title: ALDH18A1promotes the tumor progression of esophageal cancer by binding to and regulating genes associated with tumorigenesis [IRIP-seq]

status: Public on Jun 02 2024

city: Urumqi

first: Yongkang

last: Wang

address: 91 Tianchi Road, Tianshan District, Urumqi, Xinjiang

institute: People’s Hospital of Xinjiang Uygur Autonomous Region

summary: Esophageal cancer is a common tumor in the digestive system. Every year, approximately 300 000 people worldwide die due to esophageal cancer. As a potential RNA binding protein (RBP), ALDH18A1 binds to RNAs to regulate a series of biological processes. To reveal the effect of ALDH18A1 on gene expression and alternative splicing (AS) as well as its function in the occurrence and development of esophageal cancer, we used RNA-seq to analyze the ALDH18A1-alternative splicing events in ALDH18A1-silenced and control KYSE150 cells. The results showed that ALDH18A1 mediates global AS dysregulation in KYSE150 cells. We performed improved RNA immunoprecipitation and sequencing for ALDH18A1 and found that ALDH18A1 has extensive RNA binding activity and preferentially binds to the GUAAUCC and UAGCUGG motifs on RNAs. The ALDH18A1-bound transcripts highly overlap with AS genes, indicating that ALDH18A1 can globally regulate AS by binding to the transcripts in KYSE150 cells. The overlapped genes between ALDH18A1-bound and AS genes are mainly involved in transcriptional regulation, RNA splicing, DNA repair, and nuclear mRNA splicing through spliceosome. In this work, we determined that ALDH18A1 affects cell invasion and metastasis by binding to mRNA and controlling the expression of regulator gene and the level of AS, thus playing a role in the development of esophageal carcinogenesis. The findings enhance the understanding of ALDH18A1 as an RBP in AS and tumor regulation.

overall_design: As a potential RNA binding protein (RBP), ALDH18A1 binds to RNAs to regulate a series of biological processes. To reveal the effect of ALDH18A1 on gene expression and alternative splicing (AS) as well as its function in the occurrence and development of esophageal cancer, we used RNA-seq to analyze the ALDH18A1-alternative splicing events in ALDH18A1-silenced and control KYSE150 cells.We performed improved RNA immunoprecipitation and sequencing for ALDH18A1 and found that ALDH18A1 has extensive RNA binding activity and preferentially binds to the GUAAUCC and UAGCUGG motifs on RNAs.

first: Wang

last: Yongkang

first: Maimaiti

last: Yisireyili

first: Kelimu

last: Abudureyimu

first: Atsushi

last: Enomoto


title: Induction of meiosis from human pluripotent stem cells

status: Public on Jun 01 2024

city: Boston

first: Merrick

middle: Pierson

last: Smela

state: MA

address: 3 Blackfan Circle

country: USA

institute: Harvard University

type: Expression profiling by high throughput sequencing

summary: An in vitro model of human meiosis would accelerate research into this important reproductive process and development of therapies for infertility. We have developed a method to induce meiosis starting from male or female human pluripotent stem cells. We demonstrate that DNMT1 inhibition, retinoid signaling activation, and overexpression of regulatory factors (anti-apoptotic BCL2, and pro-meiotic HOXB5, BOLL, or MEIOC) rapidly activates meiosis, with leptonema beginning at 6 days, zygonema at 9 days, and pachynema at 12 days. Immunofluorescence microscopy shows key aspects of meiosis, including chromosome synapsis and sex body formation. The meiotic cells express genes similar to meiotic oogonia in vivo, including all synaptonemal complex components and machinery for meiotic recombination. These findings establish an accessible system for inducing human meiosis in vitro.

overall_design: Plasmids for constitutive expression of BCL2 and doxycycline-inducible expression of HOXB5, BOLL, and MEIOC were integrated into F2 D4TDZG, F3 D4TT2G, and PGP1 D4TR8G reporter hiPSCs. The iPSCs were seeded at 50,000 cells/cm2 on Matrigel-coated plates in mTeSR1 supplemented with 5 µM GSK3484862, 1 µg/mL doxycycline, and 10 µM Y-27632. For 6-well plates, 1.5 mL of medium was used per well. After one day, the media was replaced with APEL2 containing 5 µM GSK3484862 and 1 µg/mL doxycycline. A 50% media change was performed every 2 days, and GSK3484862 was withdrawn starting on day 7. At each day from day 0 (hiPSC) to day 15, cells were harvested for scRNAseq. Samples for scRNAseq were counted and fixed using the Parse Biosciences fixation kit. Library preparation was performed using the Parse Biosciences WT v3 kit. Sequencing was performed on two lanes of a Novaseq X Plus 25B PE150 flowcell.

last: Pierson Smela

first: Jessica

last: Adams

first: Carl

last: Ma

first: Laura

last: Breimann

first: Ursula

last: Widocki

first: Toshi

last: Shioda

first: George

middle: M

last: Church


title: RNAseq profiling of neonatal mouse Merkel cells and basal keratinocytes

city: Bethesda

first: Lingling

last: Miao

state: MD

address: 9000 Rockville Pike

department: NIAMS

institute: National Institutes of Health

summary: Merkel cells (MCs), specialized neuroendocrine touch sensors within the epidermis, play a crucial role in tactile sensation. To gain deeper insignts into their molecular characteristics, we employed RNA sequencing (RNA-seq) to explore the transcriptome of MCs in comparsion to basal keratinocytes in neonatal mouse skin.

overall_design: GFP-expression Merkel cells (GFP-positive) and control basal keratinocytes (GFP-negative, SCA1 and CD49F double positve) were isolated from the epidermis of Sox2-GFP reporter mice through Fluorescence-activated cell sorting. RNA extraction was conducted using the RNeasy® Plus Micro Kit from Qiagen. Library preparation was accomlished using the TruSeq Stranded Total RNA Library Prep – RS-122-2201 kit from Illumina. Subsequently, sequencing was performed on the HiSeq2500 platform, employing paired-end reads with a length of 125 base pairs.

first: Isaac

last: Brownell

first: Jordan

last: Jarvis


title: ALDH18A1promotes the tumor progression of esophageal cancer by binding to and regulating genes associated with tumorigenesis [RNA-Seq]

country: China


title: Dual targeting of EZH2 and Histone Deacetylases in hematological malignancies promotes transcriptional and metabolic deregulation leading to ferroptosis.

status: Public on Jul 01 2024

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Spinal motor neuron development and metabolism are transcriptionally regulated by Nuclear Factor IA [ATAC-Seq]

status: Public on May 27 2024

city: La Jolla

first: Stacey

middle: Marie

last: Glasgow

state: California

address: 9500 Gilman Dr, 3216 Pacific Hall

institute: University of California San Diego

summary: Neural circuits governing complex motor behaviors in vertebrates rely on the proper development of motor neurons and their precise targeting of limb muscles. Transcription factors are essential for motor neuron development, regulating their specification, migration, and axonal targeting. While transcriptional regulation of the early stages of motor neuron specification is well-established, much less is known about the role of transcription factors in the later stages of maturation and terminal arborization. Defining the molecular mechanisms of these later stages is critical for elucidating how motor circuits are constructed. Here, we demonstrate that the transcription factor Nuclear Factor-IA (NFIA) is required for motor neuron positioning, axonal branching, and neuromuscular junction formation. Moreover, we find that NFIA is required for proper mitochondrial function and ATP production, providing a new and important link between transcription factors and metabolism during motor neuron development. Together, these findings underscore the critical role of NFIA in instructing the assembly of spinal circuits for movement.

overall_design: Control and NFIAcKO Hb9::GFP motor neurons were isolated from E13.5 embryos using fluorescence-activated cell sorting (FACS) and analyzed using ATAC-seq

first: Julia

last: Gauberg

first: Kevin

middle: B

last: Moreno

first: Karthik

last: Jayaraman

first: Sara

last: Abumeri

first: Sarah

last: Jenkins

first: Alisa

last: Salazar

first: Hiruy

middle: S

last: Meharena


title: Single-cell RNA sequencing study of brain-derived cells from two individuals with HIV-associated neurocognitive dysfunction

status: Public on May 25 2024

city: Chapel Hill

first: Edward

middle: Patrick

last: Browne

state: NC

address: 120 Mason Farm Road

institute: UNC-Chapel Hill

summary: The high prevalence of cognitive alterations in persons with HIV (PWH)  despite effective antiretroviral therapy (ART) is associated with sustained neuroinflammation.  Here, we uncover the signaling pathways that are essential for persistent immune activation and might underly development of HIV associated Neurocognitive Disorder (HAND). We analyze the brain proteome from PWH on ART during HAND progression. We observe that 73.3% of the significantly upregulated proteins in brains from PWH and HAND (compared to PWH with normal cognition) belong to immune pathways. Among them, 36.4% of upregulated innate immune-related proteins are within the type I interferon (IFN-I) signaling, suggesting that persistent IFN-I activation is central to HAND-associated brain immune activation. Single cell (sc)RNA-seq analysis confirmed that FN-I occurs mainly in astrocytes during acute HIV infection in the microglia-containing organoid (MCO) model of HIV infection  and persistent in microglia in the brain of PLWH on ART. Of note, IFN-I persistence is independent of HIV status but associated with the induction of human endogenous retroviruses-W (HERV-W) Env during HAND progression after initial HIV infection and its associated immune activation. When induced, HERV-W Env directly activates IFN-I signaling in astrocytes, but not in microglia. Together, IFN-I signaling may be initiated directly in the astrocytes after acute HIV infection then sustained in the microglia during ART. IFN-I persists due to expression of HERV-W Env, thereby contributing to the persistent immune activation in the HAND brain on ART, independent of HIV and insensitive to ART.  Our data link the neuroinflammation of persistent IFN-I signaling to the HAND brain on ART.

overall_design: Fresh human brain tissues were collected via established rapid research autopsy procedures from the donors enrolled in “the Last Gift” program (Donor1) and the National Disease Research Interchange (Donor2). Brain tissue was dissociated using a protocol established to preferentially isolate brain microglial cells. Single-cell suspensions were loaded into the 10x Genomics chromium device for 3' single-cell RNA sequencing.

first: Guochun

last: Jiang

first: Antoine

last: Chaillon

first: Jackson

last: Peterson


title: Transcriptional profile of brain endothelial cells from forebrain, cerebellum, and spinal cord in adult mice

status: Public on Jun 16 2024

city: Monterrey

first: Raquel

last: Cuevas Diaz Duran

address: Av Morones Prieto No. 3000, Colonia Los Doctores

department: Escuela de Medicina y Ciencias de la Salud

country: Mexico

institute: Tecnologico de Monterrey

summary: In this study endothelial cells of the forebrain, cerebellum, spinal cord, lungs and liver were acutely purified by FACS. RNA-Seq was performed on isolated endothelial cells and their transcriptome was compared to identify regional blood-brain barrier specific transcripts.

overall_design: Comparison of transcriptional profiles of endothelial cells of the forebrain, cerebellum, and spinal cord

last: Cuevas-Diaz Duran

first: Marie

last: Blanchette

first: Jia

middle: Q

last: Wu

first: Richard

last: Daneman


title: miRNA profiles in muscle of IUGR and normal weight pig fetuses

status: Public on May 24 2024

city: Midlothian

first: Xavier

last: Donadeu

address: Easter Bush

country: United Kingdom

institute: Roslin Institute, University of Edinburgh

type: Non-coding RNA profiling by high throughput sequencing

summary: Intrauterine growth restriction (IUGR) is a leading cause of neonatal morbidity and mortality in humans and domestic animals. Developmental adaptations of skeletal muscle in IUGR lead to increased risk of premature muscle loss and metabolic disease later during life. Although transcriptome-wide profiles in muscle associated with IUGR have been reported, their regulation by miRNAs is not well understood. The aim of this study was to identify differences in miRNA expression in porcine skeletal muscle of IUGR and normal-weight (NW) littermates during late foetal development (day 90 of gestation).

overall_design: RNA sequencing was performed on a total of 8 semitendinous muscle samples collected from  4 pig litters at day 90 of gestation. Two male fetuses were collected from each litter, one with normal weight as defined by weight above the litter average (Large) and a IUGR fetus with weight >2 SD below the average litter weight (Small). Differentially expressed genes were identified from analyses taking account of 'litter'.

first: Yennifer

last: Cortes

first: Susanna

middle: E

last: Riley


title: CD161 expression of TRM cells counteracts the HPV-associated clinical benefit in oropharyngeal cancer immunotherapy

city: Seoul

first: Junha

last: Cha

address: Yonsei-Ro 50

department: Department of Biotechnology

country: South Korea

institute: Yonsei University

summary: Oropharyngeal squamous cell carcinoma (OPSCC), a distinct head and neck cancer subtype that develops in the oropharynx, is well known to be categorized into human papillomavirus induced (HPV+) and non-HPV induced (HPV-). While HPV+ OPSCC is reported to be clinically advantageous compared to HPV- OPSCC, the heterogeneous responses in HPV+ OPSCC during immunotherapy treatment have not been well characterized at the molecular level. In this study, we assess both tumor and immune cells of the OPSCC tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) and single-cell TCR sequencing (scTCR-seq). By dissecting the transcriptome of OPSCC tumor cells, we find that cancer cell transcriptional diversity may be a strong factor in negating HPV associated clinical benefits. By assessing immune cells, we observed molecular antiviral and anti-tumor characteristics of T cells that is associated with HPV infection, and key cell-cell interaction differences among resident memory T cells (Trm), follicular helper T cells, and B cells. Importantly, we identify a novel molecular state within the HPV+ OPSCC that is distinguished by the expression KLRB1 (CD161) in the Trm that inhibits anti-tumor activity, which may further explain the heterogeneous clinical benefits of HPV+OPSCC. Association of KLRB1 expression of Trm and immunotherapy outcome was confirmed via immunofluorescence analysis, suggesting CD161 as a novel therapeutic target to improve cancer treatment of HPV+ OPSCC.

overall_design:
20 tissue samples were analyzed by scRNAseq. 10 samples were sequenced from 5'end and the other 10 from 3' end. 6 were HPV negative and 14 were HPV positive, all from the Oropharynx tissue of the head and neck cancer tumor biopsy

UPDATE: [Aug-07-2025] The titles and hiv states of Samples GSM7080432 and GSM7080433 were changed from positive to negative, and those of Samples GSM7080442 and GSM7080443 were changed from negative to positive.

first: Gamin

last: Kim

first: Hye

first: Insuk

last: Lee


title: Different developmental pathways generate functionally distinct populations of natural killer cells

first: Avinash

last: Bhandoola

address: 10 Center Dr

institute: NCI

summary: Natural killer (NK) cells function by eliminating virus-infected cells or tumor cells. Here, we identified a NK lineage-biased progenitor population, termed early NK progenitors (ENKP), which developed into NK cells independently of common precursors for ILCs (ILCPs). ENKP-derived NK cells (ENKP_ NK cells) and ILCP-derived NK cells (ILCP_ NK cells) were also transcriptionally different. We devised combinations of surface markers that identified highly enriched ENKP_NK and ILCP_NK cell populations in wild-type mice. Furthermore, Ly49H+ NK cells that responded to mouse cytomegalovirus (MCMV) infection primarily developed from ENKPs whereas ILCP_NK cells were better IFN-g producers upon Salmonella and Herpes Simplex Virus (HSV) infections. Interestingly, human CD56dim and CD56bright NK cells were transcriptionally similar to ENKP_NK cells and ILCP_NK cells, respectively. Our findings establish the existence of two pathways of NK cell development that generate functionally distinct NK cell subsets in mice, and further suggest these pathways may be conserved in humans.

overall_design: For scRNAseq, lymphoid progenitors and mature NK cells/ILC1s were sorted from total bone marrow cells of TCF-YFP reporter mice, and submitted for capture on the 10X Chromium according to manufacturers instructions. The lineage potential of progenitor populations was assessed using adoptive transfers of TCF-YFP+ bone marrow derived  ALP, ENKP and ILCP in NSG. Donor-derived splenic NK cells from NSG mice were sorted, labelled with hashtagging antibodies and submitted for capture on the 10X Chromium platform according to manufacturers instructions.


title: Sorafenib inhibits invasion of multicellular organoids that mimic Lymphangioleiomyomatosis nodules.

status: Public on Jun 13 2024

city: Iowa City

first: Amy

middle: Leanne

last: Ryan

state: IA

address: 51 Newton Road

department: Anatomy and Cell Biology

institute: The University of Iowa

summary: Lymphangioleiomyomatosis (LAM) is a debilitating, progressive lung disease with few therapeutic options, largely due to a paucity of mechanistic knowledge of disease pathogenesis. Lymphatic endothelial cells (LECs) are known to envelope and invade clusters of LAM-cells, comprising of smooth muscle α-actin and/or HMB-45 positive "smooth muscle-like cells” however the role of LECs in LAM pathogenesis is still unknown. To address this critical knowledge gap, we investigated wether LECs interact with LAM-cells to augment their metastatic behaviour of LAM-cells. We performed in situ spatialomics and identified a core of transcriptomically related cells within the LAM nodules. Pathway analysis highlights wound and pulmonary healing, VEGF signaling, extracellular matrix/actin cytoskeletal regulating and the HOTAIR regulatory pathway enriched in the LAM Core cells. We developed an organoid co-culture model combining primary LAM-cells with LECs and applied this to evaluate invasion, migration, and the impact of Sorafenib, a multi-kinase inhibitor. LAM-LEC organoids had significantly higher extracellular matrix invasion, decreased solidity and a greater perimeter, reflecting increased invasion compared to non-LAM control smooth muscle cells. Sorafenib significantly inhibited this invasion in both LAM spheroids and LAM-LEC organoids compared to their respective controls. We identified TGFβ1ι1, a molecular adapter coordinating protein-protein interactions at the focal adhesion complex and known to regulate VEGF, TGFβ and Wnt signalling, as a Sorafenib-regulated kinase in LAM-cells. In conclusion we have developed a novel 3D co-culture LAM model and have demonstrated the effectiveness of Sorafenib to inhibit LAM-cell invasion, identifying new avenues for therapeutic intervention.

overall_design: Spatial Transcriptome sequencing libraries were prepared with 10x Genomic Visium Spatial Gene Expression Slides & reagent kit according to the manufacturers instructions

middle: L

first: Sinem

last: Koc-Gunel

first: Lalit

middle: K

last: Gautam

first: Ben

middle: A

last: Calvert

first: Shubha

last: Murthy

first: Noa

middle: C

last: Harriott

first: Janna

last: Nawroth

first: Beiyun

last: Zhou

first: Vera

middle: P

last: Krymskaya


title: Effect of B cell receptor class-switching on WSU-FSCCL lymphoma cells

status: Public on May 15 2024

city: London

first: Pavel

last: Tolar

address: Institute of Immunity and Transplantation, Rowland Hill St

institute: University College London

summary: Although immunoglobulin class-switching from IgM to IgG enhances B cell receptor (BCR) signalling and antibody responses, certain subsets of B cell lymphomas retain unswitched IgM BCRs despite signs of class-switching in the immunoglobulin heavy chain loci. This suggests that expression of the IgG BCR suppresses progression of specific lymphoma subsets. We found that inducing BCR class switching from IgM to IgG1 or IgG4 inhibits proliferation of B EZB DLBCL lymphoma cell lines. To understand changes associated with class-switching we compared transcritional profiles of isogenic WSU-FSCCL cell lines artificially class-switched to express IgM and IgG BCRs.

first: Laabiah

last: Wasim


title: Scalable, compressed phenotypic screening using pooled perturbations  (PDAC screens)

status: Public on May 13 2024

city: Cambridge

first: Alex

middle: K.

last: Shalek

address: 77 Massachusetts Ave

institute: MIT

summary: High-throughput phenotypic screens leveraging biochemical perturbations and high-content readouts are poised to advance therapeutic discovery, yet they remain constrained by limitations of scale. To address this, we establish a method of pooling exogenous perturbations followed by computational deconvolution to compress a screen’s required sample, labor, and financial input. We benchmark the approach with a bioactive small molecule library and a high-content imaging readout, demonstrating the feasibility and increased efficiency of compressed experimental designs compared to conventional approaches. To prove generalizability, we apply compressed screening in two different biological discovery campaigns. In the first, we use early-passage pancreatic cancer organoids to map transcriptional responses to alibrary oftumor-microenvironmentrecombinant protein ligands. We uncover reproducible phenotypic shifts induced by specific ligands that are distinct from canonical reference signatures and uniquely correlate with clinical outcome.In the second, we examine the modulatory effects of a known mechanism of action chemical compound library on primary human peripheral blood mononuclear cell immune responses. Through contrastive analyses, we identify molecules that potentiate and/or inhibit cell-type specific transcriptional features, uncover pleiotropic effects for individual compounds across diverse cell types, and realize a systems-level view of drug responses. In sum, our approach empowers phenotypic screens with information-rich readouts to advance drug discovery efforts as well as basic biological inquiry.

overall_design: Patient-derived pancreatic cancer (PDAC) organoids from patients with metastatic pancreatic cancer (Raghavan et al., Cell, 2021) were screened with a library of 68 macrophage-derived ligands (and DMSO control) for the compressed screen and 11 ligands (and DMSO control) for the validation experiment for 7 days and analyzed using scRNA-seq.

first: Nuo

last: Liu

first: Walaa

last: Kattan

first: Benjamin

last: Mead

first: Conner

last: Kummerlowe

first: Thomas

last: Cheng

first: Sarah

last: Ingabire

first: Jaime

middle: H

last: Cheah

first: Christian

last: Soule

first: Anita

last: Vrcic

first: Jane

last: McIninch

first: Sergio

last: Triana

first: Manuel

last: Guzman

first: Tyler

middle: T

last: Dao

first: Joshua

last: Peters

first: Kristen

last: Lowder

first: Lorin

last: Crawford

first: Ava

last: Amini

first: Paul

last: Blainey

first: William

last: Hahn

first: Brian

last: Cleary

first: Bryan

last: Bryson

first: Peter

last: Winter

first: Srivatsan

last: Raghavan


title: Parallel evolution of X chromosome-specific SMC complexes in two nematode lineages [ChIP-Seq]

status: Public on May 21 2024

city: New York

first: Avrami

last: Aharonoff

state: NY

address: 29 Washington Place

department: Biology

institute: New York University

summary: Mechanisms of X chromosome dosage compensation have been studied in model organisms with distinct sex chromosome ancestry. However, the diversity of mechanisms as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans, where dosage compensation is accomplished by an X chromosome specific condensin that belongs to the family of structural maintenance of chromosomes (SMC) complexes. By combining a phylogenetic analyses of the C. elegans dosage compensation complex with a comparative analysis of its epigenetic signatures, such as X-specific topologically associating domains (TADs) and enrichment of H4K20me1, we show that the condensin-mediated mechanism evolved recently in the lineage leading to Caenorhabditis following an SMC-4 duplication. Unexpectedly, we found an independent duplication of SMC-4 in Pristionchus pacificus along with X-specific TADs and H4K20me1 enrichment, which suggests that condensin-mediated dosage compensation evolved more than once in nematodes. Differential expression analysis between sexes in several nematode species indicates that dosage compensation itself precedes the evolution of X-specific condensins. In Rhabditina, X-specific condensins may have evolved in the presence of an existing mechanism linked to H4K20 methylation as Oscheius tipulae X chromosomes are enriched for H4K20me1 without SMC-4 duplication or TADs. In contrast, Steinernema hermaphroditum lacks H4K20me1 enrichment, SMC-4 duplication, and TADs. Together, our results indicate that dosage compensation mechanisms continue to evolve in species with shared X chromosome ancestry, and SMC complexes may have been co-opted at least twice in nematodes, suggesting that the process of evolving chromosome wide gene regulatory mechanisms are constrained.

sample_organism:
Pristionchus pacificus
Oscheius tipulae
Steinernema hermaphroditum

overall_design:
ChIP-seq for histone modifications H4K20me1 and H3K4me3, as well as IgG in the nematodes Steinernema hermaphroditum, Pristionchus pacificus, and Oscheius tipulae

Please note that the records have been updated on Aug 4, 2025 with the additional samples and revised protocol description.

first: Sevinc

last: Ercan


title: Enhanced Collagen Secretion in Epithelial Cancer Cells is associated with L1CAM Deficiency

status: Public on Jun 11 2024

city: Naples

first: Enza

last: Lonardo

address: Via Pietro Castellino 111

country: Italy

institute: Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR

summary: Collagen, a critical component of the tumor microenvironment (TME), significantly influences cancer-associated fibrosis, tissue stiffness, immune response, and metastasis. Pancreatic ductal adenocarcinoma (PDAC) is characterized by excessive collagen deposition, and effective therapies remain limited. Our research challenges conventional understanding by highlighting the remarkable ability of specific tumor epithelial populations, particularly those with low levels of L1 cell adhesion molecule (L1CAM) expression (L1low), to actively modulate collagen dynamics within the TME. Transcriptome analysis of PDAC cells with varying L1 expression reveals shifts in collagen-related pathways, with heightened expression of collagen 17A1 (COL17A1) in L1low cells. Alongside, L1low cells exhibit enhanced migratory capacity. In an orthotopic mouse model, L1low cancer cells demonstrate increased collagen deposition, resistance to gemcitabine treatment, and an elevated propensity for liver metastases. Treatment with Tranilast, an anti-fibrotic drug, significantly reduces tumor volume and collagen deposition while enhancing L1 expression. This, in turn, mitigates tumor invasiveness and suppresses metastases formation. Overall, our study uncovers a novel role for L1CAM in PDAC aggressiveness and fibrosis, revealing a new epithelial population capable of collagen secretion and challenging the traditional notion that this function is solely attributed to stromal cells.

overall_design:
To investigate the transcriptional differences between PDAC cells with different L1CAM levels, we FACS sorted the L3.6pl cells for high and low levels of L1CAM (L1CAMpositive and L1CAMnegative).
We then performed gene expression profiling analysis using data obtained from RNA-seq of the 2 different cellular populations (L3.6pl L1CAMpositive versus L3.6pl L1CAMnegative)

first: Donatella

last: Delle Cave

first: Annalisa

last: Di Domenico

first: Marco

last: Fantuz

first: Marianna

last: Ciotola

first: Maria

last: Mangini

first: Silvia

last: Buonaiuto

first: Brunella

last: Corrado

last: Corona

first: Federica

last: Saracino

first: Gennaro

last: Andolfi

first: Ilaria

last: Di Biase

first: Antonio

last: Cucciardi

first: Alessandro

last: Carrer

first: Bruno

last: Sainz

first: Vincenza

last: Colonna

first: Gabriella

last: Minchiotti

first: Annachiara

last: De Luca


title: Disentangling cell-intrinsic and extrinsic factors underlying gene expression evolution

status: Public on May 10 2024

city: Stanford

first: Hunter

middle: B.

last: Fraser

address: 371 Jane Stanford Way

institute: Stanford University

summary: Chimeras have played a foundational role in biology, for example by enabling the classification of developmental processes into those driven intrinsically by individual cells versus those driven extrinsically by their extracellular environment. Here, we extend this framework to decompose evolutionary divergence in gene expression and other quantitative traits into cell-intrinsic, extrinsic, and intrinsic-extrinsic interaction components. Applying this framework to reciprocal rat-mouse chimeras, we found that the majority of gene expression divergence is attributable to cell-intrinsic factors, though extrinsic factors also play an integral role. For example, a rat-like extracellular environment extrinsically up-regulates the expression of a key transcriptional regulator of the endoplasmic reticulum (ER) stress response in some but not all cell types, which in turn strongly predicts extrinsic up-regulation of its target genes and of the ER stress response pathway as a whole. This effect is also seen at the protein level for both genes we tested, suggesting propagation through multiple regulatory levels. We also demonstrate that our framework is applicable to a cellular trait, neuronal differentiation, and estimated the intrinsic and extrinsic contributions to its divergence. Finally, we show that many imprinted genes are dramatically mis-expressed in species-mismatched environments, suggesting that mismatch between rapidly evolving intrinsic and extrinsic mechanisms controlling gene imprinting may contribute to barriers to interspecies chimerism. Overall, our conceptual framework opens up new avenues to investigate the mechanistic basis of evolutionary divergence in gene expression and other quantitative traits in any multicellular organism.

overall_design: We used interspecies rat-mouse and mouse-rat chimeras to study intrinsic and extrinsic mechanisms controlling gene expression.  Mouse-rat (i.e. mouse cells injected into a rat blastocyst) chimeras and the wildtype rat samples were collected at embryonic day (E) 15.5 and rat-mouse chimeras and the wildtype mouse sample were collected at E13.5.  Cells from connective tissue and forebrain were FACS sorted to enrich for TdTomato+ donor cells (i.e. cells injected into the blastocyst).  Single cell RNA-sequencing was then performed using 10x v3.1 3’ chemistry and sequenced on a Novaseq X.  Wildtype mouse and rat cells were pooled together and sequenced in one WT-Mouse_WT-Rat library.  We use Mouse-Rat and MR as well as Rat-Mouse and RM interchangeably. Read 1 was trimmed in accordance with 10x recommendations.  Each library was sequenced to a low depth initially and then libraries Mouse-Rat_2, Mouse-Rat_3, and Rat-Mouse_3 were not sequenced further.  All other libraries were sequenced more deeply in a second round of sequencing and fastq files were concatenated together.

first: Alexander

last: Starr

first: Toshiya

last: Nishimura

first: Hiromitsu

last: Nakauchi


title: Tumor cell in response to CAR T cell treatment

status: Public on May 07 2024

city: PHILADELPHIA

first: Wei

last: Guo

state: PENNSYLVANIA

address: 433 S. University Avenue

institute: University of Pennsylvania

summary: To examine the response of 4662 tumor cell on MSLN-CAR T cells. Series of genes of 4662 cells treated with the conditioned media (CM) from MSLN-CAR T cells and untransduced (UTD) T cells.

overall_design: 4662 cells were treated with or without the conditioned media (CM) from MSLN-CAR T cells and untransduced (UTD) T cells. MSLN-CAR T cells or UTD T cells (2×105) were cultured in each well of the MSLN protein coated 96-well plate for 48 hrs, and supernatant was collected and centrifuged at 500 × g for 10 min.

first: Wenqun

last: Zhong


title: Transcriptional effects of co-culture on the spatiotemporal dynamics of T cell motility and cancer-T cell interactions [scRNA-seq]

status: Public on Apr 26 2024

city: Shenzhen

first: Xuefei

last: Li

address: 1068 Xueyuan Avenue, Shenzhen University Town, Nanshan

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

summary: Insufficient infiltration of cytotoxic T cells into solid tumors poses a major challenge in cancer immunotherapy, largely due to the intricate tumor microenvironment. To address this, we co-cultured mouse cancer cell lines (B16-WT or B16-OVA) with cancer-specific cytotoxic T cells (activated OT-1) in vitro to uncover the impact of cancer-T cell interactions on T cell motility, pivotal for effective tumor infiltration. To investigate the potential molecular mechanisms underlying T cell motility patterns in the two coculture contexts, we performed both bulk and single-cell RNA sequencing of cancer and T cells sorted from the co-culture systems at specific time points.

overall_design: In this experiment, we aimed to explore the quantitative effects on spatiotemporal dynamics of T cell motility within a co-culture system of murine melanoma cells and cancer-specific OT-1 CD8+ T cells. B16-F10 cells overexpressing ovalbumin and the Ca2+ sensor GCaMp6s (referred to as B16-OVA) were generated via lentivirus infection. CD8+ T cells isolated from C57BL/6J-OT-I spleens were activated using Dynabeads® Mouse T-Activator CD3/CD28. Co-cultures were established with B16-F10-WT and B16-F10-OVA cells seeded onto Poly-D-lysine-coated µ-Slide 8 well plates, followed by the addition of activated OT-1 CD8+ T cells. Fluorescence-activated cell sorting (FACS) was employed to sort cells using EpCam antibody for cancer cells and CD8 antibody for T cells. Bulk RNA sequencing was performed on cells from co-culture at 0h, 6h, and 12h, while single-cell RNA sequencing was specifically conducted on cells obtained from the 12h co-culture.

first: Xinyue

first: Taoli

last: Jin

first: Lisha

last: Wang

first: Ming

first: Weijing

last: Han


title: Transcriptional effects of co-culture on the spatiotemporal dynamics of T cell motility and cancer-T cell interactions [RNA-seq]

overall_design: In this experiment, we aimed to explore the quantitative effects on spatiotemporal dynamics of T cell motility within a co-culture system of murine melanoma cells and cancer-specific OT-1 CD8+ T cells. B16-F10 cells expressing ovalbumin and the Ca2+ sensor GCaMp6s (referred to as B16-OVA) were generated via lentivirus infection. CD8+ T cells isolated from C57BL/6J-OT-I spleens were activated using Dynabeads® Mouse T-Activator CD3/CD28. Co-cultures were established with B16-F10-WT and B16-F10-OVA cells seeded onto Poly-D-lysine-coated µ-Slide 8 well plates, followed by the addition of activated OT-1 CD8+ T cells. Fluorescence-activated cell sorting (FACS) was employed to sort cells using EpCam antibody for cancer cells and CD8 antibody for T cells. Bulk RNA sequencing was performed on cells from co-culture at 0h, 6h, and 12h, while single-cell RNA sequencing was specifically conducted on cells obtained from the 12h co-culture.


title: Therapeutic potential of human microglial transplantation in a chimeric model of CSF1R-related leukoencephalopathy

status: Public on Apr 24 2024

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 845 Health Sciences Road

department: Neurobiology and Behavior

institute: University of California, Irvine

summary: Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) is a rare, autosomal dominant primary microgliopathy caused by mutations in colony-stimulating factor 1 receptor (CSF1R). CSF1R signaling is necessary for microglial differentiation and survival. As a result, ALSP patient brains have fewer microglia and exhibit an array of neuropathologies including axonal spheroids, white matter abnormalities, reactive astrocytosis, and brain calcification. To explore the therapeutic potential of transplanting healthy human microglia, we generated ‘hFIRE’ mice, a xenotolerant mouse model of ALSP that lacks murine microglia. Remarkably, transplantation of induced pluripotent stem cell (iPSC)-derived microglial progenitors enabled rapid CNS-wide microglial engraftment, restoring a homeostatic microglial gene signature and preventing diverse ALSP-related neuropathologies. To further examine a potential autologous approach, ALSP-patient derived iPSCs were CRISPR-corrected, rescuing mutation-induced deficits in microglial proliferation, enabling brain-wide microglial engraftment, and reducing pre-existing spheroid, astroglial, and calcification pathologies within just 6 weeks. Together with the accompanying study by Munro and Colleagues, these results demonstrate the utility of FIRE mice to model diverse ALSP neuropathologies and provide initial evidence that iPSC-microglia could be further developed as a promising new therapeutic strategy for ALSP and perhaps other microglia-associated neurological disorders.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: hCSF1 and hCSF1-FIRE mice received intracerebroventricular and cortical injections of either phosphate buffered saline (n=5 hCSF1; n=4 hCSF1-FIRE) or human hematopoietic progenitor cells (n=4 hCSF1-FIRE) to examine the effects of loss of murine microglia (hCSF1-FIRE_PBS vs hCSF1_PBS) and whether these deficits were recovered following transplantation of human HPCs (hCSF1-FIRE_HPC vs hCSF1_PBS).

first: Jonathan

last: Hasselmann


title: 35S:NTL-SRDX pnet2_ab mutants

status: Public on Apr 19 2024

city: Berkeley

first: Yangnan

last: Gu

address: 371 Koshland Hall, Berkeley, CA 94720, Department of Plant & Microbial Biology

institute: UC Berkeley

summary:
Purpose: To understand the molecular mechanism between PNET2 and NTLs, we generated 35S:NTL-SRDX in pnet2_ab mutants to suppress NTL gene expression and performed the whole genome transcriptome analysis on 4-week-old plants of WT, pnet2_ab, 35S:NTL6-SRDX pnet2_ab, 35S:NTL9-SRDX pnet2_ab, and 35S:NTL12-SRDX pnet2_ab.
Conclusions: PNET2 regulates diverse responses by associating with a family of membrane-bound transcriptional factors.

overall_design: mRNA profiles of 4-week-old plants of wild type (Col-0), pnet2_ab, 35S:NTL6-SRDX pnet2_ab, 35S:NTL9-SRDX pnet2_ab, and 35S:NTL12-SRDX pnet2_ab mutants were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Yu

last: Tang


title: GeoMX WGS of Mtb-infected mouse lesions

status: Public on Apr 17 2024

city: Seattle

first: Benjamin

middle: Henry

last: Gern

state: WA

address: 307 Westlake Ave N

department: Center for Global Infectious Diseases Research

institute: Seattle Children's Research Institute

summary: To gain holistic of the immune landscape of lesions following infection with Mycobacterium tuberculosis, we aerosol infected C3HeB/FeJ mice with 1-3 CFU of Mtb (SA161 strain). 35 days following infection, lungs were harvested and fixed, then embedded and frozed in OCT. 10um sections were obtained, classified as necrotic or non-necrotic by visual inspection and brightfield imaging, then stained with markers delineating lesions, and subsequently processed and sampled using the nanostring GeoMX platform. We then compared the transcriptional environment of necrotic vs non-necrotic lesions

overall_design: 3 necrotic and 5 non-necrotric lesions from 7 mice were included. 2-4 ROIs per lesion, and one DOI from a distal area was obtain near each lesion

first: Andrew

last: Gustin

first: Michael

last: Gale Jr

middle: Y

last: Gerner

first: Kevin

last: Urdahl


title: Parallel evolution of X chromosome-specific SMC complexes in two nematode lineages [Hi-C]

first: Avrami

last: Aharonoff

sample_organism:
Pristionchus pacificus
Oscheius tipulae

platform_organism:
Pristionchus pacificus
Oscheius tipulae

overall_design: To examine the 3D genome structure of autosomes and X chromosomes in the nematodes Pristionchus pacificus and Oscheius tipulae, we performed Hi-C sequencing on early stage hermaphrodite larvae.

first: Jun

last: Kim

first: Sevinç

last: Ercan


title: A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells

status: Public on Apr 01 2024

last: Boemo

address: Tennis Court Road

department: Department of Pathology

institute: University of Cambridge

summary: Human cancer cell lines were pulsed with thymidine analogues EdU and BrdU, sequenced on the Oxford Nanopore platform, and analysed with our DNAscent software to measure DNA replication stress.

overall_design: Tissue culture followed by EdU/BrdU pulse labelling, FACS sorting, Oxford Nanopore library prep, Oxford Nanopore MinION R9.4.1 sequencing, DNAscent v3.1.2 analysis


title: KDM5A epigenetically orchestrates MHC-I associated anti-tumor immunity of immunotherapy

status: Public on Mar 31 2024

city: Beijing

first: Tantan

address: Haidian  District

institute: Tsinghua University

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

overall_design: Refer to individual Series


title: BLIMP1 controls GC B cell expansion and exit through regulating cell cycle progression and key transcription factors BCL6 and IRF4

status: Public on Mar 28 2024

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary: In B cells BLIMP1 is required for plasma cell differentiation. BLIMP1 is also expressed in some dark zone (DZ) germinal center (GC) B cells (GCBCs), yet the role of BLIMP1 in GCBCs is not understood. Here we generated mixed bone marrow (BM) chimeric mice using Prdm1+/+ CD19Cre and Prdm1fl/fl CD19Cre BM, allowing us to examine the cell-intrinsic functions of BLIMP1 in GCBC, independent of antibody or antigen levels. Strikingly, BLIMP1-deficient B cells quickly dominate GCs and persist for a much longer time compared to the wild type cells. BLIMP1 deficiency promotes positive selection of GCBC and enhances cell-cycle progression. In addition, BLIMP1 deficiency enhanced class-switching. Mechanistically, BLIMP1-deficient GCBC fail to downregulate BCL6 and to upregulate IRF4, indicating that BLIMP1 controls the expression of these transcription factors that mediate exit from the GC. These studies revealed unique functions of BLIMP1 in regulating GCBC responses that impact long-lived immune compartments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Blimp1 KO and WT GCBC.

first: Wei

last: Luo

first: Shuchi

last: Smita


title: The yeast genome is globally accessible in living cells [OxfordNanopore]

status: Public on Mar 22 2024

city: Bethesda

first: David

middle: Johannes

last: Clark

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

summary: Eukaryotic genomes are packaged into chromatin, which is composed of condensed filaments of regularly spaced nucleosomes, resembling beads on a string. The nucleosome contains ~147 bp of DNA wrapped almost twice around a central core histone octamer. The packaging of DNA into chromatin represents a challenge to transcription factors and other proteins requiring access to their binding sites. Consequently, control of DNA accessibility is thought to play a key role in gene regulation. Here, we measure DNA accessibility genome-wide in living budding yeast cells by inducible expression of DNA methyltransferases. We find that the yeast genome is globally accessible to the methylase in living cells, unlike in nuclei, where DNA accessibility is severely limited. Gene bodies are methylated at only slightly slower rates than promoters, indicating that yeast chromatin is highly dynamic in vivo. In contrast, centromeres are strongly protected in vivo. Global shifts in nucleosome positions occur in cells as they are depleted of RSC, or ISW1 and CHD1, indicating that global nucleosome dynamics are at least partly attributable to ATP-dependent chromatin remodelers. We propose that virtually all yeast chromatin is in a state of continuous flux in living cells, but static in nuclei, suggesting that chromatin packaging is not generally repressive.

overall_design: Time courses of DNA methylation by MSssI methylase in yeast cells; Nanopore long-read sequencing data. Two biological replicates.

first: Christopher

last: Coey

first: Hemant

last: Kumar-Prajapati

middle: J


title: Gene regulatory activity associated with PCOS reveals DENND1A-dependent testosterone production

status: Public on Mar 30 2024

city: Durham

first: Timothy

last: Reddy

address: 101 Science Dr

institute: Duke University

summary: Polycystic Ovary Syndrome (PCOS) is a leading cause of infertility. About 5 million women in the US have PCOS, making it the most prevalent endocrine disorder among menstruating people. Despite that prevalence, the underlying causes remain unknown. Genome-wide association studies (GWAS) have identified non-coding genetic variation associated with PCOS risk and identifying the underlying molecular mechanisms is currently a major opportunity for improving diagnosis and treatment. We report the discovery of gene regulatory mechanisms that help explain genetic association with PCOS in the GATA4, FSHB and DENND1A loci. We based those findings using a combination of high throughput reporter assays, CRISPR-based epigenome editing, and genetic association analysis from PCOS case and control populations. In addition, we found that elevated endogenous DENND1A expression causes elevated testosterone levels, a hallmark PCOS phenotype. These results further highlight the potential for combining genetic variant analyses with experimental approaches to fine map genetic associations with disease risk.

overall_design: 3 input STARR-seq libraries, 3 output STARR-seq libraries in H295R and COV434 cell lines; 2 replicates of ATAC-seq libraries for H295R and COV434 cell lines; 4 replicates each of H295R cells treated with 10uM forskolin or DMSO control

first: Laavanya

last: Sankaranarayanan

first: Kelly J

last: Brewer

first: Graham D

last: Johnson

first: Alejandro

last: Barrera

first: Revathy

last: Venukuttan

first: Ryan

last: Sisk

first: Andrea

last: Dunaid

first: Timoothy E


title: Effects on the transcriptome of mouse embryonic fibroblasts after both Son overexpression and knockdown and treatment with 3μM nintedanib, 1μM ponatinib, 3μM proflavine hemisulfate, and 1μM pyrvinium pamoate

first: Bokai

last: Zhu

address: Bridgeside Point 1, 5th Floor, 100 Technology Drive

institute: Aging Institute of UPMC/University of Pittsburgh School of Medicine

summary: Understanding how genetic and pharmacological effects that change nuclear speckle morphology affect the global transcriptome

overall_design: Comparison of gene expression profiles of mouse embroyonic fibroblasts (MEFs) after genetic manipulation of Son or the aforementioned drug treatments

first: William

last: Dion

first: Silvia

last: Liu


title: The yeast genome is globally accessible in living cells [Illumina]

overall_design: Multiple time courses of DNA methylation by Dam methylase in yeast cells and Dam titrations for yeast nuclei: Illumina paired-end data. Two biological replicate experiments.

first: Peter

middle: R

last: Eriksson

first: Paul

last: Elizalde


title: Single-cell trascriptiponal landscapes of bovine peri-implantation development

status: Public on Mar 18 2024

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: Supporting healthy pregnancy outcomes requires a comprehensive understanding of the cellular hierarchy and underlying molecular mechanisms during peri-implantation development. Here, we presented a single-cell transcriptome-wide view of the bovine peri-implantation embryo development at day 12, 14, 16 and 18, when most of the pregnancy failure occurs. We defined the development and dynamic progression of cellular composition and gene expression of embryonic disc, hypoblast, and trophoblast lineages during bovine peri-implantation development. Notably, the comprehensive transcriptomic mapping of trophoblast development revealed a previous unrecognized primitive trophoblast cell lineage that are responsible for pregnancy maintenance in bovine prior to the time when binucleate cell emerges. We analyzed novel markers for the cell lineage development during bovine early development. We also identified cell-cell communication signaling underling embryonic and extraembryonic cells interact to ensure proper early development in bovine. Collectively, our work provides foundational information to discover essential biological pathways underpinning bovine peri-implantation development and the molecular causes of the early pregnancy failure during this critical period.

overall_design: Single-cell from single elongation embryos were isolated with trypLE, resuspended in 0.04% BSA and analyzed using scRNAseq.

first: Hao

last: Ming

first: Giovanna

last: Scatolin


title: The yeast genome is globally accessible in living cells

status: Public on Mar 21 2024

first: David

last: Clark


title: CoMtb alters the immune landscape following Mtb infection [C3H scRNAseq]

status: Public on Apr 29 2024

first: Kevin

last: Urdahl

state: Washington

address: 307 Westlake Ave N #500

department: Global Infectious Disease

summary: To gain further insights into lesion development and effects of CoMtb on immune responses during infection. we performed single-cell RNA sequencing (scRNAseq) and flow cytometry analysis of lungs from Mtb-infected animals with and without CoMtb immediately pre-infection and at 10. 17 and 34 days after CD infection. We found that CoMtb induces rapid recruitment and activation of T cells. macrophage activation. and diminished late neutrophil responses.

overall_design: Single-cell RNA sequencing (scRNAseq) and flow cytometry analysis of lungs from Mtb-infected C3H mice with and without CoMtb immediately pre-infection and at 10. 17 and 34 days after CD infection. Variables tested including comparing timepoints to each other. and CoMtb vs non-CoMtb

first: Fergal

last: Duffy

first: Maxwell

last: Neal

first: Alan

last: Diercks

first: Sara

middle: B

last: Cohen

first: Courtney

last: Plumlee

first: Benjamin

last: Gern

last: Aderem

first: John

middle: D

last: Aitchison

first: Michael

last: Gerner


title: FXR and RXRA binding in mouse liver

status: Public on Mar 20 2024

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

summary: The Farnesoid-X-Receptor (FXR) is a nuclear receptor (NR) known to obligately heterodimerize with Retinoid-X-Receptor (RXR). FXR is expressed as four isoforms (α1-α4) that drive transcription from IR-1 (inverted repeat-1) DNA motifs. More recently, FXR isoforms α2/α4 were found to activate transcription predominantly from non-canonical ER-2 (everted repeat-2) DNA motifs, mediating most metabolic effects of general FXR activation.Here, we explored whether  co-occupancy of FXR and RXR in the mouse liver has an influence on DNA motif binding preference. We found RXR acts as a molecular switch, promoting FXRα2 activation from IR-1 instead of ER-2 motifs. Our results showcase FXR as the first NR with RXR-dependent and independent modes of activation, highlighting a potential new layer of complexity for other RXR-heterodimerizing NRs.

overall_design:
To investigate their binding profile and co-occupancy, we performed ChIP-seq for FXR and RXRA from male mouse liver

Please note that the following sample raw data was analyzed in the current study as described below:
Experiment Title Run BioSample
GSM1899653 FXRChIP_MVEH8 SRR2541540 SAMN04123807

first: Jose

middle: M

last: Pittol

first: Alexandra

last: Milona

first: Michal

last: Mokry

first: Danielle

last: Hollman

first: Saskia

middle: W

last: van Mil


title: Peripheral blood transcriptomic analysis identifies potential inflammation and immune signatures for central retinal artery occlusion

status: Public on Mar 07 2024

city: Wuhan

first: Xuan

last: Xiao

state: Hubei

address: Yellow Crane Tower Street

institute: Wuhan University

summary: Central retinal artery occlusion (CRAO) is an acute retinal ischaemic disease, but early diagnosis is challenging due to a lack of biomarkers. Blood samples were collected from CRAO patients and cataract patients. Gene expression profiles were distinct between arterial/venous CRAO blood (A-V group) and venous CRAO/control blood (V-C group) samples. Differentially expressed genes (DEGs) were subjected to GO and KEGG enrichment analyses. Hub genes were identified by Cytoscape and used to predict gene interactions via GeneMANIA. Immune cell infiltration was analysed by CIBERSORT. More than 1400 DEGs were identified in the A-V group and 112 DEGs in the V-C group compared to controls. The DEGs in both groups were enriched in the ribosome pathway, and those in the V-C group were also enriched in antigen processing/MHC pathways. Network analysis identified ribosomal proteins (RPS2 and RPS5) as the core genes of the A-V group and MHC genes (HLA-F) as the core genes of the V-C group. Coexpression networks showed ribosomal involvement in both groups, with additional immune responses in the V-C group. Immune cell analysis indicated increased numbers of neutrophils and T cells. Ribosomal and MHC-related genes were identified as potential CRAO biomarkers, providing research directions for prevention, diagnosis, treatment and prognosis.

overall_design: Blood samples were collected from three groups: 9 samples from cataract control patients (CON), 9 peripheral vein samples from CRAO patients (CRAO_V), and 7 arterial samples from the embolus site of CRAO patients before thrombolysis (CRAO_A).

first: Jiaqing

last: Feng

first: Ying

last: Li

first: Chuansen

last: Wang

first: Yuedan

first: Yuwei

last: Wan

first: Mengxue

last: Zheng

first: Ting

last: Chen

first: Duan


title: Traumatic brain injury modifies adult hippocampal neural stem cell fate to promote neurogenesis at the cost of astrogliogenesis.

city: Leuven

first: Araks

last: Martirosyan

address: Herestraat 49

department: Center for Brain & Disease Research

institute: VIB-KU Leuven

summary:
We aimed to assess how TBI affects hippocampal NSCs and their subsequent commitment to the neuronal or astroglial lineages. Using a controlled cortical impact model of TBI, single cell RNA sequencing and spatial transcriptomics, we observed a cell population-specific increase in NSC-derived neuronal cells and a decrease in NSC-derived astrocytic cells.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: To understand the cellular changes induced by TBI in DG NSC and their progeny we performed scRNAseq. A controlled cortical impact model was used to induce a traumatic brain injury of mild to moderate severity. Fifteen days post-surgery, DGs were micro-dissected, dissociated and single Nesin-GFP+ cells isolated using FACS (in combination with a live/dead dye to eliminate dead cells). Cells were then pooled and subjected to scRNAseq using the 10X 3’ whole transcriptome analysis workflow.

first: Pascal

last: Bielefeld

first: Arabo

last: Apresyan

first: Francisco

last: Pestana

first: Suresh

last: Poovathingal

first: Paul

last: Lucassen

first: Juan

last: Encinas

first: T

middle: G

last: Belgard

first: Matthew

last: Holt

first: Carlos

last: Fitzsimons


title: Fif3 regulates the development of Penicillium oxalicum fungi and the expression of cellulolytic genes

status: Public on Mar 13 2024

city: Qingdao 266237

first: Ma kexuan

last: Qin yuqi

state: China

address: No. 72 Binhai Road

department: State Key Laboratory of Microbial Technology

institute: Shandong University

summary: The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT) and Fif3 deletion strain (DFif3) under conditions of 1% bran + 1% microcrystalline cellulose as carbon source. The results of correlation analysis between each sample showed that the gene expression level of DFif3 was significantly different from that of the WT strain. The deletion of DFif3 significantly down-regulates the expression levels of sporulation process genes. And the absence of DFif3 can broadly up-regulate the expression level of cellulase-encoding genes, indicating that DFif3 can cause a decrease in cellulase synthesis by affecting the expression of cellulase-encoding genes.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain, Fif3 deletion mutant strain in 18h in modified Mendal’s medium with 1% bran + 1% microcrystalline cellulose as carbon sources. Three replicates were included for each samples.

first: Kexuan

last: Ma

first: Yuqi

last: Qin


title: Acute Changes in Rat Tissue Gene Expression Following Exposure to Flight Relevant Hypobaria

status: Public on Apr 08 2024

city: Baltimore

first: Apurva

last: Borcar

address: 685 W. Baltimore Street, MSTF 5-34

department: Anesthesiology

institute: University of Maryland School of Medicine

summary:
Aeromedical evacuation (AE) is an important tool for transit of injured patients, but both the hypobaria and hyperoxia associated with AE may contribute to secondary injury. We aimed to examine the effects of these acute exposures on gene expression while avoiding the inflammatory storm that would result from injury and potentially mask underlying causes of AE-related secondary injury.
We exposed healthy, young male rats to different levels of hypobaria (4000 ft or 8000 ft eqiv.) and/or hyperoxia (100% oxygen) for different durations of time (5 or 10 h). We collected heart, lung, brain (hippocampus), and blood tissue samples, processed them for RNA, and performed microarray analysis on the samples.

overall_design: Heart, lung, and blood RNA was analyzed via Rat Clariom S Assay chips, while hippocampus RNA was analyzed via Rat Gene 2.0 ST Array chips. Treatment groups were combined, outlier samples were removed, and secondary analysis was performed comparing treatment groups against control group (0 ft, 21% oxygen, 5 h) for each tissue type  (.TXT files).

first: Flaubert

last: Tchantchou

first: Amol

last: Shetty

first: Anup

last: Mahurkar

first: Gary

last: Fiskum


title: The SUMOylation inhibitor TAK-981 induces a transcriptional reprogramming in human Natural Killer cells

status: Public on Apr 15 2024

city: Montpellier

first: Denis

last: Tempé

address: 1919 route de Mende

country: France

institute: CNRS


title: Adaptive epigenetic regulation of neuronal metabolism by a mitochondrial redox signal following complex I inhibition

status: Public on Apr 07 2024

city: Onna-son

first: Marius

middle: Wilhelm

last: Baeken

address: 1919-1 Tancha

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University

summary: Different signaling pathways connect the mitochondrion with the transcriptional machinery in the nucleus. Redox events are thought to play a substantial role along this axis, however, many open questions about their specificity, quantitative importance and mode of action remain. Here, we have employed subtoxic doses of the complex I inhibitor MPP+ in human neuronal LUHMES cells to characterize the contribution of scavengeable redox signals to mito-nuclear communication. MPP+ evoked a broadly targeted transcriptional induction of nuclear-encoded respiratory chain complex (RCC) subunits. Nanomolar doses of phenothiazine (PHT), a mitochondrially active antioxidant, attenuated these transcriptional effects by approximately half, but did not modulate the bioenergetic markers ATP, NAD+, NADH, lactate, or glucose. Transcriptional induction by MPP+ was accompanied by a loss of nuclear 5-methyl-cytosine and an increase in histone H3K14 acetylation, both of which were entirely prevented by PHT. Inhibitor and PHT reversibility experiments suggested that these alterations were mediated by lowered DNMT3B and SIRT1 levels, respectively. Analysis of MPTP-treated mice recapitulated the PHT-reversible induction of histone acetylation and DNMT3B suppression in vivo. Moreover, PHT completely abrogated the statistical significance of the association of MPP+ with the selective induction of mitochondrially imported proteins and RCC subunits. We conclude that the mitochondrion employs a redox signal to announce impending, but not yet acute mitochondrial distress to the nucleus, in order to selectively upregulate mito-metabolic genes via chromatin reorganization. Our results have implications for the interpretation of the observed epigenetic changes in Parkinson’s disease and other neurodegenerative disorders.

overall_design: LUHMES cells treated with MPP+ or PHT/MPP+ and untreated controls


title: TGF-β specifies TFH versus TH17 cell fates in murine CD4+ T cells through c-Maf (Seq04, scRNA-seq)

status: Public on Mar 01 2024

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

country: Germany

institute: University Hospital Bonn

summary: Naive murine CD4+ T cells were cultured under different polarizing conditions in 96-well plates coated with anti-CD3/anti-CD28 for 0, 0.5, 1.5, 3.5 days, sorted by flow cytometry, and subjected to single-cell RNA-seq.

overall_design:
Seq04: scRNA-seq: Tfh(2)d0, Tfh(2)d0.5, Tfh(2)d1.5, Tfh(2)d3.5

MouseSampleTags	Day
MouseSampleTag01	0
MouseSampleTag02	0
MouseSampleTag03	0
MouseSampleTag04	0.5
MouseSampleTag05	0.5
MouseSampleTag06	0.5
MouseSampleTag07	1.5
MouseSampleTag08	1.5
MouseSampleTag09	1.5
MouseSampleTag10	3.5
MouseSampleTag11	3.5
MouseSampleTag12	3.5

first: Yinshui

last: Chang


title: Gene expression analyses of whole ovaries from mice that were treated with N-Cadherin antagonist CRS-006

status: Public on Mar 04 2024

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

summary: N-Cadherin is a cell surface protein that is critical for cell-cell adhesion and is essential for structural integrity of tissues. In the ovary, it is expressed by granulosa cells and cumulus cells junctions throughout ovarian development. Importantly, it is also present between oocyte (egg) and surround cumulus cells, and is the only physical type of communication that is present between the egg and its surrounding cells.

overall_design: RNA-seq was performed on ovaries for either CRS-066 treated (N= 5) or vehicle treated  (N=6)mice for comparitve analyses

first: Alaknanda

last: Emery

first: Rebecca

middle: L

last: Robker

first: Darryl

last: Russell


title: Gene expression analyses of COCs treated with N-Cadherin antagonist CRS-006

overall_design: RNA-seq was performed on pooled COCs (n=100) treated with either CRS-066 or 0.1% DMSO vehicle during In Vitro maturation assay for comparitve analyses


title: Coordinated regulation by lncRNAs results in tight lncRNA–target couplings

status: Public on Apr 05 2024

city: Houston

first: Hua-Sheng

last: Chiu

state: TX

address: 1102 Bates Avenue

institute: Baylor College of Medicine

summary: The determination of long non-coding RNA (lncRNA) function is a major challenge in RNA biology with applications to basic, translational, and medical research. Our efforts to improve the accuracy of lncRNA-target inference identified lncRNAs that coordinately regulate both the transcriptional and post-transcriptional processing of their targets. Namely, these lncRNAs may regulate the transcription of their target and chaperone the resulting message until its translation, leading to tightly coupled lncRNA and target abundance. Our analysis suggested that hundreds of cancer genes are coordinately and tightly regulated by lncRNAs and that this unexplored regulatory paradigm may propagate the effects of non-coding alterations to effectively dysregulate gene expression programs. As a proof-of-principle we studied the regulation of DICER1—a cancer gene that controls microRNA biogenesis—by the lncRNA ZFAS1, showing that ZFAS1 activates DICER1 transcription and blocks its post-transcriptional repression to phenomimic and regulate DICER1 and its target microRNAs.

overall_design:
CRISPRi screen followed by RNA-Seq: We used a high-throughput parallel CRISPRi screening platform that combines live-cell imaging with a scalable RNA-seq workflow to generate unbiased analyses of lncRNA regulation. For each lncRNA target of interest, a pool of up to 10 single-guide RNAs (sgRNAs) was produced by high-throughput in vitro transcription of sgRNA templates generated by multiplex PCR. The resulting sgRNA pools were delivered by electroporation to HEK293T cells with stable dCAS9-KRAB expression. QuantSeq RNA-seq library preparation (Lexogen) was performed according to the manufacturer’s protocol using 5 µl of cell lysate as input. Libraries were quantified by qPCR, pooled, and sequenced on a NextSeq 500 System (Illumina). FASTQ files were processed using an in-house RNA-seq analysis pipeline. FastQC (v0.11.8) was first used for data quality control, after which adapter sequences, polyA readthrough, and low-quality reads were removed by BBMap v38.26. Reads were then mapped against the hg38 reference genome with STAR v2.6.0c, and gene counts were determined by HTSeq  v.0.11.0. The number of reads for each gene was adjusted to account for differences in sequencing depth and presented as counts per million (CPM). Comparisons were made to plate-specific pooled negative-control NT sgRNAs.
siRNA followed by RNA-Seq: Three human cell lines, ECC-1, NCI-H460, and PC-3, were transfected with 25 nM siRNAs targeting ZFAS1 and DICER1 for 24 hours in 96-well plates. Quadruplicate wells containing 10,000 cells each were pooled for each sequenced sample (N = 18: 6 per cell line, non-targeting control (NT), siZFAS1, and siDICER1, each in duplicate). Subsequently, aliquots from each sample were submitted to Novogene Corporation Inc. (Sacramento, CA) for library preparation and RNA sequencing (NovaSeq). Libraries were prepared using a polyA-selected approach and yielded over 20 million high-quality, 150bp paired-end reads per sample. RNA-seq raw reads were aligned to the hg19 reference genome with GENCODE v16 gene annotation using STAR v2.3.0e. Alignment files were processed with Picard tools v1.54 (http://broadinstitute.github.io/picard/) and indexed using SAMtools v0.1.11. Transcript quantification was performed in Cufflinks v2.02 quantification mode with the GENCODE v16.gtf annotation. Transcripts Per Million (TPM) values were used for relative abundance estimation.

first: Sonal

last: Somvanshi

first: Eric

middle: d

last: de Lavergne

first: Pieter

last: Mestdagh

first: Pavel

last: Sumazin


title: Unstable EBV latency drives inflammation in multiple sclerosis patient derived spontaneous B cells [Batch3]

status: Public on Apr 04 2024

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Epidemiological studies have demonstrated that Epstein-Barr virus (EBV) is an etiologic risk factor, and perhaps prerequisite, for the development of MS. EBV establishes life-long latent infection in a subpopulation of memory B cells. Although B cells play a key role in the pathobiology of MS, EBV-associated mechanisms of B cell inflammation and disease pathogenesis in EBV (+) B cells from MS patients are not well characterized. Accordingly, we obtained lymphoblastoid lines (LCLs) and spontaneous LCLs (SLCLs), distinguished by their transformation with lab strain (B95.8) or endogenous EBV, respectively, from MS patients and healthy controls to study host-virus interactions in B cells.  Here, we use transcriptomics and genomics-based approaches to identify differences in EBV gene expression and regulation of both viral and cellular genes in LCLs compared to SLCLs and between SLCLs generated from healthy controls and MS patients during “active” or “stable” periods of disease activity. We demonstrate increased lytic gene expression in SLCLs derived from MS patient B cells, especially those generated from peripheral blood mononuclear cells (PBMCs) obtained during “active” disease.

overall_design: RNASeq of LCLs and Spontaneous LCLs from MS patients and healthy controls

first: Samantha

middle: S

last: Soldan

first: Paul

last: Lieberman


title: Transcriptome analysis of hiPSC-CMs carrying FLNC mutations

status: Public on Mar 05 2024

city: Saint-Petersburg

first: Margarita

last: Sorokina

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Centre

summary: In this study we performed transcriptome analysis of cardiomyocytes (CMs) derived from two hiPSC lines of patients with V2264M and R1267Q mutations in FLNC gene. hiPSC cell line were obtained from patient’s PBMCs with FLNC mutation using CytoTune-iPS 2.0 Sendai Reprogramming Kit (Thermo Fisher Scientific). Detailed information about iPSC line characterization can be found in hiPSCreg database: (FAMRCi011-A and FAMRCi009). Information about FAMRCi009 is earlier published DOI: 10.1016/j.scr.2021.102640.

overall_design: Libraries were prepared with TruSeq Stranded mRNA kit, samples were RNA-sequenced on Illumina NextSeq 2000, read length 51 bp.

first: Anna

middle: A

last: Kostareva

first: Ekaterina

last: Klimenko


title: Transcriptomic Signatures of Neuronally-Derived Extracellular Vesicles Reveals Presence of Olfactory Receptors in Clinical Samples of Traumatic Brain Injury Patients

status: Public on Feb 29 2024

first: Manish

last: Bhomia

address: 4301 Jones bRidge Road

department: Pathology

institute: Uniformed Services University of the Health Sciences

summary: Traumatic brain injury (TBI) is one of the major causes of death and disability worldwide. Recently, the FDA has approved blood-based biomarkers, GFAP and UCH-L1, to evaluate the need for CT scans, however, clinical translation is currently limited. Exosomes are small microcellular vesicles which are released from the cell in both normal and diseased states, as part of extracellular communication. The aim of this study was to isolate neuronal exosomes derived from the serum of patients with severe TBI and characterize the messenger RNA content of the exosomes released by the injured neurons in order to identify new potential blood-based biomarkers. RNA was isolated from neuronal exosomes and total transcriptomic sequencing was performed. RNA sequencing data from neuronal exosomes isolated from serum showed mRNA transcripts of several neuronal genes. Additionally, the RNA sequencing data revealed mRNA of several olfactory receptor genes, which were present at elevated concentrations in the neuronal exosomes. Further validation in serum samples of mild TBI patients revealed a similar upregulation of olfactory receptors. The data from these experiments suggests that damage to the neurons in the olfactory neuroepithelium and in the brain, following a TBI, may cause the release of mRNA from these receptors in the exosomes. Thus, olfactory receptors can be further investigated as potential biomarkers for TBI diagnosis.

overall_design:
To characterize the transcriptome of neuronally derived exosomes, we first isolated neuronal exosomes from serum of patients with severe TBI
RNA was exracted from the neuronal exosomes and cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with dUTP methods.

first: Yanru

last: Feng

first: Piper

last: Deleon

first: Claudia

last: Robertson

first: Firas

last: Kobeissy

first: Kevin

middle: K

last: Wang

first: Barbara

last: Knollmann-Ritschel


title: Transcriptomic analysis of local bone tissue in rats after bone fracture

status: Public on Mar 31 2024

city: Beijing

first: Shuhang

last: Guo

address: Xizhimen South Street

institute: Peking University People's Hospital

summary: In this study, transcriptome sequencing technology was used to detect and analyze the changes in transcriptome of the local injury tissue after fracture. Differentially expressed genes (DEGs) with the high degree were analyzed. Our research results identify some important genes and pathways in the process of fracture healing, and summarize the main characteristics of transcriptome changes in fractures. This laid the foundation for a deeper understanding of the relation between molecular mechanisms and biological processes involved in fracture healing. By identifying the specific time points at which various cellular events occur during the healing process, researchers can gain insights into the complex interplay between cells, signaling pathways, and extracellular matrix components that is required for successful bone healing. This knowledge can inform the development of new therapies and interventions to improve fracture healing outcomes and ultimately enhance the quality of life for patients affected by bone fractures.

overall_design: Male adult SD rats (3 months old, weighing approximately 300g, from Beijing Vital River Laboratory Animal Technology Co., Ltd) were randomly divided into five groups. Tissue samples were collected at 0(control group), 3rd, 7th, 14th, and 28th days after fracture for whole transcriptome sequencing. In this study, transcriptome sequencing technology was used to detect and analyze the changes in transcriptome of the local injury tissue after fracture. Differentially expressed genes (DEGs) with the high degree were analyzed.

first: Shaoxun

last: Yuan

first: Shen

first: Xiaofeng

last: Yin


title: Single-cell sequencing reveals the heterogeneity of pancreatic neuroendocrine tumors under the pattern of genomic instability and histological grading

status: Public on Feb 27 2024

city: Shanghai

first: Zeng

last: Ye

address: 270 Dongan Road, Xuhui District

institute: Fudan University Shanghai Cancer Center

summary: Histological grading is the key factors affecting the prognosis of patients and instructive in guiding treatment and assessing recurrence in non-functional pancreatic neuroendocrine tumor (NF-Pan-NET). Approximately one-third of patients without copy number variation (CNV) alteration and the prognosis of these patients are better than that of patients with CNV alteration. Tumor classification based on CNV also showed significant value in evaluating prognosis. However, the difference between CNV and histological grading is unclear. Here, at single cell level, we analyzed the heterogeneity of tumor cells according to two classification criteria, genomic instability (including CNV alteration and tumor mutation burden) and histological grading. We found that the classification basis on genomic instability of the bulk tissues was better than histological grading in distinguishing tumor cells at scRNA-seq. We revealed that the activated core pathways of tumor cells were significantly different under different histological gradings and genomic instability patterns. In particular, patients with liver metastases had specific activation pathways. Deciphering the differences of the tumor microenvironment through single-cell sequencing, we found that tip cells, lymphatic endothelial cells, macrophages, CD1A+ dendritic cell, Treg, MAIT, ILC and CAFs might patriciate in the process of hepatic metastases, which will facilitate the understanding of the patterns to decode the malignant potential and of NF-Pan-NET.

overall_design: Single-cell RNA-seq profiling for primary pancreatic neuroendocrine tumor tissuess, adjacent pancreas and pancreatic neuroendocrine tumor from 17 patients with pancreatic neuroendocrine tumor: 3 cases of adjacent pancreas, 2 cases of liver metastases, 15  cases of primary  tumors.

first: Yan

last: Zhou

first: Mingwei

first: Shunrong

last: Ji


title: Gene expression of sphere-derived prostate cancer stem cells

status: Public on Mar 27 2024

city: Dalian

first: Yuanyuan

last: Luo

address: No.457 Zhongshan Road

institute: Dalian institute of chemical physics

summary: We performed RNA-seq analysis of human prostate cancer cells and sphere-derived cancer stem cells (PCSCs) to analyze the differentially expressed genes between PCSCs and differentiated cells, and find the potential key factors in PCSCs

overall_design: sphere-derived PCSC cells were cultured with or without serum for 7 days, and then were collected for TRIzol lysed for RNA extraction. 6 RNAseq samples across 2 conditions: sphere, without serum (n=3) and Adh (adherent, with serum) (n=3)

first: Wangshu

last: Qin


title: The SUMOylation inhibitor TAK-981 induces a transcriptional reprogramming in human Natural Killer cells [RNA-seq]

status: Public on Feb 28 2024

first: Denis

last: Tempé

summary: SUMOylation, a post-translational modification of the ubiquitin family plays a critical role in the regulation of proteins function and fate. TAK-981 (Subasumstat) is a first-in-class inhibitor of the SUMO-activating enzyme used in various phase I/II clinical trials for solid tumors and lymphomas. In addition to its direct cytotoxic effect on cancer cells, TAK-981 activates anti-tumor immune response. We show here that TAK-981 activates human natural killer cells. TAK-981 mostly regulates genes involved in inflammation and immune response, in particular those related to the type-I and type-II interferon pathway.

overall_design: Total RNA was purified from FACS-sorted NK cells (CD56+/CD3-) sorted from 3 different healthy donors' blood treated with mock or 100 nM TAK-981 for 24 h.

first: Rawan

last: Hallal

first: Guillaume

last: Bossis


title: Single cell RNA-seq of single cell suspension from the HCC region of WT and FABP5 Hepatocyte KO mice fed CD-HFD for 15 month

status: Public on Feb 23 2024

city: New Haven

first: Jonathan

last: Sun

address: 10 Amistad St

institute: Yale University

summary: After feeding CD-HFD diet for 15 month, tumors from WT and FABP5 hepatocyte KO mice were collected and digested with collagenase to generate single cell suspension before proceeding with 10X Single Cell RNA-Sequencing.

overall_design: The tumor region of WT and FABP5 Alb-CRE-ER mice were dissected after 15 month of CD-HFD. Single cell suspension was prepared and cells were submitted for sc-RNAseq

first: Carlos

last: Fernández-Hernando


title: Single cell RNA-seq mapping of chronological obesity-HCC progression in C57BL/6 mice fed a CD-HFD

status: Public on Feb 17 2024

state: CT

summary: We perform scRNA-seq in the livers of C57BL/6 mice fed a CD-HFD or control diet for 3 months (NAFLD), 6 months (NASH) or 15 months (HCC)

overall_design: The liver of diet-fed mice were perfused with collagenase and dissociated to separate out parenchymal (hepatocytes, cholangiocytes) and non-parenchymal (endothelial cells, immune cells etc..) fractions. Parenchymal fractions were purified using a 30% percoll gradient. Non-parenchymal fraction were enriched for live cells by flourescent activated cell sorting. Purified parenchymal and non-parenchymal cells were combined at a 1:1 ratio before submission for sequencing.

last: Fernandez-Hernando


title: A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules

status: Public on Feb 21 2024

city: San Francisco

first: Hani

last: Goodarzi

department: Department of Biochemistry and Biophysics

institute: UCSF

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

overall_design: Refer to individual Series


title: Effect of FABP5 silencing or inhibition on gene expression of Huh7 human hepatoma cells after 48 hours

summary: To investigate the function of FABP5 in the regulation of metabolic reprogramming in Huh7 cells in which target gene has been silenced by siRNA or inhibited by competitive inhibitor SBFI-103.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of FABP5 silenced/inhibited and control Huh7 cells


title: EWS::FLI cooperatively binds at GGAA microsatellites via DBD-a4 helix

status: Public on Feb 01 2024

city: Columbus

first: Ariunaa

last: Bayanjargal

state: OH

address: 700 Children's Dr

institute: Nationwide Childrens Hospital

summary: Multi-omics study of DBD-a4 helix of EWS::FLI to understand the underlying mechanism of transcriptional regulation in Ewing sarcoma cell line: A673

overall_design: In A673 cells, we knock-down endogenous EWS::FLI with shRNA  (KD) and rescued with FLAG tagged DBD and DBD+ constructs. Cells are then harvested for RNA-Seq (3 bio reps), CUT&Tag (2 bio reps for CTCF and H3K27ac, 3 bio reps for FLAG), and Micro-C libraries (2 bio reps).

first: Julia

last: Selich-Anderson

first: Jesse

middle: C

last: Crow

first: Emily

last: Theisen


title: Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos

status: Public on Feb 15 2024

city: Cambridge

first: Kehui

last: Xiang

state: MA

address: 455 Main Street

institute: Whitehead Institute

summary: During oocyte maturation and early embryonic development, poly(A)-tail lengths strongly influence mRNA translation. However, how tail lengths are controlled at different developmental stages has been unclear. Here, we performed tail-length and translational profiling of mRNA reporter libraries (each with > 10 million 3ʹ-UTR sequence variants) in frog oocytes and embryos, and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5-mer. Additional sequence motifs drive stage-specific deadenylation in embryos, and UUUUA and C-rich motifs drive tail-length-independent translational repression in oocytes. A neural network model accurately predicts tail-length change during oocyte maturation in frogs, mice, and humans. Analyses of human sequence variants showed that those predicted to disrupt tail-length control have been under negative selection, implying that our insights into control of poly(A)-tail length and translation have implications for human health and fertility.

sample_organism:
Danio rerio
Xenopus laevis
Mus musculus
synthetic construct

overall_design:
Sythetic mRNA reporter libraries with random 3'-UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. Poly(A)-tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail-length changes. At the same time, poly(A)-tail lengths of endogenous mRNAs from frog oocytes and embryos, fish embryos, and mouse oocytes were measured to investiage how their tail lengths were controlled.

Please note that sample titles have been updated on Jan 6, 2024.

first: Jiimy

last: Ly

first: David

middle: P

last: Bartel


title: Mucosal Boosting Enhances Vaccine Protection Against SARS-CoV-2 in Rhesus Macaques

status: Public on Feb 14 2024

city: Boston

first: Dan

last: Barouch

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

summary: A major limitation of current SARS-CoV-2 vaccines is that they provide minimal protection against acquisition of infection with current Omicron subvariants, although they still provide protection against severe disease. It has been hypothesized that enhanced mucosal immunity will be required to block infection and onward transmission. Intranasal administration of current vaccines has proven inconsistent, suggesting that alternative immunization strategies may be required. Here we show that intratracheal boosting with a bivalent Ad26 based SARS-CoV-2 vaccine results in substantial induction of mucosal humoral and cellular immunity and near complete protection against SARS-CoV-2 BQ.1.1 challenge.

overall_design: 40 previously immunized rhesus macaques were boosted with a bivalent Ad26 vaccine by the intramuscular, intranasal, and intratracheal routes or with a bivalent mRNA vaccine by the intranasal route. Ad26 boosting by the intratracheal route led to substantial expansion of mucosal neutralizing antibodies, IgG and IgA binding antibodies, and CD8+ and CD4+ T cell responses, which exceeded those induced by Ad26 boosting by the intramuscular and intranasal routes. Intratracheal Ad26 boosting also led to robust upregulation of cytokine, NK, and T and B cell pathways in the lung. Following high-dose SARS-CoV-2 BQ.1.1 challenge, intratracheal Ad26 boosting provided near complete protection, whereas the other boosting strategies proved less effective. Protective efficacy correlated with both mucosal and systemic immune responses. These data demonstrate that novel immunization strategies can induce robust mucosal immunity, suggesting the feasibility of developing vaccines that block respiratory viral infections.

first: Malika

last: Aid

middle: H


title: Erythropoietin receptor on cDC1s dictates immune tolerance

city: Palo Alto

first: Xiangyue

last: Zhang

address: 3373 Hillview ave

institute: Stanford University

summary: Type 1 conventional dendritic cells (cDC1s) are unique in their efferocytosis and cross-presenting abilities, resulting in T cell-mediated immunity or tolerance. However, the factors that dictate whether cDC1s induce a tolerogenic or immunogenic response remain largely unknown. Here, we show that the erythropoietin receptor (EpoR) acts as a critical switch that determines the tolerogenic function of cDC1s and the threshold of Ag-specific T cell responses. In total lymphoid irradiation and anti-thymocyte serum (TLI/ATS)-induced allograft tolerance, cDC1s upregulate EpoR expression, and conditional knockout of EpoR in cDC1s diminishes antigen (Ag)-specific FOXP3+ Treg induction and expansion, resulting in allograft rejection. Mechanistically, EpoR promotes efferocytosis-induced tolerogenic maturation of splenic cDC1s towards late-stage CCR7⁺ cDC1s characterized by elevated integrin β8 gene (Itgb8) expression, and conditional knockout of Itgb8 in cDC1s impairs TLI/ATS-induced tolerance. Migratory cDC1s in peripheral lymph nodes preferentially express EpoR, and their capacity to induce FOXP3⁺ Tregs is enhanced by EPO. Reciprocally, EpoR deficiency enables immunogenic maturation of both pLN migratory and splenic CCR7⁺ cDC1s by upregulating genes essential for MHC class II-mediated Ag presentation, cross-presentation and costimulation. Loss of cDC1 EpoR reduces tumor growth by enhancing anti tumor CD8⁺ T cell immunity, particularly by promoting tumor Ag specific CD8⁺ T cell priming in tumor draining lymph nodes to generate more precursor exhausted T cells (Tpex) and by sustaining intratumoral Tpexs while decreasing Tregs. Targeting EpoR on cDC1s to either induce or inhibit immune tolerance could pave the way for novel treatments of a variety of diseases.

overall_design: To investigate the tolerogenic mechanisms employed by cDC1s, on the day after the last dose of TLI/ATS, we performed RNA-seq of XCR1+CD8a+ cDC1s that had been purified by fluorescence activated cell sorting (FACS).  To comprehensively define the tolerogenic properties of EpoR+ cDC1s, we further performed RNA-seq on EpoR+ and EpoR- cDC1s following TLI/ATS. Comparison of the transcriptome of spleen CCR7+XCR1+SIRPa- cDC1s and peripheral lymph node migratory XCR1+SIRPa- cDC1s, Eporflox/flox vs. Epor-Xcr1-Cre cKO mice.

first: Sijie

last: Chen

first: Pingping

last: Zheng


title: Multi-omics exploration of microenvironmental changes during BTK covalent inhibition in chronic lymphocytic leukemia

status: Public on Feb 07 2024

city: Barcelona

first: Daniel

last: Medina

address: Centre Cellex, 115-117 Natzaret

department: Experimental Hematology

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

summary: Continuous treatment with ibrutinib not only exerts tumor control but also enhances T cell function in patients with chronic lymphocytic leukemia (CLL). We conducted longitudinal multiomics analyses in samples from CLL patients receiving ibrutinib upfront to identify potential adaptive mechanisms to Bruton Tyrosine Kinase (BTK) inhibition during the first 12 months of continuous therapy. Wefound that in T cells, ibrutinib reduced the expression of exhaustion markers, the proportion of Tregs and Tfh cells, as well as expression of genes related to activation, proliferation, differentiation, and metabolism. In CLL cells, we observed a downregulation of immunosuppression, adhesion, and migration mechanisms. Adaptation at molecular level, characterized by an increase in cancer cell fraction of CLL cells with mutated driver genes, was observed in around half of the patients. Interestingly, BTK C481S mutations were detected as early as after 6 months of treatment, particularly enriched in subsets of malignant cells retaining migrative capacity. These CLL cells with potential migrative capacity under ibrutinib also exhibited a distinct transcriptomic profile including upregulation of mTOR-AKT and Myc pathways. We identified high expression of TMBIM6 as a potential novel independent poor prognostic factor. Of note, BIA, a TMBIM6 antagonist, induced CLL cell apoptosis and synergized with ibrutinib. In summary, our comprehensive multi-omics analysis of CLL patients undergoing ibrutinib therapy has unveiled early immunomodulatory effects on T cells and adaptative mechanisms in CLL cells. These findings can contribute to the identification of resistance mechanisms and the discovery of novel therapeutic targets.

overall_design:
To assess the transcriptomic changes in T cells from chronic lymphocytic leukemia (CLL) after 6 months of ibrutinib treatment, we isolated total RNA from T cells (CD3+ purification, negative selection) from peripheral blood mononuclear cells samples from CLL patients at before treatment and after 6 months of ibrutinib.

To assess the transcriptomic changes in migrated B cells from chronic lymphocytic leukemia (CLL) towards CXCL12 before and after 6 months of ibrutinib treatment. We previously isolated B cells (CD19+ purification, negative selection) from peripheral blood mononuclear cells samples from CLL patients at before treatment and after 6 months of ibrutinib.

last: Medina-Gil

first: Marta

last: Crespo

first: Beatriz

last: Martín-Mur

first: Anna

last: Esteve-Codina


title: Integration of hyperspectral imaging and transcriptomics from individual cells with HyperSeq

status: Public on Feb 05 2024

city: Kensington

first: Yike

last: Xie

state: NSW

address: Lowy 2, Cnr High and Botany St

institute: UNSW Sydney

summary: Microscopy and omics are complementary approaches to probe the molecular state of cells in health and disease, combining granularity with scalability. While important advances have been achieved over the last decade in each area, integrating both imaging- and sequencing-based assays on the same cell has proven challenging. In this study, a new approach called HyperSeq that combines hyperspectral autofluorescence imaging with transcriptomics on the same cell is demonstrated. HyperSeq was applied to Michigan Cancer Foundation 7 (MCF-7) breast cancer cells and identified a subpopulation of cells exhibiting bright autofluorescence rings at the plasma membrane in optical channel 13 (ex = 431 nm, em = 594 nm). Correlating the presence of a ring with the gene expression in the same cell indicated that ringed cells are more likely to express hallmark genes of apoptosis and gene silencing and less likely to express genes associated with ATP production. Further, correlation of cell morphology with gene expression suggested that multiple members of the spliceosome were upregulated in larger cells. A number of genes, albeit evenly expressed across cell sizes, exhibited higher usage of specific exons in larger or smaller cells. Finally, correlation between gene expression and fluorescence within the spectral range of Nicotinamide adenine dinucleotide hydrogen (NADH) provided preliminary insight into the metabolic states of cells.  These observations provided a link between the cell’s optical spectrum and its internal molecular state, demonstrating the utility of HyperSeq to study cell biology at single cell resolution by integrating spectral, morphological and transcriptomic analyses into a single, streamlined workflow.

overall_design: MCF-7 cells were imaged by a Hyperspectral microscope and then captured by CellCelector to 384-well PCR plates for subsequent SmartSeq2 library preparation

first: Abbas

last: Habibalahi

first: Ayad

last: Anwer

first: Kanu

last: Wahi

first: Catherine

last: Gatt

first: Emma

last: Johansson

first: Jeff

last: Holst

first: Ewa

last: Goldys

first: Fabio

last: Zanini


title: Transcription factor ZNF263 enhances EGFR-targeted therapeutic response and reduces residual disease in lung adenocarcinoma [RNAseq2]

status: Public on Jan 23 2024

first: Jiaqi

last: Liang

state: Shanghai

address: 180 Fenglin Road

institute: Zhongshan Hospital Fudan University

summary: EGF receptor (EGFR) tyrosine kinase inhibitors (TKIs) have achieved clinical successes in lung adenocarcinoma (LUAD). However, tumors often show profound but transient initial response and gain resistance. Here, we identified transcription factor ZNF263 as being significantly decreased in osimertinib-resistant or drug-tolerant persister LUAD cells and clinical residual tumor specimens. Exogenous expression of ZNF263 improved the initial response of cells and delayed the formation of persister cells with osimertinib. We elaborated that ZNF263 bound and recruited DNMT1 to the EGFR gene promoter, suppressing EGFR transcription with DNA hypermethylation. ZNF263 could also interact with nuclear EGFR (nEGFR), impairing the nEGFR-STAT5 interaction to enhance AURKA expression. Overexpressing ZNF263 also made tumor cells with wild-type EGFR expression or refractory EGFR mutations more susceptible to EGFR inhibition. More importantly, lentivirus or AAV-mediated plasmid delivery of ZNF263 synergistically suppressed tumor growth and regrowth with osimertinib in xenograft animal models. These findings suggest that enhancing ZNF263 may achieve complete response in LUAD with EGFR-targeted therapies.

overall_design: To investigate gene expression profiles in lung adenocarcinoma after osimertinib treatment, we collected clinical tumor specimens prior or post treatment of osimertinib from patients with advanced lung adenocarcinoma.

first: Guoshu

last: Bi

first: Qihai

last: Sui

first: Guangyin

last: Zhao


title: Alcohol use disorder-associated DNA methylation differences in nucleus accumbens and dorsolateral prefrontal cortex

status: Public on Jan 18 2024

city: Research Triangle Park

first: Melyssa

last: Minto

state: NC

address: 3040 E. Cornwallis Road

institute: RTI International

summary: Alcohol use disorder (AUD) has a profound public health impact and understanding of the molecular mechanisms underlying the development and progression of AUD remain limited. Many genetic risk loci have been identified for AUD or alcohol consumption, though the neurobiological mechanisms underlying these loci remain largely unknown. DNA methylation (DNAm) differences between individuals with and without AUD can provide insight into the mechanisms that predispose to AUD and consequences of AUD itself. Here, we provide Illumina HumanMethylation EPIC array data generated in nucleus accumbens and dorsolateral prefrontal cortex, both addiction relevant brain tissues, from 119 decedents of European ancestry: 61 controls and 58 cases. From these data we have conducted an epigenome-wide association study (EWAS) and identified several CpG associations with AUD. A subset of the identified CpGs map to genes that were previoulsy identified as associated with substance use behaviors in genetic studies, but the other CpGs map to genes previoulsy unassociated with substance use behaviors and are novel.

overall_design: Genome-wide DNAm data were measured in postmortem nucleus accumbens (NAc) and dorsolateral prefrontal cortex (DLPFC) tissue with the HumanMethylation EPIC BeadChip array. The dataset includes data from 119 deceased individuals: 61 controls (57 with data from NAc and DLPFC, 2 NAc only, 2 DLPFC only) and 58 DSM-5 AUD cases (56 with data from NAc and DLPFC, 0 NAc only, 2 DLPFC only).


title: Structural basis of the DEK-nucleosome complex and its functional implications (CUT&Tag)

status: Public on Jan 15 2024

city: changsha

first: shen

last: yunfan

state: hunan

address: xiangya road

institute: central south university

summary: The nuclear factor Dek is notably enriched within chromatin; nevertheless, the precise binding mechanism of Dek to the nucleosome remains elusive. In this study, we employ cryo-electron microscopy (cryo-EM) to elucidate the high-resolution structure of the Dek-Nucleosome Core Particle (NCP) complex. We identify specific domains responsible for DEK interaction with the histone octamer and DNA within the nucleosome. The veracity of these binding domains is confirmed through a series of meticulous biochemical experiments. Subsequently, cellular experiments reveal that Dek lacking nucleosome-binding capacity exhibits a deficiency in chromatin interaction. Remarkably, this impairment induces a shift towards the primitive endoderm fate in mouse embryonic stem cells, underscoring the pivotal role of Dek in determining cell fate through its nucleosomal interactions.

overall_design: Parental and DEK-knockout cells. CUT&Tag for DEK and histone modifications was employed to assess the impact of DEK on  histone modifications.

first: Yunfan

last: Shen

first: Yanhong

last: Liu

first: Hongda

last: Huang

first: Kai

last: Yuan