title: Single-cell transcriptomics reveals the role of antigen presentation in liver metastatic breast cancer

status: Public on Jan 23 2024

city: Shanghai

first: Qingtong

last: Zhou

address: No. 138 Yixueyuan Road

department: School of Basic Medical Sciences

institute: Fudan University

summary: Liver metastasis (LM) is the primary cause of cancer-related mortality in late-stage breast cancer (BC) patients. However, the complexity and diversity of the tumor microenvironment (TME) of LM have not been fully understood. Here we report an in-depth analysis of the transcriptional landscape of liver metastases of 11 patients with secondary hepatic carcinoma at single-cell resolution. Our study reveals that terminally exhausted CD4+ and dysfunctional CD8+ T cells were enriched in metastatic tumor along with low antigen presentation. We also found macrophages were associated with the infiltration profile of CD4+ T cells, while FCN3+ macrophages, type 1 conventional dendritic cells (cDC1) and LAMP3+ DC regulated T cell functions, probably via antigen processing and presentation. MHC expression in FCN3+ macrophage, cDC1 and LAMP3+ DC was reduced in LM compared to those in normal tissues and primary tumor of BC. Dysfunction of antigen presentation in these cells is linked to a worse prognosis in breast invasive carcinoma (BRCA) and liver hepatocellular carcinoma (LIHC) cohorts and identifies potentially targetable immune inhibitory pathways in secondary hepatic carcinoma. Thus, our results show a cellular diversity of TME in BC-LM, providing valuable insights into the role of tumor infiltrating T cells in liver metastatic cancers.

overall_design: Single-cell RNA-seq profiling for liver metastases of 11 patients with secondary hepatic carcinoma: 6 cases of breast cancer (BC), 2 cases of nasopharyngeal carcinoma (NPC), 2 cases of thyroid carcinoma (THCA), 1 case of cervical carcinoma (CESC), and adjacent nonmalignant tissues (used as normal control).

first: Xiaoshuang

last: Wang

first: Yan

first: Zhongen

last: Wu

first: Cao

last: Xie

first: Qiwei

last: Xu

first: Dehua

last: Yang

first: Di

last: Zhu

first: Ming-Wei

first: Lu


title: Bulk RNA-sequencing Analysis of the acute myeloid leukemia stem cells

status: Public on Jan 22 2024

city: Charleston

first: Sophie

last: Paczesny

state: South Carolina

address: 86 Jonathan Lucas Street

department: Microbiology & Immunology

country: USA

institute: Medical University of South Carolina

type: Expression profiling by high throughput sequencing

summary: By RNA-sequencing, we compared WT vs ST2 knockout leukemia stem cells (LSCs) from the bone marrow of ST2flox/flox and ST2flox/flox Mx1Cre MLL-AF9 LSCs, and found that ST2 deficiency in LSCs reprogramme the oncogenic, metabolic and cell cycle signatures which correlated with reduced leukemogenesis and maintenance.

overall_design: ST2flox/flox LSCs (control) and ST2flox/flox Mx1Cre LSCs were injected into lethally irradiated C57BL/6 mice at Day 0, and polyinosinic:polycytidylic acid (pIpC) was administrated every other days for a total of 7-doses started on the same day. BM cells were obtained and two types of LSCs following fluorescence-activated cell sorting were deliveried for RNA extraction, library construction, and RNA-sequencing.

first: Denggang

last: Fu


title: ChREBP is activated by reductive stress and mediates GCKR-associated metabolic traits

status: Public on Jan 02 2024

city: Boston

first: Russell

last: Goodman

state: MA

address: 55 Fruit st, Thier Building, 11th Floor

institute: Massachusetts General Hospital

summary: We investigate the transcriptional effect of hepatic expression of the bacterial enzyme EcSTH

overall_design: EcSTH was expressed via retroorbital injection of adenovirus. 4 days later  liver tissue was collected at which point RNAseq was performed.


title: Molecular and immune profiles linked to androgen response categories in metastatic castration-resistant prostate cancers (mCRPC)

status: Public on Mar 01 2024

city: Houston

first: Ana

last: Aparicio

state: TX

address: 1515 Holcombe Blvd

department: Genitourinary Medical Oncology

institute: MD Anderson Cancer Center

summary: Prostate cancer is a heterogenous disease and can be broadly categorized into androgen responsive and androgen indifferent groups. Robust biomarkers to identify them and enable the development of therapeutic strategies specific to each, remain to be defined. We conducted a dynamic, modular clinical trial ("DynAMo") in which 192 men with mCRPC were segregated based on Satisfactory (≥ 50% PSA decline from baseline and <5 CTC/7.5mL) versus Unsatisfactory marker status after 8-weeks of abiraterone, prednisone and apalutamide (ApA). Those with Satisfactory status (n=128, 67%) were randomized to continue ApA alone (Module 2A) or with ipilimumab (Module 2B). Median overall survival (OS) and 95% CI was 46.4 (39.2, 68.2) months and 41.4 (33.3, 49.9) months respectively. Patients with Unsatisfactory marker status (n=64, 33%) had carboplatin+cabazitaxel chemotherapy added to ApA (Module 3) and had an OS and 95% CI of 18.7 (14.3, 26.3) months. As part of this study, poly(A) RNA was extracted from 140 fresh frozen cores obtained from 136 patients during pre-treatment biopsies of metastatic sites. Of these, 21 (15.0%) yielded insufficient or poor-quality RNA. Of the 119 cores that were subject to bulk RNA sequencing, 56 (47.1%) from 56 patients passed quality control filters (i.e., RNA total reads ≥60 million, exonic rates ≥0.7, and ≥20,000  genes detected). The sequencing results from these 56 patient samples are provided here.

overall_design: bulk RNA sequencing analyses from 56 patient samples in the DynAMo clinical trial


summary: We investigate the transcriptional effect of alcohol gavages on wildtype versus ChREBP KO mice.

overall_design: Wild type or ChREBP mice were gavaged with alcohol or water, and liver tissue was collected 6 hour later at which point RNAseq was performed.


title: Defining key transcriptional regulators of extravillous trophoblast differentiation [ChIP-seq]

status: Public on Jan 16 2024

city: Austin

first: Mijeong

last: Kim

address: 2506 Speedway, NMS 4.246

institute: The University of Texas at Austin

type: Genome binding/occupancy profiling by high throughput sequencing

summary: During early human pregnancy, extravillous trophoblasts (EVT) play a central role in placental anchorage and blood vessel remodeling. Despite the essential roles in pregnancy, key factors and mechanisms underlying EVT differentiation remain largely unknown. Here, we defined key transcription factors (TFs) by monitoring the dynamics of transcriptome and enhancer usage during EVT differentiation. We confirmed the requirements of the defined TFs and identified their action mechanisms.

overall_design: ChIP-seq of H3K27ac was performed in human trophoblast stem cells (TSC), EVT differentiating cells (day 3, EVT D3), and fully differentiated EVT (day 8,  EVT D8). ATAC-seq and H3K4me3 ChIP-seq were performed in TSC and EVT D8. Time-course ChIP-seq of TFAP2C and DLX6 were performed in TSC, EVT D2, EVT D5, and EVT D8. To map genomic targets of DLX5 and ASCL2, ChIP-seq using native antibodies was conducted, and NRIP1 targets were identified by biotin-mediated ChIP-seq (bioChIP-seq). Inputs were sequenced for a control.

first: Jonghwan


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

overall_design: Refer to individual Series


title: Viral reprogramming of host transcription initiation

status: Public on Feb 01 2024

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center


title: Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells

status: Public on Feb 12 2024

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

country: France

institute: Epigenetics and Cell Fate Unit

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is an essential epigenetic mark in mammals. It controls gene expression and genome stability. Global DNA methylation pattern is abnormal in cancers. Ubiquitin like with PHD and RING finger domains 1 (UHRF1) is a key epigenetic regulator that recruits and activates DNA methyltransferase 1 (DNMT1), the methylation maintenance enzyme. UHRF1 is a proven oncogene and its overexpression transforms cells in vitro and causes cancer in animal models. Therefore, UHRF1 provides a unique entry point into the links between epigenetics and cancer. However, it is still not fully clear how UHRF1 works in cancer cells.  To understand UHRF1 functions in cancer, we employed experimental strategy to use an advanced chemical/genetic system, the auxin-inducible degron (AID) technology, whereby the degron-fused protein can be totally and rapidly degraded upon the addition of a small molecule, auxin. We chose the human CRC cell line HCT116 as our model and successfully generated UHRF1-AID and DNMT1-AID. Through this study, we made the significant discovery that UHRF1 not only regulates DNMT1, but also influences the activities of de novo methyltransferases DNMT3A and DNMT3B, as well as the active demethylase TET2.

overall_design: To elucidate the roles of UHRF1 and DNMT1 in the HCT116 cell line, we generated four distinct cell lines: wild-type (WT), UHRF1-AID, DNMT1-AID, and UHRF1-AID/DNMT1-AID. To analyze the kinetics of DNA methylation, we treated these cell lines with auxin for 0, 2, 4, 6, 8, and 12 days.

first: Kohsuke

last: YAMAGUCHI

first: Fumihito

last: MIURA

first: Pavel

last: Bashtrykov

first: Olivier

last: KIRSH

first: Albert

last: Jeltsch

first: Takashi

last: Ito


title: Macrophage-derived oncostatin M repairs the lung epithelial barrier during inflammatory damage

status: Public on Dec 15 2023

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Tissue repair programs must function alongside antiviral immunity to restore the lung epithelial barrier following infection. We found that macrophage-derived oncostatin M (OSM) counteracted the pathological effects of type I interferon (IFN-I) during infection and damage in mice. At baseline, OSM-deficient mice exhibited altered alveolar type II (ATII) epithelial cell states. In response to influenza or viral mimic challenge, mice lacking OSM exhibited heightened IFN-I responses and increased mortality. Furthermore, OSM promoted organoid formation despite the growth-inhibitory effects of IFN-I. These findings identify OSM as an indispensable macrophage-derived growth factor that maintains the homeostasis of lung epithelial cells and promotes their proliferation to overcome IFN-I-mediated immunopathology.

overall_design: To examine the impact of genetic knockout of the gene Osm on the response to influenza virus infection, littermate wild-type and knockout mice were infected with influenza (strain WSN) and lungs were harvested at 3 or 7 days post infection (as well as from uninfected controls). RNA was subsequently isolated from whole lung tissue for analysis.

first: Daisy

middle: A

last: Hoagland

first: Patricia

last: Rodríguez-Morales

first: Alexander

middle: O

last: Mann

first: Ruth

last: Franklin


title: scRNASeq Data of CD3 Negative Immune Cells in HS lesional skin, healthy skin, and matched blood

status: Public on Dec 10 2023

city: San Francisco

first: Margaret

last: Lowe

state: CA

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

summary: Hidradenitis suppurativa (HS) is an inflammatory skin disease with limited therapeutic options. We and others have previously identified an abnormal B cell infiltrate within HS lesional skin. We performed scRNASequencing on CD3 negative cells from inflammatory HS skin lesions, healthy control skin and matched blood to better understand infiltrating B cells amongst other immune cells within lesional skin.

overall_design: scRNASeq of CD3 Negative cells sort-purified from enzymatically digested skin of biopsied hidradenitis suppurativa inflammatory lesions or of healthy control skin and from matched patient blood

middle: M

first: Michael

middle: D

last: Rosenblum


title: Stress responsive mRNA isoform analysis in human and mice

status: Public on Dec 08 2023

city: Hefei

first: Xiaolin

last: Wang

address: Huangshan Road

country: China

institute: USTC

summary: To investigate functional stress responsive mRNA isoform in human and mice, we performed high-throughput RNA sequencing (RNA-seq) of HEK293T and N2a cells under ER and metabolic stresses.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We performed ribosomal RNA (rRNA) depleted RNA sequencing (RNA-seq) of human HEK293T and murine N2a cells treated with thapsigargin (TG, inducing ER stress) or glucose deprivation (GD, inducing metabolic oxidative stress).

first: Xiuzhi

last: Li


title: scRNASeq Data of CD4 Tregs and Teffectors in HS lesional skin and healthy skin

status: Public on Dec 07 2023

summary: Hidradenitis suppurativa (HS) is an inflammatory skin disease with limited therapeutic options. CD4 T Cells have been described as more inflammatory than T cells in healthy skin. To better understand alterations within the T cell compartment, we profiled CD4 Teffector cells and regulatory T cells (Treg) from inflammatory HS skin lesions and healthy control skin via scRNASequencing.

overall_design: scRNASeq of Treg and CD4 Teffector cells sort-purified from enzymatically digested skin of biopsied hidradenitis suppurativa inflammatory lesions or of healthy control skin


title: Genome-wide DNA methylation analysis of colorectal cancer and polyp

status: Public on Jan 01 2024

city: Harbin

first: Xishan

address: Xue Fu Road 246

institute: The Second Affiliated Hospital of Harbin Medical University

summary: Colorectal polyp is known a precursor of colorectal cancer (CRC) that holds an increased risk for progression to CRC. Circulating cell-free DNA(cfDNA) methylation has shown favorable performance in the detection and monitoring the malignant progression in a variety of cancers. Here, we conducted a study to discovery cfDNA methylation markers for the diagnosis of CRC. We first performed a genome-wide analysis using the Infinium HumanMethylationEPIC BeadChip array to identify differentially methylated CpGs (DMCs) between 8 CRC and 8 polyp tissues. Then, we validated DMCs in a larger tissue cohort and four methylation markers (cg04486886, cg06712559, cg13539460 and cg27541454) were selected as the methylation markers in tissue by LASSO and random forest models. A diagnosis prediction model was bulit based on the four markers and the methylaion diagnosis score (md-score) can effectively discriminate patients with CRC from polyp tissues. Finally, a single cfDNA methylation marker, cg27541454, was confirmed hypermethylated in CRC in the plasma validation cohort. Together, our findings suggested that the md-score derived from tissue could robustly detect CRC from polpy patients, and cg27541454 may be a promising candidate non-invasive biomarker for CRC early diagnosis.

overall_design: Tissue samples from colorectal cancer (n=8) and polyp (n=8) patients were hybridized by the Illumina Infinium EPIC Human Methylation BeadChip, following DNA extraction and bisulphite treatment.


title: Bulk RNAseq NIEHS P30 CURES Pilot Environmental hormonal and mutagenic stress in fluorescent-ubiquitinated cell cycle indicator (FUCCI) mESC 2021

status: Public on Dec 20 2023

city: Detroit

first: Daniel

last: Rappolee

state: MI

address: 275 E Hancock St

department: OBGYN

institute: Wayne State University

summary:
This experiment examines how toxicants can override normal stemness (NS) conditions, which LIF maintains, causing lineage imbalance and otherwise affecting cells in the early embryo.
It also compares NS to normal differentiation (ND) (without LIF/ LIF-). Sorbitol is a positive control for stress overriding LIF+. Retinoic acid (RA) modified LIF- is a positive control for 1st lineage differentiation. But RA also activates Hox gene in anterior posterior patterning at gastrulation.
The third control is NS itself, and all stimuli are compared to NS.
Other toxicants are Benzo(a)pyrene (BP) - a mutagen, Cortisol - a stress hormone, and two endocrine disruptors Diethyl phthalate (DEP), and Perfluorooctanoic acid (PFOA).

overall_design:
Bulk RNAseq of FUCCI mESC cultured for 72hr with different stimuli. Triplicate biological experiments.
Baseline maintenance media was LIF at 1,000U/mL and 15% serum which enables heterogeneous normal stemness, putatively at naïve pluripotency like the day E4.5 inner cell mass. 72hr of LIF removal for ND putatively yields formative pluripotency, a restriction of pluripotency compared with naive, but also preparing cells for the start of gastrulation.
Toxicant dose responses (1,10,100nM. 1, 10, 100uM) were performed in a live imager to determine lowest observable adverse effect level (LOAEL) for growth and IC75 level (concentration with 75% growth suppression) and these two doses were used as dose-dependent test exposures in the 72hr culture prior to cell lysis and RNAseq.
FUCCI ESC were 129/sv strain ESC with FUCCI transgenes, a gift from Dr Savatier: from Coronado, D., Godet, M., Bourillot, P.Y., Tapponnier, Y., Bernat, A., Petit, M., Afanassieff, M., Markossian, S., Malashicheva, A., Iacone, R., Anastassiadis, K., Savatier, P., 2013. A short G1 phase is an intrinsic determinant of naive embryonic stem cell pluripotency. Stem Cell Res 10, 118-131.

first: Ximena

middle: L

last: Ruden

first: Mohammed

last: Abdulhasan

first: Katherine

last: Gurdziel


title: Deubiquitinase USP13 regulates cardiac hypertrophy and dysfunction

status: Public on Dec 31 2023

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

summary: Construction of transcriptome sequencing library and transcriptome sequencing was completed by LC-Bio Technology Co., Ltd. (Hangzhou, China). The expression profile of Machado-joseph deubiquitinases (MJDs) family in heart tissues of Ang II mice.

overall_design: We performed RNA sequencing analysis on the heart tissues of Ang II mice.

first: Jibo

last: Han

first: Guang

last: Liang


title: Measuring variability in Illumina MethylationEPIC microarrays

city: Jupiter

first: Anderson

last: Butler

state: Florida

institute: VoLo Voundation

type: Methylation profiling by genome tiling array

summary: DNA methylation microarrays have become a widely used tool for investigating epigenetic modifications in various aspects of biomedical research. However, technical variability in methylation data poses challenges for downstream applications such as predictive modeling of health and disease. In this study, we measure the impact of common sources of technical variability in Illumina DNA methylation microarray data, with a specific focus on positional biases inherent within the microarray technology. By utilizing a dataset comprised of multiple, highly similar technical replicates, we identified a chamber number bias, with different chambers of the microarray exhibiting systematic differences in fluorescence intensities and their derived methylation beta values, which are only partially corrected for by existing preprocessing methods, and demonstrate that this positional bias can lead to false positive results during differential methylation testing. Additionally, our investigation identified outliers in low-level fluorescence data which might play a role in contributing to predictive error in computational models of health-relevant traits such as age.

overall_design: Whole blood from four human donors were measured with total of sixteen technical replicates, across multiple slides and chambers.


title: Single nuclei sequencing reveals C4 photosynthesis is based on rewiring of ancestral cell identity networks

status: Public on Dec 05 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: In multicellular systems changes to the patterning of gene expression drive modifications in cell function and trait evolution. One striking example is found in more than sixty plant lineages where compartmentation of photosynthesis between cell types allowed evolution of the efficient C4 pathway from the ancestral C3 state. The molecular events enabling this transition are unclear. We used single nuclei sequencing to generate a cell level expression atlas for C3 rice and C4 sorghum during photomorphogenesis. In both species a conserved cistrome was identified for each cell type and initiation of photosynthesis gene expression was conditioned by cell identity. Photosynthesis genes switching expression from mesophyll in rice to bundle sheath in sorghum acquire hallmarks of bundle sheath identity. The sorghum bundle sheath has also acquired gene networks associated with C3 guard cells. We conclude C4 photosynthesis is based on rewiring in cis that exapts cell identity networks of C3 plants.

sample_organism:
Oryza sativa
Sorghum bicolor

platform_organism:
Oryza sativa
Sorghum bicolor

overall_design: Using 10X transcriptomic, 10X multiome (ATAC+RNA seq) and sci-RNA-seq3, we analyzed the cell type gene regulatory responses of rice and sorghum seedlings as they underwent de-etiolation.

last: Swift

first: Leonie

middle: H

last: Luginbuehl

first: Tina

last: Schreier

last: Donald

first: Travis

last: Lee

last: Nery

first: Julian

last: Hibberd


title: Discovering Molecular Signatures in ATMR: Single-cell RNA Sequencing Analysis of Human Blood and Tissue Spatial Transcriptomics

status: Public on Dec 03 2023

city: Seoul

first: Minji

last: Kang

address: 103 daehak-ro

department: biomedical sciences

country: South Korea

institute: Seoul National University graduate school


title: Discovering Molecular Signatures in ATMR: Single-cell RNA Sequencing Analysis of Human Blood and Tissue Spatial Transcriptomics [Spatial Transcriptomics]

summary: Background. Acute T cell-mediated rejection (ATMR) is a significant challenge in kidney allograft. Despite this, high-resolution transcriptomic analysis of both the targeted tissue and systemic blood is lacking. To address this void, we embarked on a study employing single-cell RNA sequencing (scRNA-seq) on peripheral blood mononuclear cells (PBMCs), coupled with spatial transcriptomics analysis on graft biopsy specimens, to unveil the intricacies of ATMR. Methods. We collected paired pre- and post-operative blood samples from six kidney transplant patients. Among these, two patients exhibited a lack of rejection, while four patients bore biopsy-proven ATMR. By scrutinizing tissue samples from protocol biopsies taken two weeks post-operation in comparison to zero-time biopsies. Moreover, our investigation delved into peripheral blood samples, where we detected an expanded cell population within PBMCs, presumed to harbor numerous alloreactive T cells. This CD8+ effector memory (CD8 Tem) cell population was subsequently examined for DEGs between the two patient groups.  Results. Our comprehensive approach, which combined scRNA-seq and spatial transcriptomics results, unveiled specific genes such as LTB, GZMK, STAT1, PSME2, UBE2L6, and GBP5, which showcased heightened expression levels among ATMR patients. Network analysis underscored the interconnection of STAT1 with the other identified genes, suggesting its plausible role in the rejection process. Conclusions. Our findings demonstrate CD8+ STAT1+ hold notable significance in the context of ATMR. This subpopulation undergoes clonal expansion and retains a memory phenotype, there by contributing to a heightened and swifter inflammatory response within the graft.

overall_design: Human PBMC samples were used for single cell RNA sequencing, human kidney biopsy tissue samples were used for spatial transcriptomics

first: Jeongin

last: Song

first: Yunyoung

last: Jang

first: YongChul

last: Kim

first: HyunJe

first: SeungHee

last: Yang


title: Single-cell RNAseq analysis of CXCL12+ mesenchymal cells of the murine molar

status: Public on Dec 01 2023

first: Mizuki

last: NAGATA

address: 7500 Cambridge St

department: Orthodontics

institute: UTHealth

summary: A single cell transcriptional profile of mesenchymal cells in the murine molar marked by CXCL12-GFP, Col1a1-GFP or CXCL12-creER+ cells at postnatal day 6 or 25 (P6 or P25)

overall_design: GFP+ or tdTomato+ were FACS-isolated . 10,000 cells were loaded onto 10X Genomic Chromium Single Cell Expression Solution version 3 platform. cDNA was sequenced by Illumina HiSeq4000 or NovaSeq 6000

first: Noriaki

last: Ono

first: Wanida


title: GD3 Synthase Is a Master Regulator of Wild-Type p53–Mediated Apoptosis and Mutant p53–Mediated Tumorigenesis

status: Public on Dec 02 2023

first: Zheng

last: Yin

address: 6565 Fannin St, MC: F6-300

department: Systems Medicine and Bioengineering

institute: Houston Methodist Cancer Center

summary: We noted that the increased expression of GD3S enables breast cancer cells to evade cell death induced by the stabilization of p53 through Nutlin3A treatment, and we aim to explore the molecular mechanisms underlying these observed effects.

overall_design: Comparative gene expression profiling analysis using RNA-seq data for MCF7 cell line with or without GD3S overexpression treated with DMSO or Nutlin3A, with triplicated samples for each of the four genotype-treatment combinations

first: Vivek

last: Anand

first: Venkata

last: Lokesh Battula


title: Structural stability based deep sequencing of 5 protein targets

city: Shenzhen

first: Zhe

last: Zhang

state: Guangdong

address: Gaoke Innovation Center

department: Institute of Physical and Systems Biology

institute: Shenzhen Bay Laboratory

summary: We developed an efficient, cost-effective assay for Structural Inference By Structure-stability-based selection of deep mutation variants and high throughput sequencing (Sibs-Seq). We demonstrated that unlike naturally occurring homologous sequences evolved over billions of years, these stability-selected, artificial homologs in a single-round 24 or 36 hours of mutation selections is often sufficient for producing high-accuracy structure prediction with < 2 angstrom root-mean-squared deviation (RMSD) to the native structure.

overall_design: A target protein of interest (POI) is subjected to error prone PCR (EP-PCR) to construct a mutation library (>106) that is inserted between two assisted-complementary fragments of the murine dihydrofolate reductase. A functional mDHFR will then produce tetrahydrofolate (THF) essential for Trimethoprim(TMP) resistance and allow growth of TMP-sensitive E. coli in the presence of TMP. By contrast, if the POI is in an unstable structural state, two fragments of mDHFR would be too far apart to reconstitute into a functional mDHFR. Lacking a functional mDHFR will inhibit the growth of TMP-sensitive E. coli cells when treated with TMP. Thus, when inserting a library of randomly mutated POIs, those stably folded variants will lead to TMP-resistant E. coli that can grow in the presence of TMP. The sequence counts of each mutant available from high-throughput sequencing will allow to calculate its fitness score, which provides an estimation for its stability.

first: Jinle

last: Tang

first: Jian

last: Zhan

first: Yaoqi

last: Zhou


title: Characterization of the effect of deleting the Nrg-1(neuregulin-1) gene, using the endothelial driver line Tie2-Cre in E (embryonic day) 9.5 hearts

city: Madrid

first: Jose Luis

last: de la Pompa

state: MADRID

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: To investigate the role of Nrg-1 in heart ventricular chamber development we deleted Nrg-1 in endothelial lineages, harvested hearts at E9.5, and determined gene expression profiles, using RNA-seq.

overall_design: Gene expression profiling with RNA-seq was performed on 4 replicate samples of control (WT) and 4 replicate samples of mutant (Nrg-1flox;Tie2-Cre) heart ventricles at E9.5

first: Joaquim

last: Grego-Bessa

first: Donal

last: MacGrogan

first: Jose-Luis


title: Characterization of the effect of overexpressing the Nrg-1 (neuregulin-1) gene, using the cardiac driver line Nkx2.5-Cre, in E (embryonic day) 15.5 heart venticles

summary: To investigate the role of Nrg-1 in heart ventricular chamber development, we overexpressed Nrg-1 in cardiac lineages, harvested ventricles at E15.5, and determined gene expression profiles, using RNA-seq.

overall_design: Gene expression profiling with RNA-seq was performed on 4 replicate samples (1 ventricle per replicate) of control (WT) and 4 replicate samples of mutant (Rosa26Nrg-1;Nkx5.5-Cre) embryos at E15.5


title: Characterization of the effect of deleting the Nrg-1(neuregulin-1) gene, using the tamoxifen-inducible endothelial driver line Cdh5-CreERT in E (embryonic day) 15.5 hearts

summary: To investigate the role of Nrg-1 in heart ventricular chamber development, we induced a conditional Nrg-1 deletion in endothelial cells at E15.5, with tamoxifen, and determined gene expression profiles, using RNA-seq.

overall_design: Gene expression profiling with RNA-seq was performed on 4 replicate samples of control (WT) and 4 replicate samples of mutant  (Nrg-1flox;Cdh5-CreERT2) (1 ventricle per replicate) at E15.5


title: Role of Nrg-1 in the development of heart ventricular chamber in mice.

summary:
To investigate the role of Nrg-1 in heart ventricular chamber development, we have used RNA-Seq to characterize the effect of Nrg-1 inactivation or over-expression in mouse embryos at E9.5 and E15.5.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Modeling myelodysplastic syndromes in mice by altered Hoxa1 spliceform expression

status: Public on Nov 28 2023

city: Meblourne

first: Alistair

middle: Morgan

last: Chalk

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

summary: The homeobox gene, Hoxa1, has two different isoforms generated by alternative splicing: a full-length homeodomain-containing Hoxa1 (Hoxa1-FL), and a truncated Hoxa1 (Hoxa1-T), that lacks the homeodomain. Oncoretroviral overexpression of wildtype Hoxa1 cDNA (WT-Hoxa1), which generates both Hoxa1 isoforms, in murine hematopoietic stem and progenitor cells (HSPCs) perturbed hematopoiesis, resulting in myelodysplastic syndromes (MDS) in mice. Overexpression of a mutated Hoxa1 cDNA (MUT-Hoxa1) that generates Hoxa1-FL but not Hoxa1-T led to a more severe MDS capable of transforming to secondary acute myeloid leukemia (sAML). Similar to human MDS, DNA damage repair pathways were downregulated in Hoxa1-overexpressing hematopoietic progenitor cells. Conditional knock-in mouse models revealed a Hoxa1-FL dosage-dependent effect on MDS disease severity. Our data reveal that increased expression of Hoxa1-FL in HSPCs is sufficient to initiate MDS in mice. CD34+ cells from up to 50% of patients with MDS had elevated HOXA1-FL expression, highlighting the clinical relevance of our mouse models.

overall_design:
5000-78,000 sorted (MEP) cells with overexpression of Wild type Hoxa1 (WT- Hoxa1), Mutant Hoxa1 (MUT-Hoxa1) or control vector (MXIE) from primary recipient mice 16 weeks post transplantation.
Three vector groups (MXIE, WT-Hoxa1 and MUT-Hoxa1) were compared.
Joseph C: St. Vincent’s Institute, Melbourne, Australia
Hendy J: St. Vincent’s Institute, Melbourne, Australia
Baker EK: St. Vincent’s Institute, Melbourne, Australia
Chalk AM: Stem Cell Regulation Unit, St. Vincent’s Institute, Melbourne, Australia
Gudas LJ: Department of Pharmacology, Weill Cornell Medical College, New York, NY
Fabb SA: Monash University, Carlton, Australia
Wall M: Victorian Cancer Cytogenetics Service, St. Vincent’s Hospital, Melbourne, Australia
Walkley CR: St. Vincent’s Institute, Melbourne, Australia
Purton LE: St. Vincent’s Institute, Melbourne, Australia

first: C

last: Joseph

first: J

last: Hendy

first: E

last: Baker

first: A

first: L

middle: J

last: Gudas

first: S

last: Fabb

first: M

last: Wall

last: Walkley

middle: E

last: Purton


title: KAT5 activity regulates quiescent-like states in human gliomas.

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Quiescence cancer stem-like cells may play key roles in promoting tumor cell heterogeneity and recurrence for many tumors, including glioblastoma (GBM). Here we show that the protein acetyltransferase KAT5 is a key regulator of transcriptional, epigenetic, and proliferative heterogeneity impacting transitions into G0-like states in GBM. KAT5 activity suppresses the emergence of quiescent subpopulations with neurodevelopmental progenitor characteristics, while promoting GBM stem-like cell (GSC) self-renewal through coordinately regulating E2F- and MYC- transcriptional networks with protein translation. KAT5 inactivation significantly decreases tumor progression and invasive behavior while increasing survival after standard of care. Further, increasing MYC expression in human neural stem cells stimulates KAT5 activity and protein translation, as well as confers sensitivity to homoharringtonine, to similar levels to those found in GSCs and high-grade gliomas. These results suggest that the dynamic behavior of KAT5 plays key roles in G0 ingress/egress, adoption of quasi-neurodevelopmental states, and aggressive tumor growth in gliomas.


title: Modeling myelodysplastic syndromes in mice by altered Hoxa1 spliceform expression (CMP)

overall_design: Three vector groups (MXIE, WT-Hoxa1 and MUT-Hoxa1) were compared.


title: Transcriptomic alteration of bone-related cells in aged mice after long-term high fat diet (HFD) feeding

status: Public on Nov 15 2023

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Aging is associated with osteoporosis and remodeling of bone marrow microenvironment, skewing hematopoiesis. Obesity may accelerate aging process. We use bulk-RNA sequencing to measure the transcriptomic changes of bone cells caused by long-term HFD feeding in aged mice, which mainly includes osteocytes and other bone marrow stromal cells.

overall_design: mRNA profiles of cortical bone from 18-month old male C57BL/6J mice under 12-month chewing diet (CD) or HFD feeding.

first: Yidan

last: Pang

first: Changqing

last: Zhang


title: RNA-Seq results of oligodendrocyte model of SBMA, AR-97Q cells, compared to AR-17Q cells

status: Public on Nov 14 2023

city: Nagoya

first: Madoka

last: Iida

state: Aichi

address: 65 Tsurumai-cho Showa-ku

department: Neurology department

country: Japan

institute: Nagoya University

summary: Transcriptional changes of AR-97Q cells and AR-17Q cells were compared. RNA-seq gene expression analysis revealed that differentially expressed genes were associated with regulation of signaling and regulation of cell communication as biological process, and membrane was most relevant to the genes as cellular component.

overall_design:
Lentivirus expressing full-length human AR containing 17 or 97 CAG repeats were introduced into Oli-neu cell, thereby generating cell lines harboring AR-17Q as control cells and cell lines harboring AR-97Q as a cellular model of SBMA. Differentiation was induced by adding 1 μM PD174265 (Calbiochem) to the medium for 72 hours.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 samples from each cell line.

first: Kentaro

last: Sahashi

first: Masahisa

last: Katsuno


title: Single cell RNA-Seq result of  spinal cord of AR-97Q mice and wild-type mice at four disease stages

status: Public on Nov 27 2023

summary: To understand the early pathogenesis of SBMA and to systematically assess the role of different cells in the spinal cord of SBMA, we conducted snRNA-seq on the spinal cord of AR-97Q mice at different stages of the disease. The genes related to ion channel and synapse function were up-regulated in oligodendrocytes in early stages of SBMA although they were down-regulated at the advanced stage.

overall_design: Single-nucleus RNA sequencing (snRNA-seq) was conducted on spinal cord samples from AR-97Q mice and wild-type mice at four stages: pre-pubertal (3 weeks of age), pre-onset (6 weeks of age), early symptomatic (9 weeks of age) and advanced (13 weeks of age). Spinal cords from 4 mice per a sample were pooled for homogenization and nuclear isolation.

first: Tomohiro

last: Akashi

first: Kunihiko

last: Hinohara


title: Liebenberg syndrome severity arises from variations in Pitx1 locus topology and ectopically transcribing cells

status: Public on Mar 04 2024

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

summary: Enhancer hijacking, a common cause of gene misregulation linked to disease, occurs when non-matching enhancers and promoters interact ectopically. This interaction is made possible by genetic changes that alter the arrangement or insulation of gene regulatory landscapes. While the concept of enhancer hijacking is well understood, the specific reasons behind the variation in phenotypic severity or the point at which those phenotypes become evident remain unexplored. In this work, we expand on the ectopic activation of the hindlimb-specific transcription factor Pitx1 by one of its own enhancers, Pen, in forelimb tissues that causes the Liebenberg syndrome. We combine a previously developed in-embryo cell-tracing approach to a series of inversions and relocations to show that reduction in Pitx1-Pen relative genomic positioning leads to increased proportions of Pitx1 forelimb-expressing cells and more severe phenotypical outcomes. We demonstrate that the Pitx1 locus assumes an active topology when enhancer-promoter contacts are required for transcription and that its promoter generates consistent transcription levels across different alleles. Finally, we show that changes in 3D chromatin structure and enhancer-promoter contacts are not the result of Pitx1 transcriptional activity. In summary, our work shows that variation in enhancer-promoter interactions can lead to pathogenic locus activation in variable proportions of cells which, in turn, define phenotypic severity.

overall_design: We analysed two biological replicates of  forelimb GFP+ cells from Pitx1GFP;Inv1, Pitx1GFP;Inv2, Pitx1GFP;Rel1, Pitx1GFP;Rel2 and Pitx1GFP;Rel3 cells to compare compare to WT forelimb cells. Furthermore, we analyse two biological replicates from bulk Pitx1GFP;Rel2 and Pitx1GFP;Rel3, dCas9P300-Pitx1TSSsgRNAs and dCas9P300-noSgRNAs forelimbs.

first: Olimpia

last: Bompadre


title: Discovering Molecular Signatures in ATMR: Single-cell RNA Sequencing Analysis of Human Blood and Tissue Spatial Transcriptomics [scRNA-seq]

first: Minji

last: Kang

first: Jeongin

last: Song

first: Yunyoung

last: Jang

first: YongChul

last: Kim

first: HyunJe

first: SeungHee

last: Yang


title: Exploiting Epigenetic Targets to Overcome Taxane Resistance in Prostate Cancer

status: Public on Nov 17 2023

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

summary: The development of taxane resistance remains a major challenge for castration resistant prostate cancer (CR-PCa), despite the effectiveness of taxanes in prolonging patient survival. To uncover novel targets, we performed an epigenetic drug screen on taxane (docetaxel and cabazitaxel) resistant CR-PCa cells. We identified BRPF reader proteins, along with several epigenetic groups (CBP/p300, Menin-MLL, PRMT5 and SIRT1) that act as targets effectively reversing the resistance mediated by ABCB1. Targeting BRPFs specifically resulted in the resensitization of resistant cells, while no such effect was observed on the sensitive compartment. These cells were successfully arrested at the G2/M phase of cell cycle and underwent apoptosis upon BRPF inhibition, confirming the restoration of taxane susceptibility. Pharmacological inhibition of BRPFs reduced ABCB1 activity, indicating that BRPFs may be involved in an efflux-related mechanism. Indeed, ChIP-qPCR analysis confirmed binding of BRPF1 to the ABCB1 promoter suggesting direct regulation of the ABCB1 gene at the transcriptional level. RNA-seq analysis revealed that BRPF1 knockdown affects the genes enriched in mTORC1 and UPR signaling pathways, revealing potential mechanisms underlying its functional impact, which is further supported by the enhancement of taxane response through the combined inhibition of ABCB1 and mTOR pathways, providing evidence for the involvement of multiple BRPF1-regulated pathways. Beyond clinical attributes (Gleason score, tumor stage, therapy outcome, recurrence), metastatic PCa databases further supported the significance of BRPF1 in taxane resistance, as evidenced by its upregulation in taxane-exposed PCa patients.

overall_design:
To investigate the underlying mechanisms of taxane resistance, we established docetaxel and cabazitaxel-resistant CR-PCa cell lines (Du145 and 22Rv1). To gain insight into the molecular mechanisms underlying BRPF1-mediated reversion of drug resistance, we aimed to examine the transcriptome of docetaxel-resistant (DtxR) Du145 cells treated with siRNA-BRPF1.
We performed a gene expression profiling analysis using data obtained from RNA-seq of parental (Du145-P), docetaxel-resistant (DtxR) Du145, and cabazitaxel-resistant (CbzR) Du145 cells. We performed a gene expression profiling analysis using data obtained from RNA-seq of siRNA-Control and siRNA-BRPF1 treated docetaxel-resistant (DtxR) Du145 cells.

first: Buse

last: Cevatemre

first: Ipek

last: Bulut

first: Beyza

last: Dedeoglu

first: Arda

last: Isiklar

first: Ozlem

last: Yedier Bayram

first: Tugba

last: Bagci-Onder

first: Ceyda

last: Acilan Ayhan


title: Interferon Regulatory Factor 6 Determines Epithelial Cell Development and Immunity

status: Public on Nov 01 2023

city: Portland

first: Timothy

last: Nice

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

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


title: Cellular reprogramming is driven by widespread rewiring of promote-enhancer interactions

status: Public on Nov 03 2023

city: Tallahassee

first: Peter

last: Fraser

state: FL

address: 319 stadium Drive

institute: Florida State University

summary:
Interactions between promoters and cis-regulatory elements, such as enhancers, play a role in gene regulation. However, the role of three-dimensional (3D) chromatin structure in orchestrating changes in transcription during cell fate transition is not fully understood.
Here, we performed integrated analyses of chromosomal architecture, epigenetics and gene expression using Hi-C, promoter Capture Hi-C (PCHi-C), ChIP sequencing, and RNA sequencing during trans-differentiation of preB cells into macrophages with a β-estradiol inducible CEBPα-ER transgene. Within 1 hour of β-estradiol induction, CEBPα translocates from the cytoplasm to the nucleus and binds to thousands of promoters and putative regulatory elements, resulting in downregulation of preB cell specific genes and induction of macrophage specific genes. Hi-C results were remarkably consistent throughout transinduction, revealing only a small number of TAD boundary location changes, and A/B compartment switches despite changes in expression of thousands of genes. PCHi-C reveals changes in promoter-anchored loops with decrease in interactions parallel with their decreased expression, and new promoter-anchored interactions with macrophage specific genes concordant with their increased expression.Overall, our data demonstrate that CEBPα-induced transinduction involves few changes in genome architecture that are detectable by Hi-C, and widespread reorganization of thousands of promoter anchored loops with PCHi-C that drive changes in cell identity.

overall_design: We performed Hi-C, promoter capture Hi-C (PCHi-C) and RNAseq to investigate the 3D genome organization during transdifferentiation of Pre-B cells to macrophages.

first: Miao

last: Wang

first: Bing

last: He

first: Divyaa

last: Srinivasan

first: Yueling

last: Hao

first: Jatin

last: Shrinet


title: Interferon Regulatory Factor 6 Determines Epithelial Cell Development and Immunity 1

summary: Intestinal epithelial cells (IECs) form a primary barrier against microbial invasion. Prior studies of enteric pathogens have indicated that IEC defense mechanisms are distinct from those of other cell types. For example, antiviral defense of IECs depends on type III interferon whereas most cell types depend on type I IFN. Interferon regulatory factors (IRFs) are a family of transcription factors with well-described roles in stimulation of IFN cytokines, but IRF6 is unique in its preferential expression by epithelial lineages. IRF6 has primarily been studied in epidermal development, but has relatively unknown roles in the intestinal epithelium. Here, we found that Irf6 KO regulated IFN-stimulated antiviral immunity of IECs but had no effect on macrophages. RNseq analysis of Irf6 KO cells showed significant differences in the IFN-stimulated gene expression program that correlated with the magnitude of antiviral gene stimulation. We also found significant baseline phenotypic and transcriptional changes in Irf6 KO IECs, with reduced rate of growth and preturbation of growth and differentiation pathway genes. Knockout of Irf6 in primary IEC organoids also resulted in slower growth and smaller size. Transcriptional analysis of Irf6 KO organoids indicated reduced expression of genes in the epithelial differentiation pathwya, including Wnt and Notch pathway genes, as well as increased expression of a subset of IFN-stimulated genes. These data indicate a previously unappreciated role of Irf6 in shaping the IEC transcriptome, including baseline epithelial development genes and IFN-stimulated genes.

overall_design: Mouse IEC cell lines (derived from M2C cells, Padilla-Nash et al., 2012; doi: 10.1002/gcc.21921) were transduced with lentivirus encoding Cas9 and gRNA against Irf6 or non-targeting control, and monoclonal isolates were sequence-confirmed for disruption of the Irf6 locus. Treatments were added to cultured cells, and RNA was isolated twenty-four hours after treatments. Samples were collected in experimental triplicate.

first: Austin

middle: P

last: Wright


title: Reorganization of Lamina Associated Domains in early mouse embryos is regulated by RNA Polymerase II activity.

city: Munich

first: Maria-Elena

last: Torres-Padilla

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

summary: How the earliest events in embryogenesis, including zygotic genome activation (ZGA) during maternal-to-zygotic transition influence chromatin remodelling remains unknown. Here, we have investigated the establishment of nuclear architecture, focusing on the remodelling of Lamina Associated Domains (LADs) during this transition. We report that LADs reorganize gradually in 2-cell embryos and that blocking ZGA leads to major changes in nuclear organisation.

overall_design: LaminB1 DamID in wildtype early 2-cell embryos and in late 2-cell embryos either treated with alpha-amanitin or DRB.

first: Mrinmoy

last: Pal


title: Cytokine Polarized Bone Marrow Neutrophils Drive Axon Regeneration

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

summary: The adult central nervous system (CNS) has a limited capacity for self-repair. Severed CNS axons typically do not regrow. There is an unmet need for treatments specifically designed to enhance neuronal viability, facilitate CNS axon regeneration, and ultimately restore lost neurological functions to individuals with traumatic CNS injury, multiple sclerosis, and stroke, among other disorders. Here we demonstrate that both mouse and human bone marrow (BM) neutrophils upregulate markers of alternative activation, and acquire the ability to promote neurite outgrowth, following polarization with a combination of recombinant interleukin-4 (IL-4) and granulocyte-colony stimulating factor (G-CSF). Moreover, adoptively transferring IL-4/G-CSF polarized BM neutrophils into experimental models of CNS injury resulted in significant axon regeneration within the optic nerve and spinal cord. The findings reported in this paper hold significant implications for the future development of autologous myeloid cell-based therapies that may bring us closer to effective solutions for reversing CNS damage.

overall_design: To investigate the effect of polarization on the generation of alternatively activated immune cells, mouse Ly6G+ bone marrow neutrophils and human CD34+ bone marrow cells were polarized with or without IL-4 and/or G-CSF.

first: Jerome

last: Andrew

first: Sas

first: Wang

last: Yan

first: Atkinson

last: Jeffrey

first: Wen

last: Jing

first: Liu

last: Tom

first: Webb

last: Amy

first: Segal

last: Benjamin


title: A plasma miRNA-based classifier for small cell lung cancer diagnosis [miRNA-Seq]

status: Public on Oct 31 2023

city: Richmond

first: Michela

last: Saviana

state: Virginia

address: 1101 E Marshall St

department: Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine

institute: Virginia Commonwealth University

type: Non-coding RNA profiling by high throughput sequencing

summary: Objectives: Small cell lung cancer (SCLC) is characterized by poor prognosis and challenging diagnosis. Screening in high-risk smokers results in a reduction in lung cancer mortality, however, screening efforts are primarily focused on non-small cell lung cancer (NSCLC). SCLC diagnosis and surveillance remain significant challenges. The aberrant expression of circulating microRNAs (miRNAs/miRs) is reported in many tumors and can provide insights into the pathogenesis of tumor development and progression. Here, we conducted a comprehensive assessment of circulating miRNAs in SCLC with a goal of developing a miRNA-based biomarker classifier to assist in SCLC diagnoses. Materials and Methods: We profiled deregulated circulating cell-free miRNA in the plasma of SCLC patients. We tested selected miRs on a training cohort and created a classifier by integrating miRNA expression and patient clinical data. Finally, we applied the classifier on a validation dataset.  Results: We determined that miR-375-3p can discriminate between SCLC and NSCLC patients, and between SCLC and Squamous Cell Carcinoma patients.  Moreover, we found that a model comprising miR-375-3p, miR-320b, and miR-144-3p can be integrated with race and age to distinguish metastatic SCLC from a control group.  Conclusion: This study proposes a miRNA-based biomarker classifier for SCLC that considers clinical demographics with specific cut offs to inform SCLC diagnosis.

overall_design: A total of 38 samples were used for miRNA extraction from plasma. The cohort comprises 10 high-risk smokers that were used as control samples, 10 adenocarcinomas, 10 squamous cell carcinomas, and 8 SCLC patients. The RNA was purified from 200 uL of plasma and NGS for small RNA was performed.

first: Patrick

middle: S

last: Nana-Sinkam

first: Mario

last: Acunzo

first: Saviana

last: Michela


title: A population of  Regulatory T cells controls nociception through enkephalins to restrain skin inflammation [plate scRNA-seq]

first: Stanislav

last: Dikiy

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

summary: The skin, as a principal barrier tissue, integrates diverse signals discerned by sensory neurons and by immune cells to elicit adaptive responses to a wide range of stresses. While nociceptors, sensory neurons that initiate the sensation of pain, can mobilize and amplify the function of innate and adaptive immune effector cells, regulatory T (Treg) cells, a T cell subset expressing the transcription factor Foxp3, suppress systemic and local inflammatory responses. Considering the connectivity between nervous and immune systems for sensing and responding to damaging insults, we questioned whether Treg cells can modulate proinflammatory neuronal activity by acting directly on peripheral neurons. We found that Treg cells localized near axons innervating the skin and that short-term inactivation or ablation of Treg cells increased neuronal activation to noxious stimuli in a manner separable from their immunosuppressive function. Furthermore, a population of skin Treg cells was highly enriched for expression of Penk, the gene encoding the neuropeptide precursor for endogenous opioids enkephalins, which inhibit pain perception by inducing analgesia. Acute depletion of Penk expressing Treg cells, or inducible ablation of Penk in Treg cells increased neuronal activation in response to noxious stimuli and associated inflammation. Our study suggests that a population of Treg cells residing at barrier tissues exhibit a direct neuromodulatory activity opposing exacerbated activation of sensory neurons, at least in part through the production of an endogenous opioids, and by acting as an immune component of the neuro-immune axis, dampen responses to noxious pain stimuli and local inflammation.

overall_design: Mice were anesthetized with 2.5% isofluorane and treated with 5% Imiquimod (Perrigo) or vehicle control, applied topically to dorsal and ventral sides of ear skin. Mice (2 IMQ, 2 VEH) were treated starting on day 0 three times and euthanized for sorting on day 3.

first: Alejandra

last: Mendoza

first: Paolo

last: Giovanelli

first: Alexander

middle: Y

last: Rudensky


title: iPSC-derived Trimodal T cells engineered with CAR, TCR, and hnCD16 modalities can overcome antigen escape in heterogenous tumors

status: Public on Oct 24 2023

city: San Diego

first: Eigen

last: Peralta

address: 12278 Scripps Summit Drive

institute: Fate Therapeutics Inc. (FHQ1)

summary: Although chimeric antigen receptor (CAR) T cells have demonstrated remarkable therapeutic activity in hematopoietic malignancies, antigen escape and tumor heterogeneity have in part impeded the durable efficacy of CAR T cells and their extension into successful solid tumor treatment. To address these challenges, induced pluripotent stem cell (iPSC) - derived T (iT) cells were specifically engineered to uniformly express both CAR and T cell receptors (TCR), enabling targeting of both surface and intracellular antigens, respectively, along with a high-affinity, non-cleavable variant of CD16a (hnCD16) to support antibody-dependent cell cytotoxicity (ADCC) when combined with therapeutic antibodies. Co-expression of each of these unique anti-tumor targeting strategies on engineered iT cells enabled independent and antigen-specific tumor cell killing across a diverse set of liquid and solid tumors.  In heterogenous tumor models, coactivation of two or more of these effector modalities was required for measurable anti-tumor efficacy, with all three displaying maximal efficacy. These data highlight the therapeutic potential of an off-the-shelf engineered iPSC-derived Trimodal T cell expressing CAR, TCR, and hnCD16 to combat difficult to treat heterogeneous tumors.

overall_design: RNA were isolated from cryo vials of human Neutrophils, CD56+ NK cells, Monocytes, Macrophages, CD8+ T cells (commercially available) and human TiPSC, iTs with 3 different engineering designs (generated in house as described in M&M).

first: Bi-Huei

last: Yang

first: Alma

last: Gutierrez

first: Soheila

last: Shirinbak

first: Angela

last: Liao

first: Yu-Sheng

last: Lin

first: Wen-I

last: Yeh

first: David

last: Gonzalez

first: Bjoern

last: Gaertner

first: Mochtar

last: Pribadi

first: Hui-Yi

last: Chu

first: Pei-Fang

last: Tsai

first: Chia-Wei

last: Chang

first: Tom

last: Lee

first: Ryan

last: Bjordahl

first: Martin

last: Hosking

first: Bahram

last: Valamehr


title: Multi-chamber cardioids unravel human heart development and cardiac defects [scRNA-seq]

status: Public on Oct 30 2023

city: Vienna

first: Clara

last: Schmidt

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology GmbH

summary: The number one cause of human fetal death are defects in heart development. Because the human embryonic heart is inaccessible, and the impacts of mutations, drugs, and environmental factors on the specialized functions of different heart compartments are not captured by in vitro models, determining the underlying causes is difficult. Here, we established a human cardioid platform that recapitulates the development of all major embryonic heart compartments, including right and left ventricles, atria, outflow tract, and atrioventricular canal. By leveraging both 2D and 3D differentiation, we efficiently generated progenitor subsets with distinct first, anterior, and posterior second heart field identities. This advance enabled the reproducible generation of cardioids with compartment-specific in vivo-like gene expression profiles, morphologies, and functions. We used this platform to unravel the ontogeny of signal and contraction propagation between interacting heart chambers and dissect how genetic and environmental factors cause region-specific defects in the developing human heart.

overall_design: Human pluripotent stem cells were differentiated into five different cardioid subtypes: left ventricle, right ventricle, atria, outflow tract and atrioventricular canal. Two biological replicates (except Atria) were used per protocol.

first: Schmidt

last: Clara

first: Alison

last: Deyett

first: Sasha

last: Mendjan


title: Multi-chamber cardioids unravel human heart development and cardiac defects [RNA-Seq]

overall_design: Human pluripotent stem cells were differentiated into five different cardioid subtypes, left ventricle, right ventricle, atria, outflow tract and atrioventricular canal. Data show a time course of cardioid differentiation starting from day 1.5 until day 14. Three biological replicates and eight technical replicates were used per timepoint.


title: Multi-chamber cardioids unravel human heart development and cardiac defects

overall_design: Refer to individual Series


title: Muscle miRNAs are influenced by sex at baseline and in response to exercise

status: Public on Oct 05 2023

city: Burwood

first: Danielle

last: Hiam

state: Vic

address: 221 Burwood Hwy

department: IPAN

institute: Deakin University

summary: The aim of this study was to investigate the effect of sex on miRNA expression in skeletal muscle. MiRNAs were first screened using Taqman®miRNA arrays in skeletal muscle of 42 healthy participants from the Gene SMART study (23 males and 19 females aged 18-45 yrs). Based on this 2 candidate miRNAs, hsa-miRNA-30a-5p (miR-30a) and hsa-miRNA-30c-5p (miR-30c), were overexpressed in three female and three male primary skeletal muscle lines. Overexpression of miR-30a and miR-30c was confirmed by quantifying transcript levels using qPCR RNA sequencing to understand the transcriptome profile changes driven by these miRNAs and to explore the putative biological pathways.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for male and female donor cells lines with and without overexpression of miR-30a and miR-30c.

first: Shanie

last: Landen

first: Macsue

last: Jacques

first: Sarah

last: Voisin

first: Severine

last: Lamon

first: Nir

last: Eynon


title: Cryptic endogenous retrovirus subfamilies in the primate lineage

status: Public on Oct 23 2023

city: Kyoto

first: Xun

last: Chen

address: Faculty of Medicine Building B, Yoshidatachibanacho, Sakyo Ward

department: Institute for the Advanced Study of Human Biology (ASHBi)

institute: Kyoto University

summary: Many endogenous retroviruses (ERVs) in the human genome are primate-specific and contribute novel cis-regulatory elements and transcripts. Classification and annotation of ERVs, which are flanked by long terminal repeats (LTRs) containing sequences that control their transcriptional activity, is important to better understand their evolution and potential roles in the host. Here, we observed that many of the currently annotated LTR subfamilies spreading in the primate lineage have subsets of instances that appear to be misclassified. Focusing on the evolutionary young MER11A/B/C subfamilies, we performed a phylogenetic analysis and relied on cross-species conservation to reveal the presence of 4 phyletic groups, suggesting a new annotation for 412 (19.8%) of the MER11 instances. Next, we showed that the epigenetic heterogeneity observed within the MER11A/B/C subfamilies was better explained in the context of these new phyletic groups. Using a massively parallel reporter assay (MPRA), we also demonstrated the regulatory potential of the four phyletic groups and identified motifs that were associated with their differential activities. The MPRA combined with the use of phyletic groups across primates revealed an apes-specific gain of SOX related motifs through a single-nucleotide deletion. Finally, we applied a similar approach across all 53 simian-specific LTR subfamilies and determined the presence of 75 phyletic groups. We found that 3,807 (30.0%) instances from 26 of these LTR subfamilies changed annotation and could be characterized into one of these novel phyletic groups, many of which with a distinct epigenetic profile. This refined annotation of simian-specific LTRs could improve our understanding of the evolution of ERVs in primate genomes and reveal functional signals that would have been missed otherwise.

overall_design: Gene regulatory function of ~17,000 selected transposable element sequences was analyzed using lentivirus-based massively parallel reporter assays (lentiMPRA) in human induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs) in 3 replicates.

first: Zicong

last: Zhang

first: Yizhi

last: Yan

first: Clement

last: Goubert

first: Guillaume

last: Bourque

first: Fumitaka

last: Inoue


title: Serum miRNA Seq of Children with Asthma in Costa Rica

status: Public on Oct 09 2023

city: Boston

first: Joanne

last: Sordillo

state: MA

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

institute: Mass General Brigham

summary: Small RNA was sequenced from banked peripheral blood serum from 1,134 asthmatic children aged 6 to 14 years who participated in the Genetics of Asthma in Costa Rica Study (GACRS). We filtered the participants into high and low bronchodilator response (BDR) quartiles and used DeSeq2 to identify miRNAs with differential expression (DE) in high (N= 277) vs low (N= 278) BDR group. The putative target genes of DE miRNAs were identified, and pathway enrichment analysis was performed. Results: We identified 10 down-regulated miRNAs having odds ratios (OR) between 0.37 and 0.76 for a doubling of miRNA counts and one up-regulated miRNA (OR=2.26) between high and low BDR group. Further, functional annotation of 11 DE miRNAs were performed as well as of two replicated miRs. Target genes of these miRs were enriched in regulation of cholesterol biosynthesis by SREBPs, ESR-mediated signaling, G1/S transition, RHO GTPase cycle, and signaling by TGFB family pathways.

overall_design: Serum from children with asthma was sequenced. After QC, 1134 subjects showed a total of 317 miRNAs.

first: Rinku

last: Sharma

first: Michael

last: McGeachie


title: Mouse Mammary Tumor Models of Various Molecular Subtypes Including Basal-like and Claudin-low TNBC

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Mouse mammary tumors are diverse neoplastic growths originating in the mammary glands of mice and serve as essential models for studying human breast cancer. These tumors can be classified into distinct molecular subtypes, including luminal, basal-like, HER2-enriched, and claudin-low, reflecting the heterogeneity observed in breast cancer. With unique genetic and molecular features, these subtypes are instrumental for understanding the complexities of tumor biology. Here we sequenced the mRNA of 13 treatment-na  ve mouse mammary tumor lines for a total of 82 samples.

overall_design: Gene expression of 82 individual, untreated mouse mammary tumors from mRNAseq data. At least 2 biological replicates per individual tumor model are included here. The tumor models included in this submission are: 2153, 2208, 2224, 2225, 2250, 2336, 4T1, 9263, E0771, KPB1-A, MMTV-NEU, MMTV-PYMT, and T12.


title: Genetic polymorphisms lead to major, locus-specific, variation in piRNA production in mouse.

status: Public on Sep 22 2023

city: Badalona

first: Tanya

last: Vavouri

state: BARCELONA

address: Ctra de Can Ruti, Cami de les Escoles, s/n

institute: Josep Carreras Leukemia Research Institute

summary: PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that silence transposons in the animal germline. PiRNAs are produced from long single-stranded noncoding transcripts, from protein-coding transcripts, as well as from transposons. While some sites that produce piRNAs are in deeply conserved syntenic regions, in general, piRNAs and piRNA-producing loci turnover faster than other functional parts of the genome. To learn about the sequence changes that contribute to the fast evolution of piRNAs, we set out to analyze piRNA expression between genetically different mice. Here we report the sequencing and analysis of small RNAs from the mouse male germline of four classical inbred strains, one inbred wild-derived strain and one outbred strain. We find that genetic differences between individuals underlie variation in piRNA expression. We report significant differences in piRNA production at loci with endogenous retrovirus insertions. Strain-specific piRNA-producing loci include protein-coding genes. Our findings provide evidence that transposable elements contribute to inter-individual differences in expression, and potentially to the fast evolution of piRNA-producing loci in mammals.

overall_design:
Differential expression analysis of known and predicted piRNAs in testes and spermatogonia of genetically different mouse strains (C57BL6, CAST, 129, C3H, NOD, ICR).
RNA-seq profiling of testes and FACS sorted spermatogonia from five inbred mouse strains and one outbred mouse strain.

NOTE: The data in this series replaces data originally included in GSE121138.
The records have been updated with additional RNA-seq samples on Jul 8, 2025.

first: Eduard

last: Casas

first: Adrià

last: Mitjavila-Ventura

first: Pío

last: Sierra

first: Cristina

last: Moreta-Moraleda

first: Judith

last: Cebria

first: Ilaria

last: Panzeri

first: J. Andrew

last: Pospisilik

first: Josep

middle: C

last: Jimenez-Chillaron

first: Sonia

middle: V

last: Forcales


title: A self-renewing biomimetic skeletal muscle construct engineered using induced myogenic progenitor cells

status: Public on Sep 27 2023

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

summary: Skeletal muscle is a highly organized and regenerative tissue that maintains its homeostasis primarily by activation and differentiation of muscle stem cells. Mimicking an in vitro skeletal muscle differentiation program that contains self-renewing adult muscle stem cells and aligned myotubes has been challenging. Here, we set out to engineer a biomimetic skeletal muscle construct that can self-regenerate and produce aligned myotubes using induced myogenic progenitor cells (iMPCs), a heterogeneous culture consisting of skeletal muscle stem, progenitor and differentiated cells. Utilizing electrospinning, we fabricated polycaprolactone (PCL) substrates that enabled iMPC-differentiation into aligned myotubes by controlling PCL fiber orientation. Newly-conceived constructs contained highly organized multinucleated myotubes in conjunction with self-renewing muscle stem cells, whose differentiation capacity was augmented by Matrigel supplementation. Additionally, we demonstrate using single cell RNA sequencing (scRNA-seq) that iMPC-derived constructs faithfully recapitulate a step-wise myogenic differentiation program. Notably, when the constructs were subjected to a damaging myonecrotic agent, self-renewing muscle stem cells rapidly differentiated into aligned myotubes, akin to skeletal muscle repair in vivo. Taken together, we report on a novel in vitro system that mirrors myogenic regeneration and muscle fiber alignment, and can serve as a platform to study myogenesis, model muscular dystrophies or perform drug screens.

overall_design: Single cell transcriptional analysis of induced myogenic progenitors (iMPCs) grown on electrospun PCL substrates with or without Matrigel

first: Inseon

last: Kim

first: Seunghun

last: Lee

first: Ori

last: Bar-Nur


title: Gene expression data from colon of mice with DSS induced colitis

status: Public on Sep 16 2023

city: Columbia

first: Philip

middle: Brandon

last: Busbee

state: SC

address: 6439 Garners Ferry Road

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina School of Medicine

summary:
To ascertain whether the activation of AhR in intestinal epithelial cells (IECs) directly contributes to the enhanced production of Muc2, we generated conditional AhR knockout mice with deficiency in IECs (AhRΔIEC). Subsequently, the expression of genes involved in mucin production, along with the markers indicative of mature goblet cells and proliferation in the context of colitis, with or without I3C treatment was evaluated.
We used microarrays to detail the global programme of gene expression to identify the distinct classes of up-regulated and downlregulated genes among the experimental groups.

overall_design: Mouse colon tissues from various experimental groups were collected for RNA extraction and subsequent hybridization onto Affymetrix microarrays.To investigate the role of AhR expression in intestinal epithelial cells (IECs), we employed both IEC-specific AhR knockout (AhRΔIEC) mice and wildtype (WT) mice.All mice were subjected to treatment with DSS and I3C, after which RNA was extracted from the following four groups: WT DSS, WT DSS+I3C, AhRΔIEC DSS, and AhRΔIEC DSS+I3C.

first: Archana

last: Saxena

middle: B


title: Clinical subtyping of cancer from plasma based on comprehensive epigenomic profiling

status: Public on Sep 21 2023

first: Sylvan

last: Baca

address: 450 Brookline Ave

department: Center for Functional Cancer Epigenetics

institute: Dana Farber Cancer Institute

summary: While circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1mL of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors, and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling could unlock clinically actionable information that is currently accessible only via direct tissue sampling.

first: Matthew

last: Freedman

first: Brad

last: Fortunato


title: Single-cell profiling of acral melanoma infiltrating lymphocytes reveals a suppressive tumor microenvironment

status: Public on Sep 06 2023

city: Sapporo

first: Tomoyuki

last: Minowa

state: Hokkaido

address: west 17, south 1, Chuo-ku

department: Pathology

institute: Sapporo medical university school of medicine

summary: Acral lentiginous melanoma (ALM) is the most common melanoma subtype in non-Caucasians. Despite advances in cancer immunotherapy, current immune checkpoint inhibitors remain unsatisfactory for ALM. Hence, we conducted comprehensive immune profiling using single-cell phenotyping with reactivity screening of the T cell receptors of tumor-infiltrating T lymphocytes (TILs) in ALM. Compared with cutaneous melanoma, ALM showed a lower frequency of tumor-reactive CD8 clusters and an enrichment of regulatory T cells with direct tumor recognition ability, suggesting a suppressive immune microenvironment in ALM. Tumor-reactive CD8 TILs showed heterogeneous expression of coinhibitory molecules, including KLRC1 (NKG2A), in subpopulations with therapeutic implications. Overall, our study provides a foundation for enhancing the efficacy of immunotherapy in ALM.

overall_design: Single-cell immune profiling of tumor-infiltrating lymphocytes from primary and metastatic human acral lentiginous melanoma was conducted. Individual cells were dissociated from fresh tumor resections, and tumor-infiltrating lymphocytes were isolated by FACS based on CD3CD45 staining. Single-cell 5' RNA-seq and paired full-length TCR-seq were performed using the 10X Genomics Chromium platform, and the samples were sequenced on the Illumina NextSeq HiSeq X Ten. RNA-seq data were obtained for the parental fresh tumor samples and the tumor cell line from two patients.

first: Kenji

last: Murata

first: Yoshihiko

last: Hirohashi

first: Toshihiko

last: Torigoe


title: Transient gene melting governs the timing of oligodendrocyte maturation [ATAC-seq]

status: Public on Sep 01 2023

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

summary: Cellular maturation is a crucial step for tissue formation and function, distinct from the initial steps of differentiation and cell fate specification. In the central nervous system, failure of oligodendrocyte maturation is linked to diseases such as multiple sclerosis. Here, we report a transcriptional mechanism that governs the timing of oligodendrocyte maturation. After progenitor cells differentiate into immature oligodendrocytes, the transcription factor SOX6 redistributes from super enhancers to cluster across specific gene bodies. These sites exhibit extensive chromatin decondensation and transcription, which abruptly turn off upon maturation. Suppression of SOX6 deactivates these immaturity loci, accelerating the transition to mature, myelinating oligodendrocytes. Notably, cells harboring this immature SOX6 gene signature are enriched in multiple sclerosis patient brains. Antisense oligonucleotide-mediated Sox6 knockdown drives precocious oligodendrocyte maturation in mice. Our findings establish SOX6 as a key regulator of oligodendrocyte maturation and highlight its potential as a therapeutic target to promote myelination in disease.

overall_design: Chromatin accessibilty of pluripotent stem cell derived oligodendrocyte progenitor cells (OPCs) and oligodendrocytes (OL)

first: Kevin

last: Allan


title: TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function

status: Public on Oct 20 2023

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

summary: Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species, and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find 14% of all human TAD boundaries to be shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons, compared to species-specific boundaries. CRISPR-Cas9 knockouts of two ultraconserved boundaries in mouse models leads to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations, and showcase the functional importance of TAD evolution.

sample_organism:
Macaca mulatta
Homo sapiens
Mus caroli
Mus musculus
Mus pahari
Rattus norvegicus
Nomascus leucogenys
Hylobates moloch

overall_design: We sequenced H3K4me3, H3K27me3, H3K4me1, H3K27ac, and CTCF ChIP-seq of three rodent species liver tissue, and LCL from two gibbon species. A Male and female biological replicate were sequenced for each mark and species. To test functionality of human-specific boundaries, we used CRISPR to knock-out a human-specific TAD boundary (two replicated) in iPSC-induced neurons, and used HiC to compare chromatin interaction between wild-type (two replicated) and knock-out cells. To test functionality of ultraconserved boundaries, we used CRISPR to knock-out a candidate ultra-conserved TAD boundaries in mouse, and used Capture HiC to compare chromatin interaction in the heart of wild-type (two replicates) and knock-out mice (two replicates).

first: Jake

last: VanCampen

first: Lucia

last: Carbone


title: Transient gene melting governs the timing of oligodendrocyte maturation [ChIP-seq]

overall_design: ChIP-seq of pluripotent stem cell derived oligodendrocyte progenitor cells (OPCs) and oligodendrocytes (OL)


title: High-throughput sequencing data of circRNAs in the gastrocnemius muscle of mice with or without right sciatic nerve denervation

status: Public on Sep 08 2023

city: Shanghai

first: Jin

last: Li

address: 99 Shangda Road

institute: Shanghai University

summary: This study was to identify circRNAs responsible for muscle atrophy. Skeletal muscle wasting is a common clinical feature of many chronic diseases and also occurs in response to acute events. Circular RNAs are covalently closed RNA transcripts that are involved in various physiological and pathological processes. However, the underlying mechanisms of circRNAs implicated in muscle atrophy remains unknown. Global circRNA expression profiling indicated that many circRNAs are involved in the pathophysiological processes of muscle atrophy.

overall_design: The samples used for circular RNA sequencing were gastrocnemius muscle samples from denervated mice with muscle atrophy. The sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). For circular RNA sequencing, the total RNA were treated with ribo-zero kit and RNase R to remove ribosomal RNA and linear RNA, respectively. Then constructed cDNA library and qualified by the Agilent 2100 Bioanalyzer, the sequencing was performed by the Illumina sequencer.

first: Junjie

last: Xiao


title: Transient gene melting governs the timing of oligodendrocyte maturation [miRNA-seq]

overall_design: Small RNA transcriptional profiling of mouse pluripotent stem cell-derived oligodendrocyte progenitor cells (OPCs) and oligodendrocytes (OL) as in vivo isolated OPCs and OLs.

first: Tyler

last: Miller


title: Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate motor cortex [Macaque]

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Sequence divergence of cis-regulatory elements drives species-specific traits, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome, and chromosomal conformation profiles from a total of over 180,000 cells. For each modality, we determined species-specific, divergent, and conserved gene expression and epigenetic features at multiple levels. We find that cell type-specific gene expression evolves more rapidly than broadly expressed genes and that epigenetic status at distal candidate cis-regulatory elements (cCREs) evolves faster than promoters. Strikingly, transposable elements (TEs) contribute to nearly 80% of the human-specific cCREs in cortical cells. Through machine learning, we develop sequence-based predictors of cCREs in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Lastly, we show that epigenetic conservation combined with sequence similarity helps uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.

overall_design:
The motor cortex of  Macaque were disected and nuclei were prepared for library preparation. In-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.  The snm3C-seq samples followed the library preparation protocol detailed previously. This protocol has been automated using the Beckman Biomek i7 instrument to facilitate large-scale applications. The snm3C-seq libraries were sequenced on an Illumina NovaSeq 6000 instrument, utilizing one S4 flow cell per 16 384-well plates and employing a 150 bp paired-end mode.

This study includes samples in the following series:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241339
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219006
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219113
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219198
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE219263

first: Wenliang

last: Wang

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Jordan

last: Altshul

first: Rosa

last: Gomez Castanon

last: Nery

first: Huaming

last: Chen


title: Transient gene melting governs the timing of oligodendrocyte maturation

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


title: DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts [Ribo-Seq]

status: Public on Aug 22 2023

city: Heidelberg

first: Joschka

last: Hey

state: Deutschland

address: Im Neuenheimer Feld 280

department: Cancer epigenomics

institute: DKFZ

summary:
To investigate the effect of Decitabine and SB939 treatment on the expression of endoretroviral elements.
We treated NCI-H1299 cells with DMSO or a combination of Decitabine and SB939 and performed Ribo-seq. This data was used to identify novel ORFs expressed from endoretroviral elements derived transcripts.

overall_design: Ribosomal footprinting analysis of Ribo-seq data for NCI-H1299 cells treated with DMSO or a combination of Decitabine and SB939

first: Fabricio

last: Puch

first: Ekaterina

last: Stepanova

first: Christoph

last: Plass

first: Joshcka

first: Ashish

last: Goyal


title: DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts


title: Identification of genes regulated by loss of RRM1 in Ewing sarcoma cells.

status: Public on Aug 23 2023

city: Iowa City

first: David

middle: Jon

last: Gordon

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

summary: Ribonucleotide reductase (RNR), which is composed of RRM1 and RRM2 subunits, is the rate limiting enzyme in the synthesis of deoxyribonucleotides and required for DNA replication and DNA damage repair. We used a conditional knockout (CRISPR/Cas9) and rescue approach to target RRM1 in Ewing sarcoma cells and identify downstream pathways impacted by the loss of RNR activity. RNA-seq analysis was performed at times 0 and 48 hours after removal of doxycycline from cell culture media, which results in loss of the RRM1 protein.

overall_design: We performed RNA-seq in Ewing sarcoma cell lines with conditional knockout of RRM1.


title: Inhibition of SQLE or FDFT1 in RBE cells by shRNA, or RBE cells treated with lycorine hydrochloride

status: Public on Aug 18 2023

city: Zhongshan City

first: Fengyun

last: Zhao

address: 2 Sunwen East Road

department: Cancer Research Institute of Zhongshan City

institute: Zhongshan City People's Hospital

summary: High-throughput sequencing was performed to analyze gene expression profiles of RBE cells after the the inhibition of SQLE or FDFT1 by lentiviruses-mediated shRNA, or RBE cells treated with lycorine hydrochloride.

overall_design: RBE cells were treated for 24 hours with either DMSO, or lycorine hydrochloride (1μM), and cells were collected from each treatment group to perform high-throughput sequencing and mRNA expression profile data analyzing. For the inhibition of SQLE or FDFT1 in RBE cells, the expression of SQLE or FDFT1 was knocked down by lentiviruses-mediated shRNA, the control and SQLE or FDFT1 -deficient RBE cells were subjected to high-throughput sequencing and mRNA expression profile data analyzing.


title: Overlapping representations of food and social stimuli in VTA dopamine neurons

status: Public on Aug 21 2023

city: Princeton

first: Adelaide

last: Minerva

state: New Jersey

address: Washington Road

department: Princeton Neuroscience Institute

institute: Princeton University

summary: We used 2-photon calcium imaging to determine whether the same or different dopamine neurons of the ventral tegmental area (VTADA) encode food and social stimuli, and found statistically significant overlap in the populations responsive to both stimuli. Both hunger and opposite-sex social experience increased the proportion of neurons that respond to both stimuli, implying that increasing motivation for one stimulus further increases overlap. We used single-nucleus RNA sequencing (snRNA-seq) to examine cell type-specific gene expression changes across different hunger states and the level of co-expression of feeding- and social-hormone related genes in individual VTADA neurons.

overall_design: VTA nuclei from C57BL/6 mice were isolated and analyzed using snRNA-seq. We analyzed nuclei from control (3 male, 3 female), hungry (1 male, 1 female), and sated (1 male, 1 female) samples.

first: Lindsay

last: Willmore

first: Ben

last: Engelhardt

first: Malavika

last: Murugan

first: Brenna

last: McMannon

first: Nirja

last: Oak

first: Stephan

last: Thiberge

first: Catherine

last: Peña

first: Ilana

last: Witten


title: Transient gene melting governs the timing of oligodendrocyte maturation [RNA-seq]

first: Paul

last: Tesar

overall_design: Transcriptional profiling of pluripotent stem cell derived oligodendrocyte progenitor cells (OPCs) and oligodendrocytes (OL), control and SOX6 knockout conditions

first: Kevin

last: Allan

first: Tyler

last: Miller


title: RNA-Seq and 16S rRNA seq data of cecal digesta in goats infusion of three short-chain fatty acids

status: Public on Aug 13 2023

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

institute: Yangzhou University

overall_design: Refer to individual Series


title: Proteasome inhibition reprograms chromatin landscape in breast cancer

status: Public on Aug 24 2023

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS


title: RNA-Seq data of colonic epithelial tissue in goats infusion of three short-chain fatty acids

summary: Emerging data has highlighted the importance of short-chain fatty acids (SCFAs) on ruminal microbiome and derived metabolism profiling, and ruminal epithelial health and nutritional absorption in ruminants. However, little is known about the roles of SCFAs on hindgut profiles. Here, we firstly combined infusion of three SCFAs, to study their different roles in hindgut microbiome succession and derived metabolism profiling, as well as colonic epithelial transcriptome sequencing patterns using a in vivo goat model.

overall_design: A total of 24 healthy female goats (47.44 ± 3.38 kg, 1.5 years old) at latter half of gestation period were selected in our study. All goats were commenced on a standard diet and were fed 2 times a day, the ingredient and chemical composition were shown in Tab. S1. Goats were housed individually in their tie stalls and had free access to water and feed. After ad libitum for 14 days continuous stable feeding, goats were randomly assigned to 4 groups (n = 6/group) to receive different infusion treatments. Goats in CON group received normal saline infusion at 0.8 g/kg body weight (BW) as normal control group, while in SA group received sodium acetate infusion at 0.8 g/kg BW, in SP group received sodium propionate infusion at 0.8 kg/kg BW, and in SB group received sodium butyrate infusion at 0.5 kg/kg BW. Total volume of 1 L infusion solutions was slowly perfused through oral daily before morning feeding of each goat, and the infusion lasted for 12 days. After slaughter, the  colonicl epithelial tissue samples were rapidly frozen in liquid nitrogen and stored at -80 °C for transcriptome sequencing analysis.


title: 16S rRNA sequencing data of cecal digesta in goats infusion of three short-chain fatty acids

summary: Emerging data has highlighted the importance of short-chain fatty acids (SCFAs) on ruminal microbiome and derived metabolism profiling, and ruminal epithelial health and nutritional absorption in ruminants. However, little is known about the roles of SCFAs on hindgut profiles. Here, we firstly combined infusion of three SCFAs, to study their different roles in hindgut microbiome succession and derived metabolism profiling, as well as colonic epithelial transcriptome sequencing patterns using a in vivo goat model. .

overall_design: A total of 24 healthy female goats (47.44 ± 3.38 kg, 1.5 years old) at latter half of gestation period were selected in our study. All goats were commenced on a standard diet and were fed 2 times a day, the ingredient and chemical composition were shown in Tab. S1. Goats were housed individually in their tie stalls and had free access to water and feed. After ad libitum for 14 days continuous stable feeding, goats were randomly assigned to 4 groups (n = 6/group) to receive different infusion treatments. Goats in CON group received normal saline infusion at 0.8 g/kg body weight (BW) as normal control group, while in SA group received sodium acetate infusion at 0.8 g/kg BW, in SP group received sodium propionate infusion at 0.8 kg/kg BW, and in SB group received sodium butyrate infusion at 0.5 kg/kg BW. Total volume of 1 L infusion solutions was slowly perfused through oral daily before morning feeding of each goat, and the infusion lasted for 12 days. After slaughter, the cecal digesta samples were immediately collected and stored at -80 °C for microbiome analysis.


title: Transposable elements as lineage-specific enhancers in endodermal-lineage cancers (ATAC-Seq)

status: Public on Aug 11 2023

city: Helsinki

first: Konsta

last: Karttunen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Transposable elements (TE) are repetitive genomic elements that harbor binding sites for human transcription factors (TF). A regulatory role for TEs has been suggested in embryonal development and diseases such as cancer but systematic investigation of their functions has been limited by their widespread silencing in the genome. Here, we have utilized unbiased massively parallel reporter assay data using whole human genome library to identify TEs with functional enhancer activity in two human cancer types of endodermal lineage, colorectal and liver cancers. We show that the identified TE enhancers are characterized by genomic features associated with active enhancers, such as epigenetic marks and TF binding. Importantly, we identified distinct TE subfamilies that function as tissue-specific enhancers, namely MER11- and LTR12-elements in colon and liver cancers, respectively. These elements are bound by distinct TFs in each cell type, and they have predicted associations to differentially expressed genes. In conclusion, these data demonstrate how different cancer types can utilize distinct TEs as tissue-specific enhancers.

overall_design: Transcription factor binding and chromatin accessibility were determined by ChIP-seq and ATAC-seq in GP5d cells. Gene expression profiling for GP5d and primary colon epithelial cells (DMSO treated or DNMT-HDAC inhibited) was performed by RNA-seq.

first: Divyesh

last: Patel

first: Jihan

last: Xia

first: Liangru

last: Fei

first: Kimmo

last: Palin

first: Lauri

last: Aaltonen

first: Biswajyoti

last: Sahu


title: Transposable elements as lineage-specific enhancers in endodermal-lineage cancers (RNA-Seq)


title: Transposable elements as lineage-specific enhancers in endodermal-lineage cancers (Hi-ChIP-Seq)


title: DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts [RNA-Seq]

first: Joschka

last: Hey

summary:
To investigate the effect of Decitabine and SB939 treatment on the expression of endoretroviral elements.
We treated 9 cell lines with DMSO, Decitabine, SB939 or a combination of Decitabine and SB939 and performed RNA-seq. This data was used to generate a denovo transcriptome assembly to identify novel mRNAs expressed from endoretroviral elements.

overall_design: Comparative mRNA expression profiling analysis of RNA-seq data for NCI-H1299, OCI-AML3, HL60, NCI-H2122, A172, T98G, NCI-H1395, HCT116, and SW480 cells treated with DMSO, Decitabine, SB939 or a combination of Decitabine and SB939

first: Christoph

last: Plass

first: Ashish

last: Goyal


title: Transposable elements as lineage-specific enhancers in endodermal-lineage cancers (ChIP-Seq)


title: Transposable elements as lineage-specific enhancers in endodermal-lineage cancers (STARR-Seq)


title: Macrophage-Endothelial Cell Crosstalk Orchestrates Neutrophil Recruitment in Inflamed Mucosa scRNA-Seq

status: Public on Aug 08 2023

city: Chicago

first: Connor

last: Lantz

state: IL

address: 303 E. Chicago Ave. Ward 4-075

institute: Northwestern University

summary: Rapid neutrophil (PMN) mobilization to sites of insult is critical for host defense and requires crossing of the vascular wall. PMN transendothelial migration (TEM) involves several well-studied sequential adhesive interactions with vascular ECs, however what initiates or terminates this process is not well-understood. Our findings identified a new mechanism where mucosal interstitial macrophages are recruited to interact with the vascular wall and locally prime endothelial cell (EC) responses to accommodate PMN TEM. Using real-time intravital microscopy (IVM) on lipopolysaccharides (LPS)-inflamed intestines in CX3CR1-EGFP macrophage-reporter mice, complemented by whole-mount tissue imaging and flow cytometry, we demonstrate that macrophage presence was critical for the initiation of PMN-EC adhesive interactions and subsequent PMN TEM and accumulation in the intestinal mucosa. Anti CSFR-1 antibody-mediated macrophage depletion in the lamina propria and at the vessel wall significantly reduced PMN adhesion and TEM in inflamed intestines. Vessel associated macrophages (VAMs) were found to trigger localized upregulation of EC ICAM-1 expression and their removal resulted in elimination of the ICAM-1 “hot spots”, impeding PMN-EC interactions. Further mechanistic studies using human clinical specimens, TNFa knockout macrophage chimeras, TNFa/TNF receptor (TNFR) neutralization and multi-cellular macrophage-EC-PMN cocultures revealed a new role for macrophage TNFa and EC TNFRII axis in regulating EC adhesion molecule expression and PMN TEM. As such, our findings identify new, clinically relevant mechanism by which macrophage regulate PMN trafficking in inflamed mucosa.

overall_design: CD45-/Live1-/CD31+ ECs were flow-sorted from LPS-stimulated colon lamina propria with and without macrophage depletion and subjected to mRNA sequencing.

first: Xingsheng

last: Ren

first: Laura

last: Manzanares

first: Ronen

last: Sumagin


title: Transposable elements as lineage-specific enhancers in endodermal-lineage cancers [NaNoME-seq]