA treatment, 3 biological replicates of U2AF2 shRNA treatment, 3 biological replicates of DMSO treatment, 3 biological replicates of OTS964 (OTS) treatment, 3 biological replicates of Pladienolide B (PB) treatment, 3 biological replicates of 25uM control AMO treatment, and 3 biological replicates of 25uM U1 AMO treatment. All samples were prepared from HEK293T cells.

Examination of 42 samples by 4sU-seq. There are 3 biological replicates of 50uM control AMO treatment, 3 biological replicates of 50uM U2 AMO treatment, 3 biological replicates of control shRNA treatment, 3 biological replicates of U2AF1 shRNA treatment, 3 biological replicates of U2AF2 shRNA treatment, 3 biological replicates of DMSO treatment, 3 biological replicates of OTS964 (OTS) treatment, 3 biological replicates of Pladienolide B (PB) treatment, 3 biological replicates of 25uM control AMO treatment, and 3 biological replicates of 25uM U1 AMO treatment. All samples were prepared from wild-type HEK293T cells. In addition, we generated a HEK293T cell line in which a FKBP12 F36V-degron was fused to the N-terminus of INTS11 via CRISPR/Cas9. We performed 4sU-seq in this cell line following treatment with 25 µM control AMO + DMSO (3 replicates), 25 µM control AMO + dTAG to induce INTS11 degradation (3 replicates), 25 µM U1 AMO + DMSO (3 replicates), and 25 µM U1 AMO + dTAG to induce INTS11 degradation (3 replicates).

Examination of 41 samples by mRNA-seq. There are 3 biological replicates of 50uM control AMO treatment, 3 biological replicates of 50uM U2 AMO treatment, 3 biological replicates of control shRNA treatment, 3 biological replicates of U2AF1 shRNA treatment, 3 biological replicates of U2AF2 shRNA treatment, 3 biological replicates of DMSO treatment, 3 biological replicates of OTS964 (OTS) treatment, 3 biological replicates of Pladienolide B (PB) treatment, 3 biological replicates of 25uM control AMO treatment, and 2 biological replicates of 25uM U1 AMO treatment. All samples were prepared from wild-type HEK293T cells. In addition, we generated a HEK293T cell line in which a FKBP12 F36V-degron was fused to the N-terminus of INTS11 via CRISPR/Cas9. We performed mRNA-seq in this cell line following treatment with 25 µM control AMO + DMSO (3 replicates), 25 µM control AMO + dTAG to induce INTS11 degradation (3 replicates), 25 µM U1 AMO + DMSO (3 replicates), and 25 µM U1 AMO + dTAG to induce INTS11 degradation (3 replicates).

middle: V

last: Soles


title: Differential roles of copper-binding transcription factors and the subfamilies of the SWI/SNF complex in the transcriptional regulation of the skeletal muscle lineage

status: Public on Oct 26 2024

city: Pittsburgh

first: David

last: Klein

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh


title: Loss of polarity by CDC42 depletion and oncogenic Kras activation in the intestine lead to a necrotizing enterocolitis (NEC)-like disease

status: Public on Apr 12 2025

city: Cincinnati

first: Zheng

last: Zhang

state: OH

address: 8760 Sturbridge Dr

department: Division of Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Cdc42 is a key regulator of cell polarity that modulates cytoskeletal dynamics, morphology, and directional movement and plays a important role in maintaining epithelial integrity. Loss of Cdc42 in the small intestine causes disrupted polarity, hyperplasia, and mislocalization and expansion of transit-amplifying (TA) cells at the expense of intestinal stem cells (ISCs). KRAS, on the other hand, is essential for intestinal cell proliferation and differentiation, and oncogenic KRAS mutations can lead to disrupted epithelial homeostasis and contribute to gastrointestinal transformation. A human cancer database analysis suggests that loss of polarity mutations and oncogenic KRAS mutations are mutually exclusive in colon cancer patients. We found that intestinal epithelium-specific deletion of Cdc42 combined with oncogenic Kras expression in inducible Villin-CreER mice causes severe defects in the small intestine leading to lethality. Mice with Cdc42 deletion and oncogenic Kras expression in the intestinal epithelium exhibited reduced weight, disrupted villous mucosal structure, altered tight junction protein expression, reduced proliferation, loss of ISCs, inflammation, and enterocyte necrosis. These defects resemble Necrotizing Enterocolitis (NEC), a severe gastrointestinal disorder affecting preterm infants characterized by inflammation and necrosis of the small intestine epithelial cells. Single cell RNAseq analyses revealed that Cdc42 loss combined with oncogenic Kras expression resulted in disrupted intestinal polarity machinery with altered hippo signaling, exacerbated inflammation highlighted with elevated IL1 expression, and necroptosis. Targeted inhibition of necroptosis, IL-1 receptor, or YAP signaling rescues NEC-like defects. Additionally, ISCs-specific deletion of Cdc42 and oncogenic Kras expression induced by an intestinal stem cell driver, Omlf4-CreER, led to similar NEC-like defects in the mouse intestinal epithelium. These findings present a mechanism involving YAP-IL1-necroptosis signaling by combined disruption of polarity and oncogenic cues such as Kras in intestine function and provide insights into the effects of hyperactivation of these pathways in disrupting intestinal epithelia.

overall_design: intestinal epithelium-specific deletion of Cdc42 combined with oncogenic Kras expression in inducible Villin-CreER mice to generate CDC42KO/Kras sample, while WT, CDC42 KO, and Kras are used as control. After harvesting using described methods (Barker et al., 2007), villi/crypts were resuspended in mixed medium comprised of 30% 10x TrypLE and 70% Advanced DMEM/F12 , incubated at 37 degree for 30-45 min. Mixing and passaging through a glass pipette was preformed every 10 min and suspensions were monitored with a microscope. After disruption of the cell aggregates, cells were filtered through a 40 um filter and then pelleted by centrifugation (5 min at 300–400g), washed once with Advanced DMEM/F12, and resuspended in the same medium for 10x genomics sc-RNA seq.

first: Cuiqing

last: Fan

first: Ryan

last: Jorgensen

first: Mike

last: Adam

first: Yi

last: Zheng


title: Transcriptomic profiling of MCF-7 breast cancer cells under normoxic and hypoxic conditions

status: Public on Oct 21 2024

city: Shenyang

first: Huanyu

last: Wu

state: Liaoning

address: No. 77 Puhe Road

department: Pathology Teaching and Research Office of Basic Medical College

country: China

institute: China Medical University

summary: This RNA-sequencing study was designed to characterize transcriptional changes induced by hypoxia in MCF-7 breast cancer cells and to identify hypoxia-responsive genes and pathways associated with ZNF207 signaling. MCF-7 cells were cultured under normoxic conditions or exposed to 2% O₂ for 24 h, with three independent biological replicates per condition. Differential expression and pathway enrichment analyses were performed to compare the two conditions. The dataset itself does not contain drug-treated samples. Findings from separate functional assays in the associated manuscript indicate that ZNF207 is linked to breast cancer progression and chemotherapy response.

overall_design: Comparative RNA-sequencing analysis of MCF-7 breast cancer cells cultured under normoxic conditions or hypoxic conditions (2% O2 for 24 h). Aerobic treatment of MCF-7 cells rep1, rep2, rep3;Treatment of MCF-7 cells with 2% O2 for 24 hours rep1, rep2, rep3


title: Differential roles of copper-binding transcription factors and the subfamilies of the SWI/SNF complex in the transcriptional regulation of the skeletal muscle lineage [CUT&RUN]

summary: Copper (Cu)-binding transcription factors are emerging as important regulators of gene expression during skeletal muscle differentiation. Our group has shown that the classic Metal Transcription Factor 1, MTF1, works cooperatively with the myogenic factor MyoD to promote skeletal muscle differentiation and ensure viability of murine primary myoblasts. Preliminary evidence showed that MTF1 interacts with members of the mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) family of ATP-dependent chromatin remodeling enzymes to promote differential gene expression in proliferating and differentiating myoblasts. mSWI/SNF complexes are assembled into three major subfamilies that are distinguished by the presence of mutually exclusive subunits: cBAF (canonical BRG1 or BRM-Associated Factor), PBAF (Polybromo containing BAF), or ncBAF (non-canonical BAF). The mechanisms by which each subfamily contributes to the establishment or function of specific cell lineages are poorly understood. We determined the contributions of the BAF, ncBAF, and PBAF complexes to myoblast proliferation, differentiation, and metal homeostasis via knock-down (KD) of a distinguishing subunit of each complex (Baf250A, Brd9, and Baf180, respectively). Biochemical, molecular and RNA-seq analyses showed that Baf250A KD reduced myoblast proliferation rate and differentiation. Brd9 KD resulted in a minor proliferation defect and a delay in myogenesis. KD of Baf180 and other PBAF-specific subunits did not impact proliferation or differentiation but affected the maintenance of metal homeostasis in myoblasts. The data support a model for differential roles and interactions between MTF1 and a novel category of Cu-binding transcription factors and the SWI/SNF enzymes in the development and homeostasis of the skeletal muscle lineage.

overall_design: Three replicates of CUT&RUN targeting MTF1 or untargeted IgG control were performed on proliferating myoblast cells treated with either copper or no treatment.

first: Monserrat

last: Olea-Flores

middle: C

first: Nick

last: Carulli

first: Yaje

last: Nshanji

first: Cat

last: McCann

first: Sabriya

last: Syed

first: Anthony

middle: N

last: Imbalzano

middle: J

last: Hainer

first: Teresita

last: Padilla-Benavides


title: Differential roles of copper-binding transcription factors and the subfamilies of the SWI/SNF complex in the transcriptional regulation of the skeletal muscle lineage [RNA-seq]

overall_design: Two replicates of RNAseq were performed for knockdowns targeting the Baf180, Baf250, Brd9 genes (and a SCR control). Within each of these knockdowns, cells were treated with addition of Cu, Zn, or no treatment.

first: Sarah


title: Transcriptomic profiling of MDA-MB-453 breast cancer cells following ZNF207 overexpression

status: Public on Oct 16 2024

summary: This RNA-sequencing study was designed to characterize transcriptional changes associated with ZNF207 overexpression in MDA-MB-453 breast cancer cells and to identify downstream pathways. MDA-MB-453 cells transfected with a control vector or a ZNF207-overexpression construct were analyzed, with three independent biological replicates per group. Differential expression and pathway enrichment analyses were performed to compare ZNF207-overexpressing cells with control cells. The dataset itself does not contain drug-treated samples. Findings from separate functional assays in the associated manuscript indicate that ZNF207 is linked to breast cancer progression and chemotherapy response.

overall_design: Comparative RNA-sequencing analysis of MDA-MB-453 breast cancer cells transfected with control vector or ZNF207-overexpression construct. Three independent biological replicates were analyzed per group: vector control, n=3; ZNF207 overexpression, n=3; total n=6.


title: Mutant-p53 stimulates Cxcl1 Expression from Distal Enhancers to Suppress Immune Response to Pancreatic Cancer [CUT&RUN]

status: Public on Oct 09 2024

city: Cambridge

first: Dig

middle: B

last: Mahat

email: mahat@mit.edu, dbm222@cornell.edu

state: MA

address: Koch Institute, MIT, 500 Main St, Building 76, #417

department: Koch Institute for Integrative Cancer Research

institute: Massachusetts Institute of Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer without effective treatments. It is characterized by activating KRAS mutations and p53 alterations. However, how these mutations alter cell-intrinsic gene programs to influence the immune landscape of the tumor microenvironment (TME) remains poorly understood. Here, we demonstrate that p53R172H enhances tumor growth, establishes a suppressive TME by inducing immune evasion, and blunts the effectiveness of immune checkpoint inhibitors (ICIs). We discovered that the oncogenic function of p53R172H is mediated by upregulation of the immunosuppressive chemokine Cxcl1. Mechanistically, we show that p53R172H binds to the distal enhancers of the Cxcl1 gene and increases enhancer activity and Cxcl1 expression. NF-kB also occupies Cxcl1 enhancers, and p53R172H binds these enhancers in an NF-kB-dependent manner, suggesting a role of NF-kB in commuting p53R172H to the Cxcl1 enhancers. Our findings elucidate how a common mutation in a critical tumor-suppressor gene exploits enhancers to modulate chemokine gene expression and foster an immunosuppressive TME in PDAC that undermines the efficacy of ICI.

overall_design:
To investigate the role of p53R172H in pancreatic ductal adenocarcinoma (PDAC), we generated isogenic Trp53-/- PDAC cells (KrasG12D/+; Trp53-/-) using CRISPR-Cas9. We compared transcriptional programs via RNA-seq and PRO-seq, exonic mutations using Exome-seq, and genome occupancy with CUT&RUN between Trp53R172H/- and isogenic and syngenic Trp53-/- cells, as well as Trp53-/- cells with ectopically expressed p53R172H.
We orthotopically implanted the PDAC cells into the pancreas of mice and evaluated tumor growth, size, and the immune landscape. We further treated the mice with immune checkpoint inhibitors and monitored their survival.
To explore the role of Cxcl1 and its enhancers, we generated Cxcl1-/- cells and Cxcl1 enhancer knockout cells. We then assessed gene expression, immune profiling, and the response to immune checkpoint inhibitors in these models.

first: Heena

last: Kumra

last: Castro

first: Emily

last: Metcalf

first: Kim

last: Nguyen

first: Ryo

last: Morisue

first: William

middle: W

last: Ho

first: Ivy

last: Chen

first: Brandon

last: Sullivan

first: Leon

last: Yim

first: Arundeep

last: Singh

first: Jiayu

last: Fu

first: Sean

last: Waterton

first: Yu-Chi

last: Cheng

first: Enrico

last: Moiso

first: Vikash

last: Chauhan

first: Hernandez

last: Moura Silva

first: Stefani

last: Spranger

first: Rakesh

last: Jain

first: Phillip

last: Sharp


title: Mutant-p53 stimulates Cxcl1 Expression from Distal Enhancers to Suppress Immune Response to Pancreatic Cancer [EXOME-seq]

first: Dig

last: Mahat

first: Heena

last: Kumra

first: Sarah

last: Castro

first: Emily

last: Metcalf


title: Mutant-p53 stimulates Cxcl1 Expression from Distal Enhancers to Suppress Immune Response to Pancreatic Cancer [RNA-seq]

first: Kim

last: Nguyen

first: Ryo

last: Morisue

first: William

last: Ho

first: Ivy

last: Chen


title: LSK immunophenotype hematopoietic stem cells after irradiation at day 2

status: Public on Oct 07 2024

city: 重庆Chongqing

first: Zeyu

last: Fu

state: 重庆Chongqing

address: 高滩岩正街

department: College of Preventive Medicine

institute: AMU

summary: To investigate the impact of radiation damage on hematopoietic stem cell fate decision, we conducted a longitudinal study, collecting single-cell data on days 2 post-radiation exposure. This approach enabled us to observe changes in the subpopulations of hematopoietic stem cells at the LSK level in mice over time. Additionally, we assessed alterations in their fate determination and lineage differentiation tendencies throughout the recovery process.

overall_design: To perform 10X Genomics single-cell sequencing on mouse bone marrow LSK cells, begin by euthanizing the mouse following ethical guidelines and extracting the femurs and tibias. Flush the bone marrow using a syringe with buffer PBS with 2% FBS, to obtain a single-cell suspension. Filter this suspension through a 40 µm cell strainer to remove debris and clumps. Next, enrich the LSK (Lineage^-, Sca-1^+, c-Kit^+) cells using fluorescence-activated cell sorting (FACS). Count the cells and assess viability using trypan blue staining. Adjust the concentration of LSK cells to the required density 700-1200 cells/µL, for optimal performance in the 10X Genomics Chromium Controller. Load the single-cell suspension, reagents, and gel beads into the appropriate wells of a 10X Genomics Single Cell 3' Chip and run the chip in the Chromium Controller to encapsulate single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs). Perform reverse transcription within the GEMs to generate barcoded cDNA from the mRNA of individual

first: Shilei

first: Song

last: Wang

first: Xinhai

last: Yang

first: Junping


title: Mutant-p53 stimulates Cxcl1 Expression from Distal Enhancers to Suppress Immune Response to Pancreatic Cancer [PRO-seq]

first: Brandon

last: Sullivan

first: Leon

last: Yim

first: Arundeep

last: Singh

first: Jiayu

first: Sean

last: Waterton

first: Yu-Chi

last: Cheng

first: Enrico

last: Moiso

first: Vikash

first: Hernandez


title: A massively parallel reporter assay library to screen short synthetic promoters in mammalian cells

status: Public on Oct 08 2024

city: Salt Lake City

first: Justin

last: English

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

summary: Cellular transcription enables cells to adapt to various stimuli and maintain homeostasis. Transcription factors bind to transcription response elements (TREs) in gene promoters, initiating transcription. Synthetic promoters, derived from natural TREs, can be engineered to control exogenous gene expression using endogenous transcription machinery. This technology has found extensive use in biological research for applications including reporter gene assays, biomarker development, and programming synthetic circuits in living cells. However, a reliable and precise method for selecting minimally-sized synthetic promoters with desired background, amplitude, and stimulation response profiles has been elusive. In this study, we introduce a massively parallel reporter assay library containing 6184 synthetic promoters, each less than 250 bp in length. This comprehensive library allows for rapid identification of promoters with optimal transcriptional output parameters across multiple cell lines and stimuli. We showcase this library’s utility to identify promoters activated in unique cell types, and in response to metabolites, mitogens, cellular toxins, and agonism of both aminergic and non-aminergic GPCRs. We further show these promoters can be used in luciferase reporter assays, eliciting 50-100 fold dynamic ranges in response to stimuli. Our platform is effective, easily implemented, and provides a solution for selecting short-length promoters with precise performance for a multitude of applications.

sample_organism:
Homo sapiens
Mesocricetus auratus
Mus musculus
synthetic construct

overall_design: Multiple mammalian cell lines were transfected with the TRE-MPRA library for 24 hours and were then treated with growth factors or specific compounds for six hours. For some experiments, cells were co-transfected with specific G protein-coupled receptors and treated with receptor agonsists for six hours. Some treatments contained multiple technical replicates, while others were performed once. RNA and DNA barcode abundance was determined via Illumina next-generation sequencing.

first: Adam

last: Zahm


title: Rhesus immune reference atlas (RIRA): a comprehensive single-cell atlas of rhesus macaque immune cells

status: Public on Sep 24 2024

city: Beaverton

first: Benjamin

last: Bimber

state: OR

address: 505 NW 185th Ave

summary: This is a single-cell RNA-seq atlas comprised of 10x genomics data from 47 macaques and 7 tissues

overall_design:
This dataset contains single-cell RNA-seq from bulk immune cells from rhesus macaque tissues
Please note that the series supplementary .rds data files have been updated on Feb 7, 2025.


title: Hepatokine ORM2 suppresses pathological ferritinophagy to prevent acute tissue injury

status: Public on Sep 22 2024

city: Shanghai

first: Hongyi

last: Tang

address: Chongqing Nan Road 280

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University School of Medicine

summary: Acute tissue injuries trigger rapid cellular damage, but cell-intrinsic protective programs attenuate pathology through regulatory axes. Here, we demonstrate that Orosomucoid 2 (ORM2), a hepatokine, is significantly upregulated during drug-induced acute liver injury. Knock out Orm2 exacerbates liver damage, while its overexpression provides protection, identifying ORM2 as an endogenous hepatoprotective factor during acute liver injury. Mechanistically, ORM2 disrupts the FTH-NCOA4-TAX1BP1 interaction, thereby blocking ferritinophagy and preventing iron overload-induced cytotoxicity. Furthermore, acute ischemia-reperfusion injuries in other organs also trigger hepatic ORM2 upregulation and secretion, demonstrating liver-organ crosstalk via the circulatory system. Exogenous administration of ORM2 effectively ameliorates ferroptosis and tissue damage in multiple ischemia-reperfusion injury models. Collectively, our results identify the hepatokine ORM2 as a key suppressor of pathological ferritinophagy. This function positions ORM2 protein as a potential therapeutic candidate for acute tissue injuries driven by ferritinophagy-mediated iron overload.

overall_design: WT and Orm2 KO mice were injected with APAP or PBS, and liver tissues were collected 24 hours later for RNA-seq.

first: Xuxu

last: Sun

first: Bing

last: Zhou

first: Jun

last: Wu

first: Jie


title: Transcriptomic Analysis of Hofbauer Cells from Human Placental Tissue Infected with HIV, CMV, and ZIKV

status: Public on Sep 20 2024

city: Atlanta

first: Erica

middle: L

last: Johnson

state: GA

address: 720 Westview Drive SW

department: Department of Microbiology, Biochemistry, and Immunology

institute: Morehouse School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: This study involves the isolation of Hofbauer cells from human placental tissue at different gestation periods and their infection with HIV, CMV, and ZIKV. The transcriptomic profiles of these infected cells were analyzed using RNA-sequencing to identify differentially expressed genes and pathways.

overall_design: Hofbauer cells were isolated from human placental tissue and infected with HIV, CMV, and ZIKV. RNA was extracted, and RNA-sequencing was performed to analyze transcriptomic changes.

first: Viviane

last: Schuch

first: Daniel

last: Hossack


title: Bulk RNAseq of adult Drosophila melanogaster whole brains with neuronal specific knock down of brummer.

status: Public on Sep 19 2024

city: Vancouver

first: Elizabeth

last: Rideout

state: BC

address: 2350 Health Sciences Mall

department: Department of Cell and Physiological Science

institute: University of British Columbia

summary: Lipids are essential for neuron development and physiology. Lipid droplets (LD) play a central role in coordinating cellular lipid distribution and metabolism in non-neuronal cells; however, there is no general consensus on a role for neuronal LD under normal physiological conditions. We have previously shown that neuronal LD exists in wildtype flies under normal physiological condition, and that the loss of a triglyceride lipase, brummer, increases neutral lipids in the brain (Wat et al., 2020). To investigate the importance of brummer in regulating neuronal metabolism and function in a sex-specific manner, we performed transcriptomic profiling in adult male and female whole brain with RNAi-mediated neuron-specific knock down of brummer.

overall_design: To assess the transcriptomic effects of brummer knock down in either males or females, we raised male and female flies with neuron-specific expression of RNAi targeting brummer transcripts (elav-GAL4>UAS-bmm-RNAi). Adult whole brains were dissected at day 5 to 6 after eclosion for transcriptomic profiling. We also profiled the transcriptome of whole brains from elav-GAL4>+ and +>UAS-bmm-RNAi males and females as controls.

first: Colin

last: Miller

first: Serena

last: Hollman

first: Charlotte

last: Chao


title: LSK immunophenotype hematopoietic stem cells in Dapp1 knockout mice

status: Public on Sep 18 2024

first: Zeyu

last: Fu

summary: To investigate the impact of perturbing key differentiation driver genes on hematopoietic stem cell fate decision, we employed a Dapp1 gene knockout approach. This allowed us to observe changes in the subpopulations of hematopoietic stem cells at the LSK level in mice. Additionally, we assessed alterations in their fate decision and lineage differentiation tendencies

overall_design:
We conducted an in-depth single-cell RNA sequencing study using the 10X Genomics platform to analyze mouse bone marrow LSK (Lin^⁻Sca-1^⁺c-Kit^⁺) cells. Starting with ethically euthanized mice, we extracted femurs and tibias to harvest the bone marrow. The marrow cells were flushed out using a syringe with PBS containing 2% FBS to create a single-cell suspension. This suspension was filtered through a 40 µm cell strainer to eliminate debris and cell clumps, ensuring a pure population of cells for analysis. To isolate our target LSK cells, we employed fluorescence-activated cell sorting (FACS), selecting for Lineage-negative, Sca-1-positive, and c-Kit-positive cells. We assessed the viability of these cells using trypan blue staining and adjusted the concentration to approximately 1,000 cells/µL, optimizing conditions for the 10X Genomics Chromium Controller. We then loaded the purified single-cell suspension, along with the necessary reagents and gel beads, into a 10X Genomics Single Cell 3' Chip. Running the chip in the Chromium Controller, we encapsulated individual cells into Gel Bead-In-Emulsions (GEMs), enabling the barcoding of mRNA from each cell during reverse transcription within the GEMs. Following emulsion breakage, we purified the barcoded cDNA and performed PCR amplification. The amplified cDNA was evaluated for quality and quantity using an Agilent Bioanalyzer to ensure downstream sequencing success. Constructing sequencing libraries from the high-quality cDNA, we followed the 10X Genomics protocol meticulously. These libraries were then sequenced on an Illumina NovaSeq platform, adhering to the recommended read lengths and depths to achieve comprehensive single-cell transcriptional coverage.
The sequencing data generated were processed using the 10X Genomics Cell Ranger pipeline, which aligned reads and produced a gene expression matrix for each cell. For data analysis, we utilized various bioinformatics tools, prominently featuring our novel scRL (single-cell Reinforcement Learning) framework. This advanced analytical approach allowed us to identify distinct cell populations and gene expression patterns with high precision. Most critically, employing scRL enabled us to obtain quantitative indicators of the strength of cell lineage differentiation fate decisions—a level of insight not achievable with existing methods.

first: Song

last: Wang

first: Shilei

last: Chen

first: Junping


title: The role of Cebpb in Alcohol-associated Liver Disease development and resolution

status: Public on Sep 12 2024

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

institute: University of Kansas Medical Center

summary: Abstinence is an important therapeutic intervention for patients with alcohol-associated liver disease (ALD). However, fibrosis improvement after cessation is not uniform and some patients do not improve. We aimed to use scATAC-seq analysis in a mouse model of ALD to define the mechanism of poor ALD resolution. We analyzed differentially accessible regions in livers from control, ALD, or 4 weeks post alcohol cessation mice and identified transcription factors activated in ALD that remained activated after alcohol withdrawal. The top hit was C/EBPβ. We found that hepatocyte specific Cebpb knockout prevented ALD development, while knockout at the time of alcohol cessation promoted fibrosis resolution.

overall_design: Whole liver mRNA analysis in alcohol fed (WDA - western diet with alcohol in the drinking water) Cebpb floxed mice treated with  AAV-Cre vectors

first: Michal

middle: P

last: Schonfeld


title: Spatial Mapping of Mouse Brain Aging through Indexed Sequencing

city: New York

first: Abdulraouf

last: Abdulraouf

state: NY

address: 1230 York Ave

institute: Rockefeller University

summary: Here, we have developed a novel methodology called IRIS (Imaging Reconstruction using Indexed Sequencing) that enables cost-effective spatial transcriptomics profiling without relying on optical imaging. Through neighborhood interaction-based reconstruction, IRIS allows extensive analysis of large tissue sections and many replicates with adjustable mapping resolution at only a fraction of the cost of other commercial platforms. With the IRIS platform, we reconstructed a large area spatial area with two whole mouse brain coronal sections. Moreover, we also created a spatially resolved transcriptome atlas of the mouse brain and identified aging-associated changes in gene expression and spatial organization across various brain cell types. Further analysis of cell-cell interaction changes identified aging-associated foci in white matter regions enriched with inflammatory subtypes of microglia and oligodendrocytes. Overall, the IRIS methodology cost-effective and ease-of-use approach makes it broadly applicable to the studies of spatial gene expression changes in various systems.

overall_design: Utilizing the IRIS platform, we conducted a comprehensive spatial analysis of molecular profiles and spatial arrangements of cell types in mouse brains. To study the aging-associated transcriptome changes, here we collected brain tissues from adult (4-month) and the aged (23-month) wild-type C57BL/6 mice, with three replicates per age group.

first: Weirong

last: Jiang

first: Zihan

last: Xu

first: Zehao

last: Zhang

first: Tanvir

last: Raihan

first: Wei

first: Junyue

last: Cao


title: Therapeutic silencing Spp1 in cardiac macrophages suppresses atrial fibrillation

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

summary: Atrial fibrillation (AFib) and the risk of its lethal complications are worsened by atrial fibrosis. A recent study implicates osteopontin (encoded by Spp1) secreted by atrial TREM2+ macrophages in this fibrosis. Here, we show that silencing Spp1 in TREM2+ cardiac macrophages using an antibody-siRNA conjugate (ARC) reduces atrial fibrosis and suppresses AFib, thus offering a new immunotherapy for this common arrhythmia.

overall_design:
Single-nucleus RNA sequencing was used to investigate the transcriptomic differences between nuclei isolated from left atrial tissues collected from 3 vehicle- and 3 anti-Trem2-siSpp1-treated HOMER mice.
Bulk RNA sequencing was used to investigate the transcriptomic differences between mouse bone marrow-derived macrophages treated with vehicle (lipofectamine) or siSpp1 for 24 hours.

first: Noor

last: Momin

first: Steffen

last: Pabel

first: Kamila

last: Naxerova

first: Matthias

last: Nahrendorf

first: Maarten

last: Hulsmans


title: Small RNA sequencing of 50 laryngeal squamous cell carcinoma and paired adjacent normal tissues

status: Public on Sep 09 2024

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

summary: Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer with poor prognosis. However, the mechanism underlying the pathogenesis of LSCC remains unclear. We performed high throughout sequencing to identify miRNA that associated with LSCC progression.Small RNA libraries were constructed followed by sequencing on a cohort of LSCC tissues (50 samples) and paired adjacent normal mucosa tissues (50 samples).

overall_design: Expression of miRNA in 50 LSCC and 50 paired adjacent normal mucosa tissues was examination by high throughout sequencing.

last: Gao

first: Binquan

first: Xiwang

last: Zheng


title: The proteomic landscape and temporal dynamics of human and mouse gastruloid development

status: Public on Sep 06 2024

city: Seattle

first: Riddhiman

last: Garge

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Gastrulation is the highly coordinated process by which the early embryo breaks symmetry, establishes germ layers and a body plan, and sets the stage for organogenesis. As early mammalian development is challenging to study in vivo, stem cell-derived models have emerged as powerful surrogates, e.g. human and mouse gastruloids. However, although single cell RNA-seq (scRNA-seq) and high-resolution imaging have been extensively applied to characterize such in vitro embryo models, a paucity of measurements of protein dynamics and regulation leaves a major gap in our understanding. Here we sought to address this by applying quantitative proteomics to human and mouse gastruloids at four key stages of their differentiation (naïve ESCs, primed ESCs, early gastruloids, late gastruloids). To the resulting data, we perform network analysis to map the dynamics of expression of macromolecular protein complexes and biochemical pathways, including identifying cooperative proteins that associate with them. With matched RNA-seq and phosphosite data from these same stages, we investigate pathway-, stage- and species-specific aspects of translational and post-translational regulation, e.g. finding peri-gastrulation stages of human vs. mice to be discordant with respect to the mitochondrial transcriptome vs. proteome, and nominating novel kinase-substrate relationships based on phosphosite dynamics. Finally, we leverage correlated dynamics to identify conserved protein networks centered around congenital disease genes. Altogether, our study showcases the potential of intersecting proteomics and in vitro embryo models to advance our understanding of early mammalian development in ways that may not be possible through transcriptomics alone.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To map the temporal changes underlying gastruloid development, we performed multi-omic phenotyping on 4 stages of gastruloid differentiation namely Naive ESCs, Primed ESCs, Early gastruloids and Late gastruloids.

first: Valerie

last: Lynch

first: Rose

last: Fields

first: Silvia

last: Casadei

first: Sabrina

last: Best

first: Jeremy

last: Stone

first: Matthew

last: Snyder

first: Connor

last: Kubo

first: Arata

last: Wakimoto

first: Zukai

last: Liu

first: Chris

middle: D

last: McGann

first: Jay

last: Shendure

first: Lea

last: Starita

first: Nobuhiko

last: Hamazaki

first: Devin

last: Schweppe


title: Constitutively activating MEK1 mutations drive treatment refractory histiocytic neoplasms but confer response to ERK inhibition

status: Public on Sep 03 2024

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

summary: Histiocytic neoplasms are clonal disorders of the monocyte/macrophage lineage defined by mutations activating MAP kinase signaling, including BRAFV600E mutations in ~50% of patients, which confer robust responses to BRAF inhibition. More recently, the MEK inhibitor cobimetinib was FDA-approved for BRAFV600-wild-type histiocytosis patients. Here following genomic analysis of 500 pediatric and adult patients with diverse histiocytoses, the most common alteration following BRAFV600E was MEK1E102_I103 in-frame deletion. MEK1E102_I103del and related RAF-independent MEK mutants were associated with an aggressive multi-system clinical phenotype with worse progression-free survival with MEK inhibition as compared to patients with other classes of MEK1/2 mutations. Given that cancer-associated MEK1/2 mutations have not been modeled in vivo and the clinical importance of MEK1 mutations in histiocytoses, we generated MEK1E102_I103del conditional knock-in mice. Using three distinct hematopoietic Cre drivers, these mice developed a 100% penetrant, lethal disorder by 6 weeks of age with expansion of classical and non-classical monocytes, macrophages, and Cd11b+ conventional dendritic cells which infiltrated hematopoietic organs, liver, and skin. MEK1-mutant mice were sensitive to single-agent treatment with the oral ERK inhibitor ulixertinib. We consequently treated five MEK1E102_I103del-mutant patients with ulixertinib on prospective IRB-approved Single Patient Use Expanded Access protocols, four of whom had disease refractory to MEK inhibition. Four of five patients experienced objective clinical and/or radiological responses to ulixertinib. These data reveal the impact of oncogenic MEK kinase mutations in vivo, identify patients with likelihood of resistance to MEK inhibition, and nominate ERK inhibition as a therapeutic approach to overcome resistance to MEK inhibition in histiocytoses.

overall_design: Sorted live cells were harvested from frozen/thawn bone marrow and spleen samples from Mx1-cre-Map2k1-E102_I103del mutant (n=3) and control mice (n=3) mice for 3' scRNA sequencing.

first: Eli

last: Diamond

first: Jean-François

last: Emile

first: Julien

last: Haroche

first: Anne

middle: S

last: Reiner

first: Dana

last: Bossert

first: Michael

last: Singer

first: Alexander

last: Lewis

first: Salima

last: Benbarche

first: Nina

last: Fox

first: Cynthia

last: Castro

first: Steven

last: Tittley

last: Witkowski

first: Neal

last: Rosen

first: Omar

last: Abdel-Wahab

first: Benjamin

last: Durham


title: Single cell RNA sequencing analysis of Mig-6 mutant mouse reveals progesterone susceptibility genes for uterine receptivity

status: Public on Mar 21 2025

city: Columbia

first: Shamsun

last: Nahar

state: MO

address: 1030 Hitt Street

department: Obstetrics, Gynecology and Women’s Health

institute: University of Missouri

summary: The majority of pregnancy losses result from implantation failure. Successful embryo implantation involves a delicate interaction between the receptive uterus and an implantation-competent blastocyst. Understanding the mechanisms regulating the endometrial receptivity during preimplantation are essential for improving pregnancy outcomes. Mitogen-inducible gene 6 (MIG-6) is a key mediator of progesterone signaling in the endometrium.MIG-6 loss results in implantation failure due to non-receptive endometrium. We applied single cell RNA sequencing to determine the composition of different cell types and functions within non-receptive endometrium from uterine specific Mig-6 knock-out (Pgrcre/+Mig-6f/f; Mig-6d/d) mice. Mig-6d/d mice revealed altered gene expression in the epithelial and stromal cells. We identified key gene expression changes in the non-receptive endometrium of Mig-6d/d mice, providing valuable insights into the role of progesterone signaling in implantation.

overall_design: At pregnancy day 3.5, the scRNA-seq was performed using Mig-6f/f and Mig-6d/d (Pgrcre/+ Mig-6f/f) mouse uterus (n=1). Immunohistochemistry was done to varify the changes between clusters Mig-6f/f and Mig-6d/d.

first: Kim

last: Tae Hoon

first: Jeong

last: Jae Wook


title: Transcriptomic analysis of spinal V1 interneurons informs their multifunctional role in motor output

status: Public on Sep 02 2024

city: Memphis

first: Jay

last: Bikoff

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: We present a transcriptomic atlas of spinal V1 interneurons across postnatal development (P0, P14, P28, and P56) in the mouse using single-nucleus RNA sequencing (snRNA-seq). We also present transcriptomic data comparing V1 interneurons in En1 heterozygous and En1 KO mice at age P0 only.

overall_design: V1 nuclei were genetically labeled by crossing En1::Cre mice in either the heterozygous or homozygous (KO) state to RC.lsl.Sun1-sfGFP (INTACT) mice, and GFP+ nuclei were isolated by flourescence activated cell sorting. snRNA-seq was performed on the 10X Genomics Chromium 3' platform  (v3.1).

first: Alexandra

last: Trevisan

first: Katie

last: Han

first: Phillip

last: Chapman

first: Anand

last: Kulkarni

first: Jennifer

last: Hinton

first: Cody

last: Ramirez

first: Ines

last: Klein

first: Graziana

last: Gatto

first: Mariano

middle: I

last: Gabitto

first: Vilas

last: Menon


title: Transcriptomic analysis and high throughput functional characterization of human induced pluripotent stem cell derived sensory neurons (bulk RNA-Seq)

status: Public on Aug 26 2024

city: Minneapolis

first: Vincent

last: Truong

state: MINNESOTA

address: 2112 Broadway ST NE, STE 135

institute: Anatomic Incorporated

summary: Peripheral sensory neurons are a primary effector in pain neurotransmission, and have become a useful cellular model for the study of pain. While rodent tissue has historically served as a source of these neurons, it has become increasingly clear that pain mechanisms in rodents and humans are substantially divergent. Sensory neurons harvested from cadaveric human tissue serve as a superior translational model for studying pain mechanisms, however their relative paucity limits their widespread utility. Theoretically, sensory neurons manufactured from human pluripotent stem cells (hPSCs) could help bridge this translational gap given their relative abundance and potential similarity to primary human tissue. However, hPSC-derived sensory neurons manufactured with the most common methodologies correlate poorly to human tissue both transcriptionally and functionally. In the present work, we compare a novel population of hPSC-derived sensory neurons to previously published datasets and find this novel population to more closely resemble human primary dorsal root ganglia transcriptionally. Furthermore, we evaluate the heterogeneity of this novel population via single nucleus RNA sequencing and find it resembles specific nociceptor and mechanoreceptor subsets found in vivo. Finally, we assay the functionality of this population with high throughput automated patch clamp electrophysiology with respect to voltage-gated sodium (Nav) and potassium channels (Kv), and ligand-gated ionotropic GABA and P2X receptors. Overall, we find this population of hPSC-derived sensory neurons to be of relatively high fidelity, and suitable for interrogating numerous potential pain targets on a fully humanized platform.

overall_design: Three lots of RealDRG manufactured from the same hiPSC line were thawed in Senso-MM (Anatomic Incorporated, #1030) at 100,000 neurons/cm2 in T25 format. Total RNA was collected at weekly timepoints for each line through four weeks.

first: Patrick

last: Walsh

first: Jackson

last: Brougher

first: Dale

last: George


title: Lentinula edodes Cultured Extract Intake at Puberty Mitigates Inflammatory Signals at the Mammary Glands by the Involvement of Epigenetic Mechanisms.

status: Public on Mar 15 2025

city: ottawa

first: Hamed

last: Yasavoli Sharahi

state: ontario

address: 451 Smyth Rd

institute: university of ottawa

type: Methylation profiling by genome tiling array

summary: Exposure to immune stress or lipopolysaccharide (LPS) during critical developmental stages, particularly puberty, may result in gut microbiome dysbiosis and disturb epigenetic regulation in mammary glands. This disruption can affect gene expression and potentially increase breast cancer susceptibility later in life. While the adverse effects of LPS on intestinal and brain function are documented, its impact on mammary glands is not well understood. An immunocompetent murine model (BALB/c mice) was administered an acute dosage of LPS during the pubertal stage. The study aimed to comprehensively evaluate the enduring effects of LPS exposure, as well as LPS exposure in combination with AHCC (Lentinula Edodes Cultured Extract), on various parameters, including DNA methylation patterns, cytokine profiles, and microRNA expression within the mammary gland during adulthood, at the age of 9 weeks. Analysis was carried out using DNA methylation sequencing, multiplex immunoassays, quantitative PCR, and image processing.Our findings revealed significant and enduring dysregulation in DNA methylation patterns, cytokine levels, and microRNA expression in the mammary glands exposed to LPS during puberty. These dysregulations significantly impacted critical signaling pathways related to mammary gland growth and potential breast cancer development. Notably, we observed hypermethylation of the transcriptional start sites (TSS), promoters, and 5' UTRs of critical genes, including Vav3, Pdgfa, Pdgfc, Jag2, Hras, Ksr1, Il2rb, Il17b, and Il17rb in the LPS group, whereas hypomethylation was evident in the prebiotic+LPS group. The multiplex immunoassays and quantitative PCR confirmed these findings. LPS exposure during puberty causes long-lasting epigenetic and inflammatory alterations in the mammary glands, which could influence breast cancer risk. The use of AHCC as a mitigating factor suggests potential for dietary interventions to prevent or reduce these effects.

overall_design: This study investigates the long-term effects of pubertal exposure to lipopolysaccharide (LPS) and prebiotic supplementation on the gut microbiota and immune system in female BALB/c mice. A total of 36 mice were divided into two dietary intervention groups: the prebiotic group, which received AHCC (2 g/kg BW/day) in drinking water, and the control group, which received regular drinking water. At the onset of puberty, defined by vaginal opening at five weeks of age, half of the mice in each group were intraperitoneally injected with LPS (1.5 mg/kg body weight) to induce inflammation and gut dysbiosis, while the remaining half received sterile PBS as a control. This resulted in four experimental groups, with nine mice per group: control + PBS, control + LPS, prebiotic + PBS, and prebiotic + LPS. The dietary intervention continued for one week after injection, followed by a standard diet until early adulthood. At nine weeks of age, the mice were sacrificed, and mammary gland tissue samples were collected for molecular analysis. DNA methylation profiling was performed using the Infinium™ Mouse Methylation BeadChip (Illumina), cytokine expression was measured using a multiplex Luminex immunoassay, and gene expression analysis was conducted via RT-qPCR for microRNA profiling. The study includes biological replicates (n=9 per group) and was designed to evaluate the impact of LPS exposure and prebiotic supplementation on immune modulation and epigenetic alterations. Control and experimental conditions were carefully structured to enable comparisons of differential methylation, cytokine expression, and miRNA regulation across the treatment groups.

last: Yasavoli-Sharahi

first: Roghayeh

last: Shahbazi

first: Nawal

last: Alsadi

first: Nasim

last: Bondar Sahebi

first: Cyrille

last: Cuenin

last: Cahais

first: Felicia

last: Fei-Lei Chung

first: Zdenko

last: Herceg

first: Chantal

last: Matar


title: ZMAT1 promotes osteoclast formation and bone loss through TRIM46 mediated YAP1 degradation II

status: Public on Aug 22 2024

first: Yijin

last: Hou

address: No. 168, Changhai Road

institute: Department of Traumatic Orthopedics, Changhai Hospital, Naval Medical University

summary: Osteoclasts and osteoblasts play a critical role in bone remodeling, and their dysregulation leads to pathological bone loss. However, precise regulation of their differentiation remains not fully elucidated. This study investigates the role of transcriptional regulator Zinc Finger Matrin-Type 1 (Zmat1) in both osteoclastogenesis and osteoblastogenesis. Zmat1 deficiency resulted in decreased osteoclast activity, and reduced bone resorption. Mechanististically, ZMAT1 was significantly upregulated during osteoclast differentiation and acted as a transcriptional repressor of the E3 ubiquitin ligase TRIM46, which then regulates YAP1 degradation via K48-linked ubiquitination. Furthermore, Zmat1 deficiency also enhanced osteoblast activity and bone formation. These findings highlight a novel ZMAT1/TRIM46/YAP1 axis, providing new insights into the transcriptional regulation of both osteoclast and osteoblast differentiation, and present potential therapeutic targets for osteoporosis.

overall_design: Extract bone marrow-derived macrophages from Zmat1 knockout mice and their wild-type littermate controls, and stimulate them with M-CSF for 3 days. Then, induce osteoclast development. The control groups are set as follows: 1WT-d0, 2WT-d0, 3WT-d0. The experimental groups are set up as follows: Without RANKL stimulation: 1KO-d0, 2KO-d0, 3KO-d0. After RANKL stimulation for 1 day: 1WT-d1, 2WT-d1, 3WT-d1; 1KO-d1, 2KO-d1, 3KO-d1. After RANKL stimulation for 3 days: 1WT-d3, 2WT-d3, 3WT-d3; 1KO-d3, 2KO-d3, 3KO-d3.

first: Xinyu

last: Chang


title: Transcriptomic analysis and high throughput functional characterization of human induced pluripotent stem cell derived sensory neurons  (scRNA-Seq)


title: Inherited functional regulatory risk variants for common human cancers [MPRA]

city: Stanford

first: Paul

last: Khavari

state: CA

address: 269 Campus Drive, CCSR, Room 2150

department: Dermatology

institute: Stanford University

summary: Single nucleotide variants (SNVs) in regulatory DNA are linked to inherited cancer risk. Massively parallel reporter assays (MPRA) of 5,031 SNVs linked to 14 neoplasms comprising >90% of human malignancies were performed in pertinent diploid cell types then integrated with matching chromatin accessibility, looping, and eQTL data to identify 411 regulatory SNVs and their putative target eGenes. The latter highlighted specific protein networks in lifetime cancer risk, including mitochondrial translation, proliferation, signaling, adhesion, and immunity. This cancer SNV compendium underscores the importance of studying pathogenic variants in disease-relevant cells and implicates specific dysregulated gene networks in cancer predisposition. It also indicates that inherited cancer risk can impact the same gene via orthogonal genetic mechanisms of dysregulated expression as well as protein coding sequence alteration and demonstrates that a subset of germline-encoded risk genes also enable tumor growth of established cancers.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Massively parallel reporter assay of cancer associated risk variants in 14 cell types

first: Laura

last: Kellman


title: Inherited functional regulatory risk variants for common human cancers

overall_design: CRISPR knockout screen of genes implicated in colon cancer by massively parallel reporter assay


title: ZMAT1 promotes osteoclast formation and bone loss through TRIM46 mediated YAP1 degradation.

status: Public on Aug 15 2024

overall_design: Extract bone marrow-derived mononuclear macrophages from wild-type C57BL/6 mice and stimulate with M-CSF for 3 days. Set up control groups: Control_1, Control_2, Control_3. The experimental groups are set up as follows: stimulate with LPS for 3 days: LPS_3d_1, LPS_3d_2, LPS_3d_3; stimulate with LPS for 4 hours: LPS_4h_1, LPS_4h_2, LPS_4h_3; stimulate with RANKL for 3 days: RANKL_3d_1, RANKL_3d_2, RANKL_3d_3; stimulate with RANKL for 4 hours: RANKL_4h_1, RANKL_4h_2, RANKL_4h_3.


title: ZMAT1 promotes osteoclast formation and bone loss through TRIM46 mediated YAP1 degradation. [CUT&Tag]

overall_design: There are no relevant reports on the role of Zmat1 as a transcription factor in osteoclast differentiation. To clarify the role of Zmat1 as a transcription factor in osteoclastogenesis, we constructed a Zmat1-overexpressing RAW264.7 cell line and set up a control group. Under RANKL stimulation, cells were collected, incubated with antibodies, and DNA was extracted. The DNA was then sequenced using Second Generation high-throughput sequencing technology. The results indicated that Zmat1 plays a regulatory role in gene transcription one sample were set up for each group.


title: Transcriptome profiling of cell lines from Ixodes scapularis

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: The goal of this study was to identify and compare baseline mRNA expression levels for a set of Ixodes scapularis cell lines originally reported in Munderloh et al. 1994 Journal of Parasitology 80(4):533-43. Three unmodified I. scapularis cell lines were included in the study:  ISE6, IDE2, and ISE18. In addition, one cell population modified by insertion of a transgenic cassette using Sleeping Beauty transposition was also included:  ISE18SB. The ISE18SB cells are a non-clonal cell population fully enriched for expression of a DsRed fluorescent marker gene included within the transposon insertion cassette. For all replicate samples, cells were collected after reaching approximately 60% confluency under standard culture conditions, then processed for RNA-seq analysis.

overall_design: Cells were cultured in airtight-capped flasks at 34 degrees C in a normoxic cell culture incubator in standard I. scapularis cell line media (Munderloh and Kurtii 1989 Experimental & Applied Acarology, 7:219-229) made in-house in our laboratory. For all replicate samples, cells were collected after reaching approximately 60% confluency (i.e., at Day 4 after seeding to fresh media). Approximately 5.5 x 10^6 cells per replicate sample were collected and processed for bulk RNA-seq analysis. All replicates were collected and processed together. RNA was extracted using Trizol and Zymo Research Direct-zol RNA Miniprep Kits. RNA was analyzed at the Biopolymers Facility at Harvard Medical School using an Agilent TapeStation as a quality control step. RIN analysis was not possible given the species; however, for all samples, the results of electrophoretic analysis profiles and quantitative PCR (qPCR) were consistent with high-quality RNA. KAPA mRNA HyperPrep Kits were used to build poly-A selected mRNA libraries. NGS was performed using an Illumina NovaSeq 6000 sequencing system with an SP flow cell. Reads were mapped to I. scapularis reference genome GCF_016920785.2 using STAR version 2.7.9a. Gene count extraction was done using FeatureCounts version 2.0.1. Normalization and conversion to FPKM values were performed using DEseq2 version 1.40.2.

first: Matthew

last: Butnaru

first: Weihang

last: Chen

first: Srishti

last: Goswami

first: Norbert

last: Perrimon

first: Stephanie

last: Mohr


title: Smad7-based biologic targeting epidermis and stroma promotes healing of diabetic wounds in mice and pigs

status: Public on Aug 13 2024

city: Aurora

first: Ben-Zheng

last: Li

state: CO

department: Department of Physiology and Biophysics

institute: University of Colorado Anschutz Medical Campus

summary: Impaired healing of diabetic wounds causes significant morbidity and mortality. This study aimed to identify novel mechanisms of diabetic wound healing defects and test a therapeutic intervention using diabetic mouse and pig models. We found Smad7 transgene expression in mouse epidermis promoting wound healing in diabetic db/db mice, with reductions in obesity and blood glucose. To isolate effects of Smad7 on wounds, we created a Smad7-based biologic (Tat-PYC-Smad7) that penetrates wound cells. Topical application of Tat-PYC-Smad7 to diabetic pig and mouse wounds accelerated healing compared to controls. RNAseq analysis of mouse wound samples showed reduced TGFβ/NFκB signaling, leading to faster re-epithelialization and better extracellular matrix remodeling. Tat-PYC-Smad7 also attenuated neutrophil degranulation and NETosis by blocking histone 3 citrullination and inhibiting myeloperoxidase activities. Our study reveals that Tat-PYC-Smad7 promotes diabetic wound healing by targeting keratinocytes and neutrophils, providing insight into cellular mechanisms of diabetic wound healing defects targetable by Smad7-based therapy.

overall_design: To understand the molecular basis of Tat-PYC-Smad7 effects, we performed RNA-seq on db/db mouse wound samples excised at identical locations treated with vehicle or Tat-PYC-Smad7 on days 9 and 11.

first: Yao

last: Ke

first: Fulun

first: Donna

last: Wang

first: Suyan

first: Sam

middle: T

last: Hwang

first: Scott

last: Simon

first: Sean

middle: R

last: Collins

first: Christian

last: Young

first: Xiao-Jing


title: Molecular differentiation between complete and incomplete responders to neoadjuvant therapy in rectal cancer

status: Public on Aug 09 2024

city: Birmingham

first: Fengyuan

last: Huang

state: AL

address: University Blvd

institute: University of Alabama at Birmingh

summary: Neoadjuvant chemoradiotherapy (nCRT) is the standard treatment for locally advanced rectal cancer, but less than half of patients have a clinical complete response to this treatment. To define the molecular features that are associated with response to neoadjuvant therapy, we generated and collected genomic and transcriptomic data from 712 cancers prior to treatment from our own data and from publicly available data. We found that patients with a complete response have decreased risk of local recurrence and future metastasis. We identified multiple differences in DNA mutations and transcripts between complete and incomplete responders. Complete responder tumors have a higher tumor mutation burden and many more significant co-occurring mutations than the incomplete responder tumors. In addition, mutations in DNA repair genes (across multiple mechanisms of repair) were enriched in complete responders and they also had lower expression of these genes indicating that defective DNA repair is associated with complete response to nCRT. Using logistic regression, we identified three significant predictors of complete response: tumor size, mutations within specific network genes, and the existence of three or more concurrent mutations. In tumors that do not completely respond to nCRT, abnormal cell-cell interaction and increased cancer associated fibroblasts were associated with recurrence. Additionally,gene expression analysis identified a subset of immune hot tumors with worse outcomes and upregulation of immune checkpoint proteins. Overall, our study provides a comprehensive understanding of the molecular features associated with response to nCRT and the molecular differences in non-responder tumors that later reoccur. This knowledge may provide critical insight into the development of precision therapy for rectal cancer.

overall_design: To investigate the transcriptomic differences between complete and incomplete responders to neoadjuvant therapy in rectal cancer,  we collected pre-treatment biopsy samples and isolated RNA from the samples. We then perfored gene expression profiling analysis using data obtained from RNA-seq of 15 samples from 7 patients.

first: Karin

last: Hardiman

first: Zechen

last: Chong

first: Marshall

last: McLeod

first: Regin

last: Irwin

first: Mary

last: Smithson

first: Zongliang

last: Yue

first: Min

last: Gao


title: Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read and single-molecule resolution

status: Public on Mar 05 2025

city: Irvine

first: Annie

last: Trinh

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

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

overall_design: Refer to individual Series


title: Deterioration of multi-level 3D genome organization during breast cancer progression

status: Public on Aug 07 2024

city: Oslo

first: Roberto

last: Rossini

address: Blindernveien 31

country: Norway

institute: University of Oslo

summary: Breast cancer progression entails intricate, multi-level alterations in genome organization and expression. To gain insights into the modifications in chromatin's three-dimensional (3D) structure during breast cancer progression, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) remain largely stable, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observed a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identified a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene becomes inserted into a highly active region on chromosome 10. This insertion event leads to the formation of de novo enhancer contacts and activation of the oncogene, illustrating how structural variants can interact with the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the degradation of genome organization at multiple scales during breast cancer progression revealing the complex interplay between genomic structure and oncogenic processes.

overall_design: We sequenced the transcriptome of MCF10A, MCF10AT1, and MCF10Ca1a cell lines to investigate changes in gene expression during breast cancer progression.

first: Mohammadsaleh

last: Oshaghi

first: Maxim

last: Nekrasov

first: Aurélie

last: Bellanger

first: Renae

last: Domaschenz

first: Yasmin

last: Dijkwel

first: Philippe

last: Collas

first: David

last: Tremethick

first: Jonas

last: Paulsen


title: Persistent changes in nociceptor translatomes govern hyperalgesic priming in mouse models

status: Public on Aug 06 2024

city: Dallas

first: Theodore

last: Price

state: TX

address: 800 W Campbell Rd

institute: The University of Texas at Dallas

summary: Hyperalgesic priming is a model system that has been widely used to understand plasticity in painful stimulus-detecting sensory neurons, called nociceptors. A key feature of this model system is that following priming, stimuli that do not normally cause hyperalgesia now readily provoke this state. We hypothesized that hyperalgesic priming occurs due to reorganization of translation of mRNA in nociceptors. To test this hypothesis we used paclitaxel treatment as the priming stimulus and translating ribosome affinity purification (TRAP) to measure persistent changes in mRNA translation in Nav1.8+ nociceptors. TRAP sequencing revealed 161 genes with persistently altered mRNA translation in the primed state. We identified Gpr88as upregulated, and Metrn as downregulated. We confirmed a functional role for these genes wherein a GPR88 agonist causes pain only in primed mice, and established hyperalgesic priming is reversed by Meteorin. Our work demonstrates that altered nociceptor translatomes are causative in producing hyperalgesic priming.

overall_design: Paclitaxel (Sigma Aldrich, Y0000698) was dissolved in a 1:1 solvent mixture of Kolliphor EL (Sigma-Aldrich) and ethanol. Female Nav1.8-TRAP mice were administered paclitaxel diluted in sterile Dulbecco’s phosphate buffered saline (DPBS; Thermo Scientific) or vehicle solvent intraperitoneally at a dosage of 4 mg/kg every other day, resulting in a cumulative dosage of 16 mg/kg. The animals were tested fro mechanical hypersensitivity until they reached back to baseline measurement. The animals were euthanized, and all dorsal root ganglion were dissected and trap sequencing was performed. The input and the immunoprecipitate fractions were bulk sequenced.

first: Ishwarya

last: Sankaranarayanan

first: Diana

last: Ferreira


address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

overall_design: The aim of this section of the overall project is to deterine the extent to which regions of the genome interacting with lamin B1 (lamina-associated domains, or LADs) vary, and to what extent topologically-associated domains (TADs) interact with lamin B1 in an in vitro model of breast cancer progression. The model consists of MCF10A, MCF10A and MCFCA1 cells cultured under prliferation conditions. LAD data were collected in parallel to chromatin interaction data using Hi-C, and trnascriptomic data using RNA-seq, in each cell type. Hi-C and RNA procedures and datafiles are described in associated GEO metada submissions.

first: Mohamed

last: Abdelhalim


title: Multimodal analysis reveals cellular diversity and divergent circuits of the zona incerta

status: Public on Aug 02 2024

city: Cambridge

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

summary: The zona incerta (ZI) plays an important role in diverse behavioral functions and is an emerging clinical target for deep brain stimulation to treat neurological conditions. Despite their importance, the cell type composition of the ZI and the anatomical circuit organization linking specific ZI cell types to brain-wide circuits remain unclear. In this study, we used single-nucleus RNA-sequencing, spatial RNA profiling, ex vivo electrophysiology, and anatomical circuit mapping to generate a multimodal cellular atlas of the ZI and to characterize the brain-wide monosynaptic inputs to specific ZI cell types. We define four genetically distinct populations of ZI GABAergic neurons that display unique spatial distributions, specialized intrinsic electrophysiological properties, divergent efferent projections, and cell-type dependent synaptic input patterns. Finally, using fiber photometry we reveal response divergence between distinct ZI cell types in a novel behavioral assay that centers around approach-avoid conflict produced by innately appetitive and aversive stimuli. This study thus provides a foundational resource for the design and interpretation of future experiments aimed at understanding the organization and function of the ZI.

overall_design: The GEO dataset comprises single-nucleus RNA-sequencing data of neurons of the zona incerta (ZI) from three adult (8-12 weeks old) C57Bl/6J mice.

first: Ryan

last: Kast

first: Sean

last: Simmons

first: Nita

last: Rome

first: Xian

last: Adiconis

first: Lisa

last: Melamed

first: Kate

last: McCabe

first: Dongqing

last: Wang

first: Alexandra

last: Krol

first: Magdalena

last: Krubner

first: Vincent

last: Prevosto

first: Kirsten

last: Levandowski

first: Ubadah

last: Sabbagh

first: Heather

last: Sullivan

first: Ian

last: Wickersham

first: Fan

middle: Z

first: Zhanyan

last: Fu

first: Guoping

last: Feng


title: Role of the STAR proteins in early mammalian development [Ribosome profiling]

city: Barcelona

first: Elias

last: Bechara

address: Dr Aiguader 88

country: Spain

institute: CRG

summary: RNA binding proteins (RBPs), are emerging as important master regulators of the biology of stem cells in both pluripotency and differentiation. The Signal transduction and activation of RNA (STAR) is family of proteins shown to be involved in mammalian development. We characterized the role of two members of the family, Sam68 and Quaking (QKI), in pluripotency and differentiation of mouse embryonic stem cells (mESCs) by making use of CRISPR-Cas9 generated knock-out (KO) cell lines along with RNA-sequencing, ribosome profiling and RNA crosslinking followed by immunoprecipitation (iCLIP2). Our results indicate that both proteins are important in the regulation of mESCs cell cycle and self-renewal and are indispensable for proper cardiomyocyte differentiation by regulating expression, alternative splicing and translation of the cardiogenic  factors GATA4. This work highlights the importance of the RBPs during the differentiation of mESCs.

overall_design: 6 samples in biological triplicate: a wild type E14 cell line of reference and KO lines (Sam68 or Qauking) of the same genetic background. Each line was analyzed in 2 time points: day 0 and day 10 of Embryoid body differentiation

first: Alessandro

last: Dasti

first: Maria

last: Antonelli


title: Role of the STAR proteins in early mammalian development


title: Role of the STAR proteins in early mammalian development [RNA-seq]

status: Public on Aug 01 2024

overall_design: 9 samples in biological triplicate: a wild type E14 cell line of reference and KO lines (Sam68 or Qauking ) of the same genetic background. Each line was analyzed in 3 time points: day 0, day3 and day 10 of Embryoid body differentiation


title: Library-based single-cell analysis of CAR signaling reveals drivers of in vivo persistence

status: Public on Jul 13 2024

first: Caleb

last: Perez

email: crperez@mit.edu, mbirnb@mit.edu

address: 77 Massachusetts Ave

department: Biological Engineering

institute: MIT

summary: The anti-tumor function of engineered T cells expressing chimeric antigen receptors (CARs) is dependent on signals transduced through intracellular signaling domains (ICDs). Different ICDs are known to drive distinct phenotypes, but systematic investigations into how ICD architectures direct T cell function—particularly at the molecular level—are lacking. Here, we use single-cell sequencing to map diverse signaling inputs to transcriptional outputs, focusing on a defined library of clinically relevant ICD architectures. Informed by these observations, we functionally characterize transcriptionally distinct ICD variants across various contexts to build comprehensive maps from ICD composition to phenotypic output. We identify a unique tonic signaling signature associated with a subset of ICD architectures that drives durable in vivo persistence and efficacy in liquid, but not solid, tumors. Our findings work toward decoding CAR signaling design principles, with implications for the rational design of next-generation ICD architectures optimized for in vivo function.

overall_design: CD3+ T cells expressing a library of 35 distinct ICD architectures following various tumor perturbations were single-cell sequenced via Chromium Next GEM Single Cell 5' Kit v2, generating gene expression libraries, CAR BC libraries (see below), and, for samples stained with CITE-seq antibodies, feature barcoding libraries. Each CAR variant is barcoded by a unique 8bp sequence in the 5'UTR, allowing deconvolution of the ICD architecture expressed by each cell. The resulting libraries were pooled to achieve approximately 30000, 5000, and 1000 reads per cell, respectively. Reads were aligned to the Genome Reference Consortium Human Build 38 (GRCh38), and a cell–feature matrix was generated using the CellRanger pipeline (10X Genomics; v6.1.2–7.0.1). Downstream analysis was performed using the Seurat package (v4.3.0.1). Several different scRNA-seq datasets are presented, with sample-specific treatments given in the description for each sample.

first: Andrea

last: Garmilla

first: Avlant

last: Nilsson

first: Hratch

last: Baghdassarian

first: Khloe

last: Gordon

first: Louise

last: Lima

first: Blake

middle: E

last: Smith

first: Marcela

last: Maus

first: Douglas

last: Lauffenburger

first: Michael

last: Birnbaum


title: DOGMA-seq of opioid addiction treatment in HIV-1 infected individuals

status: Public on Jul 01 2024

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: BCMM 349, 295 Congress Ave, BCMM 349

department: Microbial Pathogenesis

institute: Yale University School of Medicine

summary: Opioid use and HIV-1 infection a impact immune function independently, but their impact on the immune system together is unknown. To understand the impact of opioids on immune function in HIV-1 infected individuals we used DOGMA-seq to examine the transcriptome, chromatin accessibility, and surface protein expression in HIV-1-infected individuals undergoing opioid addiction treatment.

overall_design: 12 individuals were sampled at time 0 and after 3 months of treatment with an opioid replacement therapy consisting of either methadone,  bueprenoropine with naloxone, or naltrexone. Both PBMC and negative selection  isolated CD4 + T cells were profiled using DOMGA-seq with the Biolegend TotalSeq™-A Human Universal Cocktail, V1.0.

first: Jack

last: Collora


title: Prenatal inflammation remodels lung immunity and function by programming ILC2 hyperactivation

status: Public on Jun 24 2024

city: Salt Lake Ciy

first: Anna

last: Beaudin

state: Utah

address: 2001 Circle of Hope Drive

department: Hematology/HCI

institute: University of Utah

summary: We examined how prenatal inflammation shapes tissue function and immunity in the lung by reprogramming tissue-resident immune cells from early development. Maternal, but not fetal, type I interferon-mediated inflammation provoked expansion and hyperactivation of group 2 innate lymphoid cells (ILC2s) seeding the developing lung.  Hyperactivated ILC2s produced increased IL-5 and IL-13, were associated with acute Th2 bias, decreased Tregs, and persistent lung eosinophilia into adulthood. ILC2 hyperactivation was recapitulated by adoptive transfer of a fetal liver precursor following prenatal inflammation, indicative of developmental programming at the fetal progenitor level. Reprogrammed ILC2 hyperactivation and subsequent lung immune remodeling, including persistent eosinophilia, was associated with worsened histopathology and increased airway dysfunction equivalent to papain exposure, indicating increased asthma susceptibility in offspring. Our data elucidate a potential mechanism by which early-life inflammation results in increased asthma susceptibility, driven by hyperactivated ILC2s that drive persistent changes to lung immunity during perinatal development.

overall_design: Single-cell RNA sequencing of ILC2s sorted from neonatal (postnatal day 14) mouse lung after prenatal saline or poly(I:C) treatment (embryonic day E14.5).

first: Diego

last: López

first: Aleah

last: Griffin

first: Lorena

middle: M

last: Aguilar

first: Cassandra-Deering

last: Rice

first: Elizabeth

last: Myers

first: Kristi

last: Warren

first: Robert

last: Welner


title: The Characteristics of cell in Psoriatic Resolved Lesions Revealed and Onsite Recurrent by Single-cell Transcriptome

status: Public on Jul 29 2024

city: Guangzhou

first: Lu

last: peng

address: No.106, Zhongshan 2nd Road

institute: Guangdong Provincial People's Hospital

summary: Skin biopsy from the previously resolved region (PN), the autologous on-site recurrence with psoriatic plaque (PP)and the non-lesion control (CN) were obtained from the lower back of four male plaque psoriasis patients. Single-cell RNA sequencing (scRNA-seq) was performed after cell dissociation. In our article, sub-clustering and characterization of T cells were demonstrated, functional comparisons of T-cell subsets were conducted further among PN, PP and CN.

overall_design: The previously resolved region (PN), the autologous on-site recurrence with psoriatic plaque (PP)and the appearing-normal control (CN) were obtained from the lower back of four male plaque psoriasis patients. Single-cell RNA sequencing (scRNA-seq) were performed after cell dissociation. The specimen named “CN” has combinated the cells of appearing-normal control from Patient D1 and Patient D2.

last: Peng

first: Wenqi

last: Liu

first: Yufan

last: Cheng

first: Ling

last: Chen

first: Zhu

last: Shen


title: Fecal microbiota transfer from autoimmune dry eye disease model mice to conventional mice induces ocular surface inflammation and stereotypic B cell receptor repertoire development in lacrimal gland

status: Public on Jun 26 2024

city: Seoul

first: Soobin

last: Lee

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea

country: South Korea

institute: Seoul National University

summary: In this study, we transferred gut microbiota of SS-like autoimmune dry eye disease model mice to conventional B6 mice (NOD-FMT). After the transfer, NOD-FMT mice experienced a dramatic change in the gut microbiomes and showed clinicopathological features of SS, including increased corneal fluorescein staining score, decreased tear production, elevated levels of IL-6 mRNA, decreased levels of MUC5AC mRNA encoding mucin. Additionally, we observed that NOD-FMT mice shared stereotypic B cell receptor (BCR) clonotypes with a much higher frequency compared to control group. B cell clones encoding these stereotypic BCR clonotypes developed and expanded locally in the lacrimal gland, and achieved systemic presence in certain clonotypes.

overall_design: Feces were collected from 30 NOD.B10.H2b mice older than 20 weeks with autoimmune dry eye disease, and their microbiomes were transferred to ten mice (NOD-FMT group). In parallel, ten mice were orally gavaged with PBS (PBS-T group), and five mice from the same cohort received no treatment (NC group).

first: Soyeon

last: Ju

first: Sunghoon

last: Kwon

first: Junho

last: Chung

first: Mee Kum

last: Kim


first: Roberto

last: Rossini

overall_design:
We generated Hi-C datasets for MCF10A, MCF10AT1, and MCF10Ca1a cell lines to investigate changes in 3D genome conformation during breast cancer progression.

***Please note that the records have been updated with additional/replacement processed data files on Aug 9, 2024****

first: Mohammadsaleh

last: Oshaghi

first: Maxim

last: Nekrasov

first: Aurélie

last: Bellanger

first: Renae

last: Domaschenz

first: Yasmin

last: Dijkwel

first: Philippe

last: Collas

first: David

last: Tremethick

first: Jonas

last: Paulsen


title: Single-cell multiomics of neuron activation reveals context-specific genetics of brain disorders [022]

status: Public on Feb 20 2025

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: Most causal variants for neuropsychiatric disorders (NPD) remain unknown. A major hurdle is that disease variants may act in specific contexts, such as during neuronal activation, which is difficult to study in vivo at the population level. We profiled single-nucleus neuron-activation multiomics in human induced pluripotent stem cell-derived neurons from 100 donors, revealing the NPD-relevant transcriptomic and epigenomic landscape of neuronal activation. We identified abundant genetic variants associated with activity-dependent gene expression and chromatin accessibility, the latter explaining larger proportions of NPD heritability. Integrating multiomics data with genome-wide association studies further revealed NPD risk variants and genes with effects detected only upon stimulation, such as activity-dependent cholesterol metabolism. Our work highlights the power of cell stimulation to reveal context-specific "hidden" genetic effects.

overall_design: Raw FASTQ files complies 10x Genomics multiome scARC (scRNA-seq + scATAC-seq) standard. Library generated using cultured glutamatergic and GABAergic neurons derived from iPS cells with Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit. The output folders, including all matrices files, of Cell Ranger 2.0.2 were packaged and compressed sample-wise in according to their BioSample and SRA metadata

first: Siwei

last: Zhang


title: The chondrocyte “mechanome”: Activation of the mechanosensitive ion channels TRPV4 and PIEZO1 drives unique transcriptional signatures

status: Public on Jun 05 2024

city: Saint Louis

first: Farshid

last: Guilak

address: 660 S Euclid Ave, Campus Box 8233

department: Dept of Orthopedics

institute: Washington University in St. Louis

summary: The mechanosensitive ion channels Transient Receptor Potential Vanilloid 4 (TRPV4) and PIEZO1 transduce physiologic and supraphysiologic magnitudes of mechanical signals in the chondrocyte, respectively. TRPV4 activation promotes chondrogenesis, while PIEZO1 activation by supraphysiologic deformations drives cell death. The mechanisms by which activation of these channels discretely drives changes in gene expression to alter cell behavior remains to be determined. To date, no studies have contrasted the transcriptomic response to activation of these channels, nor has any published data attempted to correlate these transcriptomes to alterations in cellular function. This study used RNA sequencing to comprehensively investigate the transcriptomes associated with activation of TRPV4 or PIEZO1, revealing that TRPV4 and PIEZO drive distinct transcriptomes, but also exhibit unique co-regulated clusters of genes. Notably, activation of PIEZO1 through supraphysiologic deformation induced a transient inflammatory profile that overlapped with the interleukin (IL)-1-responsive transcriptome and contained genes associated with cartilage degradation and osteoarthritis progression. However, both TRPV4 and PIEZO1 were also shown to elicit anabolic effects. PIEZO1 expression promoted a pro-chondrogenic transcriptome under unloaded conditions, and daily treatment with PIEZO1 agonist Yoda1 significantly increased sulfated glycosaminoglycan deposition in vitro. These findings emphasize the presence of a broad “mechanome” with distinct effects of TRPV4 and PIEZO1 activation in chondrocytes, suggesting complex roles for PIEZO1 in both the physiologic and pathologic responses of chondrocytes. The identification of transcriptomic profiles unique to or shared by PIEZO1 and TRPV4 (distinct from IL-1-induced inflammation) could inform future therapeutic designs targeting these channels for the management and treatment of osteoarthritis.

overall_design: To study the TRPV4-responsive transcriptome, primary chondrocytes were cast in 2% agarose to form tissue engineered cartilage constructs. Constructs were stimulated for 3 hours with cyclic, unconfined compressive loading (10% peak-to-peak deformation, 1 Hz) with or without TRPV4 antagonist GSK205 (10 uM) or treated with TRPV4 agonist GSK101 (1 nM) or 1 ng/mL of IL-1. Vehicle controls were exposed to DMSO (1:1000 in media) but left free swelling. For both TRPV4 and IL-1 stimulation groups, tissue constructs were taken down at 3 hours and 9 hours post stimulation onset, flash frozen, and stored at -80C (n=4 per group). To study the PIEZO1-responsive transcriptome, chondrocytes were plated at 500k cells per well in a 6 well plate and transfected (DharmaFECT Transfection Reagent, Dharmacon) with siRNA targeting PIEZO1 (siPIEZO1), a non-targeting control siRNA (siNTC), or left non-transfected (NT). All transfection groups were cast in 2% agarose to form tissue engineered cartilage constructs. Constructs were subjected to a single round of quasi-static unconfined compression to 80% deformation (supraphysiologic range) at 1.9% deformation/min (~0.73 um/sec), treated with PIEZO1 agonist Yoda1 (5 uM), or standard media with a DMSO vehicle control (1:1000) but left free swelling.  In response to stimulation, tissue constructs were taken down at 3 hours and 9 hours post stimulation onset, flash frozen, and stored at -80C (n=4 per group).

first: Robert

last: Nims

first: Daniel

last: Palmer

first: Jordan

last: Kassab

first: Bo


title: Pioneer neurons are molecularly distinct, and their axon targeting is regulated by retinoic acid signaling (WT 30 h)

status: Public on Jun 01 2024

city: Portland

first: Alex

last: Nechiporuk

state: OR

address: 3181 SW Sam Jackson Park Road

institute: Oregon Health and Science Univ

summary: During nervous system development, pioneer neurons are the first to extend their axons into target tissues, creating a scaffold for follower neurons. Despite years of study, whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line (pLL) sensory neurons during axon growth using single-cell RNA sequencing (scRNA-seq) revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state, whereas “pioneer” is a later developmental state. The scRNA-seq data revealed active retinoic acid (RA) signaling in followers, but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret, which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development.

overall_design: Thirty hour old TgBAC(neurod1:EGFP)nl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium-free Ringer’s solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES pH 7.0), by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre-warmed protease solutions (0.25% trypsin, 1 mM EDTA, pH 8.0, PBS) and collagenase P/HBSS (100 mg/mL) was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution (6X, 30% calf serum, 6 mM CaCl2, PBS) was added and samples were centrifuged (350xg, 4° C for 5 minutes). Supernatant was removed and 1 mL of chilled suspension solution was added (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, 0.05 mg/mL streptomycin, DMEM). Samples were centrifuged again (350g, 4° C for 5 minutes) and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer (50 μl PBS/ 2% BSA) in a siliconized 1.5mL tube.

first: Benjamin

last: Woodruff

first: Lauren

last: Miller

first: Lindsey

last: Royer

first: Nicholas

last: Calistri

first: Laura

last: Heiser