title: Transcriptome analysis of A.baumannii 98-37-09 wild type compared to YhaK Tn mutant under antibiotic treatment in human serum.

city: Rochester

first: Mikaeel

middle: Imran

last: Young

state: New York

address: 601 Elmwood Ave, Rm 211311B , MRBX

department: Microbiology and Immunology

institute: University of Rochester

summary: We report the transcriptomic information of wild type (Lab-WT) A.baumannii 98-37-09 and A1S_3277 transposon mutant during the growth in human serum with 0.15 µg/mL levofloxacin

overall_design: Examination of A.baumannii 98-37-09 and A1S_3277 transposon mutant grown in human serum and treated with 0.15 µg/mL levofloxacin until mid-exponential phase. Samples were performed in duplicate. Total RNA was isolated from both samples, sequenced using NovaSeq and differential gene analysis conducted to investigate the role of A1S_3277 (YhaK).

first: Paul

last: Dunman


title: USP7 represses lineage differentiation genes of mouse embryonic stem cells through both catalytic and non-catalytic activity [CUT&Tag]

status: Public on Aug 08 2023

city: Hangzhou

first: Chao

last: Liu

state: State...

address: Zhejiang University

country: China

institute: Zhejiang University

summary: USP7, a ubiquitin-specific peptidase (USP), plays an important role in many cellular processes through its catalytic deubiquitination of various substrates. However, its nuclear function to regulate gene expression in mouse embryonic stem cells (mESCs) remains largely unknown. Here, we report that USP7 maintains mESCs identity through both catalytic activity-dependent and -independent repression of lineage differentiation genes. Usp7 depletion attenuates SOX2 level and derepresses lineage differentiation genes thereby compromising mESCs identity. Mechanistically, USP7 deubiquitinates and stabilizes SOX2 to repress mesoendodermal (ME) lineage genes. Moreover, USP7 assembles into RYBP-variant polycomb repressive complex 1 (vPRC1) and contributes to Polycomb chromatin domain-mediated repression of ME lineage genes in a catalytic activity-dependent manner. However, USP7 deficient in its deubiquitination function is able to maintain RYBP binding on chromatin to represses primitive endoderm-associated genes in mESCs. Overall, our study demonstrates that USP7 harbors both catalytic and non-catalytic scaffold activity to repress lineage differentiation genes thereby revealing a previously unrecognized role in controlling gene expression and maintaining mESCs identity.

overall_design: different antibodies for CUT&Tag of mESCs with auxin inducible degradation to rapidly deplete Usp7 protein, and overexpressed a Usp7 with HA-C224S enzyme catalytic center mutation (HA-C224S) and a HA-Usp7 wild type full length (HA-Usp7-FL)  after IAA addition for 3 days.

first: Junfeng

last: Ji


title: Selective IL-27 production by intestinal regulatory T cells permits gut-specific regulation of Th17 immunity [RNA-Seq]

city: La Jolla

first: Li-Fan

last: Lu

state: CA

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

country: USA

institute: University of California, San Diego

type: Expression profiling by high throughput sequencing

summary: Regulatory T (Treg) cells are instrumental in establishing immunological tolerance. However, the precise effector mechanisms by which Treg cells control a specific type of immune response in a given tissue remains unresolved. By simultaneously studying Treg cells from different tissue origins under systemic autoimmunity, here we show that IL-27 is specifically produced by intestinal Treg cells to regulate Th17 immunity. Selectively increased intestinal Th17 responses in mice with Treg cell-specific IL-27 ablation led to exacerbated intestinal inflammation and colitis-associated cancer, but also helped protect against enteric bacterial infection. Furthermore, single-cell transcriptomic analysis has identified a CD83+TCF1+ Treg cell subset that is distinct from previously characterized intestinal Treg cell populations as the main IL-27 producers. Collectively, our study uncovers a novel Treg cell suppression mechanism crucial for controlling a specific type of immune response in a particular tissue, and provides further mechanistic insights into tissue-specific Treg cell-mediated immune regulation.

overall_design: Foxp3GFP-CD4+ conventional T cells (Tconv), Foxp3Thy1.1+CD4+ regulatory cells (Treg) isolated from spleen, lung and gut in DT- or control PBS-treated Foxp3DTR mice

first: Chia-Hao

last: Lin

first: Cheng-Jang

last: Wu

first: Sunglim

last: Cho

first: L-Fan


title: A feedback loop between heterochromatin and the nucleopore complex controls germ-cell to oocyte transition during Drosophila oogenesis [mRNA-Seq]

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

institute: RNA Institute

summary: Germ cells differentiate into oocytes that become totipotent upon fertilization. How the highly specialized oocyte acquires this distinct cell fate is poorly understood. During Drosophila oogenesis, H3K9me3 histone methyltransferase SETDB1 translocates from the cytoplasm to the nucleus of germ cells concurrent with oocyte specification. Here, we discovered that nuclear SETDB1 is required to silence a cohort of differentiation-promoting genes by mediating their heterochromatinization. Intriguingly, SETDB1 is also required for the upregulation of 18 of the ~30 nucleoporins (Nups) that comprise the nucleopore complex (NPC). NPCs in turn anchor SETDB1-dependent heterochromatin at the nuclear periphery to maintain H3K9me3 and gene silencing in the egg chambers. Aberrant gene expression due to loss of SETDB1 or Nups results in loss of oocyte identity, cell death and sterility. Thus, a feedback loop between heterochromatin and NPCs promotes transcriptional reprogramming at the onset of oocyte specification that is critical to establish oocyte identity.

overall_design: mRNA-seq of duplicate samples of ovaries from germline SETDB1  KD, wde KD and Nup154 KD as a developmental control

first: Kahini

last: Sarkar

first: Noor

last: Kotb

first: Alex

last: Lemus

first: Elliot

middle: T

last: Martin

first: Alicia

last: McCarthy

first: Justin

last: Camacho

first: Ayman

last: Iqbal

middle: M

last: Valm

first: Morgan

last: Sammons


title: Effects of culture condition on small RNA transcriptomes in extracellular vesicles released by human bone marrow stromal cells

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

type: Non-coding RNA profiling by high throughput sequencing

summary: Various culture media that can rapidly expand bone marrow stromal cells (BMSCs) are currently available. However, the effects of those culture media on the contents of extracellular vesicles released by bone marrow stromal cells have not been fully understood. Using BMSCs from 6 healthy donors were cultured in two different culture media and characterized the small RNA profiles in extracellular vesicles.

overall_design: Total 12 samples were analyzed; BMSCs (#3-#8) were cultured in either DMEM+10% FBS (D) or high perfomance medium (R)

first: Amanda

middle: L

last: Scheiber

first: Cierra

middle: A

last: Clark

first: Takashi

last: Kaito

first: Masahiro

last: Iwamoto

first: Edwin

last: Horwitz

middle: I

last: Kawasawa

first: Satoru

last: Otsuru


title: RNAseq study of latency prevention with Vorinostat

city: Chapel Hill

first: Edward

middle: Patrick

last: Browne

state: NC

address: 120 Mason Farm Road

institute: UNC-Chapel Hill

summary: Primary CD4 T cells were activated ex vivo and infected with HIV-dGFP/Thy1.2. Thy1.2 positive cells were isolated by immuno-magnetic enrichment and cultured for 21 days in the presence or absence of 500nM Vorinostat. At the end of the 21 day culture period cells were collected and subjected to RNA-seq.

overall_design: Study done in biological triplicate. Cells from three independent HIV-negative donors were infected, isolated, and cultured in parallel with or without Vorinostat treatment condition.

first: Jackson

last: Peterson

first: Sam

last: Burgos


title: Comparing the cerebellar transcriptome of Sacs KO versus WT mice

city: Milan

first: Francesca

last: Maltecca

state: Milan

address: Via Olgettina, 58

department: Division of Neuroscience

country: Italy

institute: Ospedale San Raffaele

summary: Autosomal Recessive Spastic Ataxia of Charlevoix-Saguenay (ARSACS) is caused by mutations in SACS gene encoding sacsin. ARSACS patients and mouse models display early degeneration of cerebellum in agreement with high sacsin expression in this organ. We performed unbiased transcriptomic of cerebella from Sacs KO mice versus controls to dissect the mechanisms underlying cerebellar degeneration in ARSACS.

overall_design: Cerebella derived from 5 Sacs KO versus 5 WT littermates at 5 months of age.

first: Andrea

last: Del Bondio


title: A feedback loop between heterochromatin and the nucleopore complex controls germ-cell to oocyte transition during Drosophila oogenesis [Cut&Run]

first: Prashanth

last: Rangan

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Sequencing of duplicate samples after performing CUT&RUN of ovaries  from WT, germline SETDB1  KD and Nup154 KD for H3K9me3

first: Kahini

last: Sarkar

first: Noor

last: Kotb

first: Alex

last: Lemus

first: Elliot

last: Martin

last: McCarthy

last: Camacho


title: A feedback loop between heterochromatin and the nucleopore complex controls germ-cell to oocyte transition during Drosophila oogenesis

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

overall_design: Refer to individual Series


title: Transcriptome data of bone marrow regulatory T cells (Tregs) with premature aging

city: Chongqing

first: Weinian

last: Liao

address: Gaotanyan street 30

institute: Army Medical University

summary: Bone marrow (BM) is normally maintained in an immune-privileged and anti-inflammatory state, kept in check principally by regulatory T cells (Tregs). Thus, it is reasonable to expect that Tregs will help shield hematopoietic stem cells (HSCs) from excessive inflammation and thereby counteract HSC aging. Understanding how BM Tregs are adapted to the aged BM and whether they are endowed with unique functions to modulate HSC aging will identify targets for prevention of HSC aging. To identify the phenotype switching and function variation in BM Tregs with physiological and premature aging, we performed RNA-seq of Tregs from the bone marrow of mice at three months post irradiation (IR) and their age-matched control mice (Ctrl).

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of BM Tregs (CD3+CD4+NK1.1–Foxp3+) of control or IR mice.

first: Changhong

last: Du

first: Junping

last: Wang


title: Anthocyanin-treated osteoblast cells [mRNA-seq]

city: Chicago

first: Gail

middle: B

last: Mahady

state: Il

address: 833 S Wood St

department: Pharmacy Practice

institute: University of Illinois

summary: Our preliminary data shows that dietary ACNs increased osteoblast differentiation and function in human osteoblasts, as well as increased osteoblast differentiation and reduced bone resorption in transgenic medaka. In cultured human osteoblasts, ACNs and resveratrol enhanced growth, reduced apoptosis and increased the expression of HDACs and PGC-1, suggesting that ACNs alter epigenetic regulation and mitochondrial biogenesis

overall_design: mRNA-seq

first: Pinal

last: Kanabar


title: Post-fast refeeding enhances intestinal stem cell mediated regeneration and tumorigenesis through mTORC1 signaling and polyamine

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: For more than a century, fasting regimens have been shown to improve health, lifespan, and tissue regeneration in diverse model organisms and humans. However, important questions remain regarding how fasting and refeeding cycles stimulate stem cell output and how this influences their role in early tumor formation. Here, we demonstrate that in the mammalian intestine, a short 24-hour fast followed by a 24-hour refeeding period (that is, post-fast refeeding) and not fasting itself elevates the stemness program and regenerative capacity of Lgr5+ intestinal stem cells (ISCs).  Furthermore, loss of the tumor suppressor APC in post-fast refed ISCs significantly boosts tumor incidence in the small intestine and colon compared to those in the fasted or ad libitum fed states. Mechanistically, robust induction of insulin-PI3K-mTORC1 signaling as well as elevated intestinal polyamines level increase protein synthesis in post-fast refed ISCs to mediate these changes as inhibition of mTORC1, polyamine, or protein synthesis abrogate the regenerative or tumorigenic effects of post-fast refeeding. Thus, our data indicate that post-fast refeeding leads to a burst not only in stem cell-driven regeneration but also in tumorigenicity and that careful consideration be given to fast-refeeding cycles when planning diet-based strategies.

overall_design: One replicate each of intestinal stem  and progenitor cells isolated from mice feeding at will (al), fasted for 24 hours (f), fasted followed by refeeding at will for 24 hours (rf) and refeeding plus Rapamycin.

first: Imada

last: Shinya

first: Omer

last: Yilmaz


title: JAML is a novel immunotherapy target for tissue-resident memory T cells [scRNA-seq]

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

summary: Tumor-infiltrating CD8+ T cells express high levels of the co-stimulatory molecule JAML, which can be exploited for cancer immunotherapy.

overall_design: Single-cell RNA-seq was performed from CD45+JAML+ T cells isolatied from murine tumor (n = 3)

first: Simon

last: Eschweiler

first: Alice

first: Ciro

last: Ramírez-Suástegui

first: Adrian

last: von Witzleben

first: Serena

middle: J

last: Chee

first: Hayley

last: Simon

first: Monalisa

last: Mondal

first: Matthew

last: Ellis

first: Gareth

last: Thomas

first: Vivek

last: Chandra

first: Christian

middle: H

last: Ottensmeier


title: Chronic Lymphocytic Leukemia MEC1 SF3B1 K700E and Wild Type Cell Lines' RNA-seq after Treatment with H3B-8800 Splicing Modulator.

city: Barcelona

first: Estefania

last: Mancini

state: Barcelona

address: C/ Dr. Aiguader, 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Centre for Genomic Regulation

summary: To study the impact of SF3B1 mutations on alternative splicing and the effect of H3B-8800 splicing modulator in wild type and SF3B1-mutant chronic lymphocytic leukemia cells, we established SF3B1 K700E MEC1 CLL isogenic cell line and carried out RNA deep sequencing in SF3B1 wild type and K700E MEC1 cell lines upon H3B-8800 treatment.

overall_design: MEC1 SF3B1 wild type and SF3B1 K700E chronic lymphocytic leukemia cell lines treated for 6 hours with H3B-8800 75nM.

first: Irene

last: López-Oreja

first: Sophie

last: Bonnal


title: JAML is a novel immunotherapy target for tissue-resident memory T cells


title: JAML is a novel immunotherapy target for tissue-resident memory T cells [bulk RNA-seq]

overall_design: Single-cell RNA-seq was performed from CD45+JAML+ T cells isolatied from murine tumor (n = 3); bulk RNA-seq of tumor-infiltrating CD4+FOXP3+ Treg cells and CD8+ T cells

last: Wang


title: RNA-Seq of baboon kidney cortex biopsies

city: Winston Salem

first: Laura

last: Cox

address: 1 Medical Center Blvd

department: Internal Medicine

institute: Wake Forest School of Medicine

summary: Sex differences in baboon kidney cortex gene expression.

overall_design: This study utilizes weighted gene coexpression network analysis to investigate underlying sex differences of gene networks in the primate kidney cortex transcriptome. Establishing sex differences in baboon kidneys is essential for translating understanding of its role to human physiology and disease and for development of precision medicine.

first: Angelica

last: Riojas

first: Kimberly

last: Spradling-Reeves


title: Whole-genome transcriptome analysis of tomato and Arabidopsis roots in the shade

city: Cold Spring Harbor

first: Ullas

middle: V.

last: Pedmale

address: 1 Bungtown RD

department: Pedmale

institute: Cold Spring Harbor Laboratory

summary: RNA-seq analysis of arabidopsis and tomato roots in shaded and unshaded seedlings.

sample_organism:
Arabidopsis thaliana
Solanum lycopersicum

overall_design: Time-course RNA-seq analysis in Arabidopsis and tomato roots unshaded or exposed to shade

middle: V

first: Daniele

last: Rosado


title: Analysis of micro-RNA expression profiles in human islets and islet-derived exosomes during cytokine mediated β cell stress and death

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

summary: Biomarkers capable of monitoring β cell stress during the evolution of type 1 diabetes (T1D) are currently lacking. MicroRNAs (miRNAs) are a class of small non-coding RNAs ~22 nucleotides in length that modulate gene expression by binding to the 3’untranslated region of target mRNAs.  Given their stability in biological fluids and enrichment in cell-derived EVs, we hypothesized that miRNAs from human islet and islet-derived EVs could identify β-cell stress/death and be leveraged in T1D biomarker strategies. To test this, human islets were obtained from 10 cadaveric donors (5 male/5 female) and treated with or without cytokines (IL-1β and IFN-γ) for 24 hrs, as an ex vivo model of T1D. Small RNA sequencing was performed and  identified 1110 and 890 miRNAs in total and 20 and 14 differentially expressed (DE) miRNAs (fold change≥1.5 and p<0.05) from islets and EVs, respectively. These findings were validated in an independent set of cytokine-treated islets and islet-derived EVs (7M and 5F donors). Interestingly, miRNA expression pattern was strikingly different between male and female donors at baseline and under cytokine stress with < 10% overlap among the DE miRNAs. miR-155-5p and miR-146a-5p were the only two miRNAs that were upregulated in cytokine-treated islets and EVs in both the sexes. Functional enrichment analysis of DE miRNAs identified pathways such as insulin signaling, ER stress and apoptosis. Taken together, these data suggest that miRNA expression patterns change dynamically in both human islets and islet-derived EVs in response to pro-inflammatory cytokine stress. EV miRNAs were largely distinct from those in the islet fraction, suggesting that miRNAs are selectively packaged into EVs in response to extrinsic cues. Finally, these data highlight the importance of considering sex as a biological variable when defining T1D biomarkers.

overall_design: Identification of differentially expressed miRNAs from human islets and islet-derived exosomes treated with/without proinflammatory cytokines (IL-1B + IFN-g)

first: Farooq

last: Syed

first: Preethi

last: Krishnan


title: Next Generation Sequencing analysis using SPOP mutant (F133V)-transduced RM-1-BM mouse prostate cancer cells and RAW264.7 mouse macrophage cells

status: Public on Aug 07 2023

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

summary: In this experiment, we analyzed the gene expression profiles of SPOP mutant (F133V)-transduced (and vector control) RM-1-BM mouse prostate cancer cells and RAW264.7 macrophage cells in transwell coculture and monoculture in the context of olaparib (or vehicle) treatment by RNA sequencing.

overall_design: Fresh SPOP mutant (F133V)- and vector control-transduced RM-1-BM mouse prostate cancer cell and RAW264.7 mRNA profiles from olaparib- or vehicle-treated transwell cocultures and monocultures were generated by deep sequencing, in triplicate

first: Manchao

last: Zhang

first: Chuandong

last: Geng

first: Sanghee

last: Park

first: Patrick

last: Pilie

first: Timothy

last: Thompson


title: Revisiting chromatin packaging in mouse sperm [Nanopore-methylation]

city: Boston

first: Qiangzong

last: Yin

address: 3 Blackfan St, CLS building 440A

department: Medicine

institute: BIDMC/Harvard Medical School

type: Methylation profiling by high throughput sequencing

summary: Mammalian sperm exhibit an unusual and heavily-compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression in the early embryo. Scores of genome-wide surveys in sperm have reported patterns of chromatin accessibility, histone localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low levels of cell-free chromatin. In the absence of proper sperm lysis we readily recapitulate multiple prominent genome-wide surveys of sperm chromatin, suggesting that these profiles primarily reflect contaminating cell-free chromatin. Removal of cell-free DNA, along with appropriate lysis conditions, are required to reveal a sperm chromatin state distinct from any yet reported. Using ATAC-Seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with genes expressed during late spermiogenesis. Histone modification and chromosome folding studies also strongly support the hypothesis that prior studies suffer from contamination, but technical challenges associated with reliably preserving the architecture of the compacted sperm head prevent us from confidently assaying true localization patterns for these epigenetic marks. Together, our studies strongly argue that our knowledge of mammalian chromosome packaging remains largely incomplete, and motivate future efforts to more accurately characterize genome organization in mature sperm.

overall_design: DNA methylation and chromatin accessibility profiling in untreated sperm using Oxford Nanopore long-read sequencing

first: Chih-Hsiang

last: Yang

first: Olga

middle: S

last: Strelkova

first: Yu

last: Sun

first: Sneha

last: Gopalan

first: Liyan

first: Job

last: Dekker

first: Thomas

middle: G

last: Fazzio

first: Xin

middle: Z

last: Li

first: Johan

last: Gibcus

first: Oliver

last: Rando


title: Revisiting chromatin packaging in mouse sperm [Hi-C]

overall_design: 3D genome profiling in mouse sperm samples that are pre-treated with Dnase or DTT using Hi-C


title: Pancreatic acinar cell fate relies on system xc- to prevent ferroptosis during stress

city: Brussel

first: Zhaolong

last: Pan

address: Laarbeeklaan 103

country: Belgium

institute: Vrije Universiteit Brussel

summary: Acinar cell dedifferentiation is one of the most notable features of acute and chronic pancreatitis. It can also be the initial step that facilitates pancreatic cancer development. In the present study, we further decipher the precise mechanism and regulation using murine experimental models. Our RNAseq analysis indicates that, early acinar cell dedifferentiation is accompanied by multiple pathways related to cell survival that are highly enriched, and where SLC7A11 (xCT) is transiently upregulated. xCT is the specific subunit of the cystine/glutamate antiporter system xC-. Acinar cells with depleted or reduced xCT function show an increase in ferroptosis relating to lipid peroxidation. Lower glutathione levels and more lipid ROS accumulation could be rescued by the antioxidant N-acetylcysteine or the ferroptosis inhibitor Ferrostatin-1. In caerulein-induced acute pancreatitis in mice, xCT also prevents lipid peroxidation in acinar cells. In conclusion, during stress, acinar cell fate seems to be poised for avoiding several forms of cell death. xCT specifically prevents acinar cell ferroptosis by fueling the glutathione pool and maintaining ROS balance. The data suggest that xCT offers a druggable tipping point to steer the acinar cell fate in stress conditions.

overall_design: Fresh isolated pancreatic acinar cells of WT or xCT KO mouse were cultured in vitro to allow dedifferentiation. Samples were collected at day0, day1 and day4. For each timepoint, 3 biological replicates were examined. Comparative gene expression profiling analysis of RNA-Seq data between genotypes and among differnet timepoints were performed.

first: Marco

last: Mambretti

first: Ilse

last: Rooman


title: Uptake of an aluminum-containing food color in human cells and its implications for human health

city: Linz

first: Marlene

last: Rezk

address: Krankenhausstraße 7A

country: Austria

institute: Johannes Kepler Universität

summary: Food colors contain Aluminium (Al) to change the color’s solubility in water, but these Al containing versions of the food colors have never been investigated towards their pathophysiological effects in humans, but are assumed to behave like the Al-free version. We compared the food color carminic acid (CA) with its Al-containing version carmine (Car, both used as E 120) and could see a clear difference between gene expression profiles of Caco-2 cells exposed to Car, CA or control. Genes which were only dysregulated through Car treatment, but not with CA treatment, lead to a significant suppression of oxidative phosphorylation, which is known to be impaired in neurodegenerative diseases.

overall_design: We investigated the gene expression of differentiated Caco-2 cells after treatment with Carminic Acid, Carmine or Control for 24 hours (triplicates for each treatment)

first: Clara

last: Ganhör

first: Christian

last: Doppler

first: David

last: Bernhard


title: Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis [mRNA-Seq]

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

summary: MicroRNAs (miRNAs) play an important role in gene regulation. In Arabidopsis thaliana, mature miRNAs are processed from primary miRNA transcripts by Dicing complex, which contains DCL1, SE and HYL1 and forms nuclear dicing bodies (D-bodies) through SE phase separation. Here we report that Cyclophilin 71 (CYP71), a peptidyl-prolyl isomerase (PPIase), positively regulates miRNA processing. We show that CYP71 directly interacts with SE and enhances its phase separation, thereby promoting the formation of D-body and increasing the activity of Dicing complex. We further show that the PPIase activity is important for the function of CYP71 in miRNA production. Our findings reveal orchestration of miRNA processing by a cyclophilin protein and suggest the involvement of proline cis-trans isomerization, a structural mechanism, in SE phase separation and miRNA processing.

overall_design: To evaluate the impact of CYP71 mutations on miRNA and miRNA target gene expression profile, we performed small RNA-seq and mRNA-seq in triplicate using 2-week-old Col-0, cyp71-2, cyp71-3 seedlings.


title: Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis


title: ENPP1 is an innate immune checkpoint of the anticancer cGAMP-STING pathway

city: Palo Alto

first: FEIQIAO

middle: Brian

last: YU

address: 3181 Porter Dr.

department: Multi-Omics

institute: Arc Institute

summary: ENPP1 expression correlates with poor prognosis in many cancers, and we previously discovered that ENPP1 is the dominant hydrolase of extracellular cGAMP: a cancer-cell-produced immunotransmitter that activates the anticancer STING pathway. However, ENPP1 has other catalytic activities and the molecular and cellular mechanisms contributing to its tumorigenic effects remain unclear. Here, using single cell RNA-seq (scRNA-seq), we show that ENPP1 overexpression drives primary tumor growth and metastasis by synergistically dampening extracellular cGAMP-STING mediated antitumoral immunity and activating immunosuppressive extracellular adenosine (eADO) signaling. In addition to cancer cells, stromal and immune cells in the tumor microenvironment (TME) also express ENPP1 which functions as a gate keeper to block cGAMP sensing in these cells. Enpp1 knockout in both cancer cells and normal tissues slowed primary tumor growth and prevented metastasis in an extracellular cGAMP- and STING-dependent manner. Lastly, an ENPP1 knock-in mutation that selectively abolishes ENPP1’s cGAMP hydrolysis activity phenocopied total ENPP1 knockout, demonstrating that restoration of paracrine cGAMP-STING signaling is the dominant anti-cancer mechanism of ENPP1 inhibition. In summary, selectively blocking ENPP1’s cGAMP hydrolysis activity is a promising therapeutic approach for treating cancer.

overall_design: Primary orthotopic breast tumors and lungs containing metastases of BALB/cJ mice implanted with ENPP1-WT-OE or ENPP1-T238A-OE 4T1 breast cancer cells, two mice per condition, were isolated and analyzed using scRNA-seq

first: Songnan

last: Wang

first: Lingyin

first: Feiqiao

last: Yu

first: Jason

last: Swinderman


title: GENE EXPRESSION WITHIN A HUMAN CHOROIDAL NEOVASCULAR MEMBRANE USING SPATIAL TRANSCRIPTOMICS

city: Iowa City

first: Andrew

middle: P

last: Voigt

state: IA

address: 375 Newton Road

institute: University of Iowa

summary:
Purpose: The goals of this study were to identify expression patterns in human macular neovascularization with spatial transcriptomics
Methods: Independent libraries were prepared two human donors: one with macular neovascularation (MNV) and one healthy control. Three tissue sections were taken from the MNV donor and two from the control donor.  From the right eyes of both donors, a 4 mm diameter macular punch was collected centered on the fovea centralis, as was a 4 mm peripheral punch approximately 12 mm superotemporal from the macula. Both central and peripheral punches (spanning retina, choroid and sclera) were placed in optimal cutting temperature compound (OCT) and were rapidly snap frozen in liquid nitrogen and stored at -80C.   Final libraries were sequenced on an Illumina NovaSeq system. Sequenced reads were mapped to the human genome build hg38 with CellRanger(v7.0.0). Feature selection was performed with the variance stabilizing transformation with Seurat (v4).
Results: Spots from the MNV and control donor were deconvoluted with CSIDE, which estimated the percent RNA contribution to each spot from different cell types. Differential expression was performed between the MNV and control donors. Within the area of neovascularization, endothelial cells were predicted to increase expression of genes related to Rho family GTPase signaling and integrin signaling. Likewise, VEGF and TGFB1 were identified as potential upstream regulators that could drive the observed gene expression changes produced by endothelial and retinal pigment epithelium cells in the macular neovascularization donor.
Conclusions: Overall, this study spatially analyzes gene expression across the retina, retinal pigment epithelium, and choroid in health and describes a set of candidate molecules that become dysregulated in macular neovascularization.

overall_design: mRNA profiles were spatially acquired for one donor with MNV and one control donor using the 10X Visium system followed by sequencing on an Illumina NovaSeq.

first: Robert

middle: F

last: Mullins


title: single nucleus RNA-seq of early development in P. miniata and S. purpuratus

city: PITTSBURGH

first: Hinman

last: Veronica

address: 587 S Negley Ave, Apt 17

institute: Carnegie Mellon University

sample_organism:
Strongylocentrotus purpuratus
Patiria miniata

overall_design: Refer to individual Series


title: MicroRNA expression study on samples from surgically treated breast cancer patients

city: Morgantown

first: Dajie

last: Luo

state: West Virginia

address: P.O. Box 9300 Room 2816 HSS

institute: West Virginia University

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling of a total of 677 genes in 52 breast cancer samples.

overall_design: In the study presented here, a consecutively operated, well-defined cohort of 52 breast cancer cases and 4 matched normal breast tissues, was used to acquire expression profiles of a total of 677 unique genes, leading to the successful construction of supervised classifiers.

first: Nancy

last: Guo

first: Rebecca

last: Raese


title: An ILK/STAT3 pathway controls plasticity in a neural stem cell model of glioblastoma.

city: Edinburgh

first: Alexander

last: Loftus

address: Crewe Road

country: United Kingdom

institute: The University of Edinburgh

summary: Glioblastomas (GBM) are driven by malignant neural stem-like cells that display extensive heterogeneity and phenotypic plasticity, which drives tumour progression and therapeutic resistance. Here we show that the nodal extracellular matrix-cell adhesion protein integrin-linked kinase (ILK) is a key determinant of phenotypic plasticity and the mesenchymal-like, invasive cell state in mouse GBM stem cells. We found that an ILK-STAT3 signalling pathway is required for plasticity that enables the transition of GBM stem cells to an astrocyte-like state both in vitro andin vivo. GBM cells genetically depleted of ILK become predominantly stabilised in a transcriptionally-defined progenitor-like state that is characterised by lack of response to differentiation cues and constitutive proliferation. Loss of ILK or interference with STAT3 impairs differentiation potential, reducing phenotypic plasticity of tumour cell populations; additionally, ILK loss causes a mesenchymal- to epithelial-like morphological transition and suppression of malignancy-associated features. Our work defines ILK as a central regulator of multiple GBM phenotypes including phenotypic plasticity and mesenchymal state.

overall_design: We established ILK-knockout and ILK re-expressing GBM stem cells and compared their transcriptomes before and after treatment with the astrocyte-differentiating factor BMP-4.

middle: E

first: Margaret

middle: C

last: Frame


title: Revisiting chromatin packaging in mouse sperm [CUT&Tag]

first: Qiangzong

last: Yin

overall_design: Histone modification profiling in mouse sperm samples that are pre-treated with Dnase or DTT using CUT&Tag

first: Chih-Hsiang

last: Yang

first: Olga

last: Strelkova

first: Yu

last: Sun

first: Sneha

last: Gopalan

first: Liyan

first: Job

last: Dekker

first: Thomas

last: Fazzio

first: Xin

last: Li

first: Johan

last: Gibcus

first: Oliver

last: Rando


title: Dual immune checkpoint blockade induces analogous alterations in the dysfunctional CD8+ T cell and activated Treg compartment

city: Amsterdam

first: Joleen

last: Traets

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Immune checkpoint blockade has shown clinical activity in a range of cancer types. To dissect the effect of neoadjuvant PD-1 and CTLA4 blockade on intratumoral T cells in treatment-naïve head and neck squamous cell carcinoma, we analyzed immune infiltrates in tumor biopsies from responding and non-responding patients. At baseline, a higher ratio between active (4-1BB/OX-40+) and inactive regulatory CD4+ T cells was associated with response to therapy. Furthermore, upon therapy, this active Treg population showed a profound decrease in responding patients. In an analogous process, the intratumoral dysfunctional CD8+ T cell compartment displayed a decrease in the expression of activity and dysfunction-related genes in responding patients, while in clinically non-responding patients, NK cells showed an increased cytotoxic transcriptional profile early upon treatment. These data reveal the immunological changes in response to dual PD-1 and CTLA4 blockade, including a parallel remodeling of presumed tumor-reactive T cell compartments in responding patients, and indicate that the presence of an activated Treg compartment at baseline may be associated with response.

overall_design:
We performed single cell RNA and TCR sequencing (10x Genomics)  on immune infiltrates (CD45+ cells) from 18 HNSCC patients enrolled in the IMCISION trial (Vos et al. 2021). Viable immune cells were isolated from pre-treatment and on-treatment primary tumor biopsies of 10 patients responding (1 partial pathological response and 9 major pathological responses) and 7 patients non-responding to anti-PD-1 and anti-CTLA4 combination immunotherapy. One patient treated with anti-PD-1 monotherapy (1 major pathological response) was included in the dataset.
*** Raw sequencing data will be deposited on EGA. ***

first: Anne

middle: M

last: van der Leun

first: Joris

middle: L

last: Vos

last: Elbers

first: Sanne

last: Patiwael

first: Xiaohang

last: Qiao

first: Mercedes

last: Machuca-Ostos

first: Daniela

last: Thommen

first: John

last: Haanen

first: Ton

middle: N

last: Schumacher

first: Charlotte

last: Zuur


title: Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory CD8+ T cell differentiation in vitro

city: Bethesda

first: Peter

last: McGuire

state: MD

address: 10 Center Dr

institute: NHGRI

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


title: Disulfiram blocks inflammatory TLR4 signaling by targeting MD-2

city: Shanghai

first: Yang

last: Bai

address: Yueyang Road No.320

institute: Chinese Academy of Sciences

summary: Toll-like receptor 4 (TLR4) sensing of lipopolysaccharide (LPS), the most potent pathogen-associated molecular pattern of gram-negative bacteria, activates NF-κB and Irf3, which induces inflammatory cytokines and interferons that trigger an intense inflammatory response, which is critical for host defense but can also cause serious inflammatory pathology, including sepsis. Although TLR4 inhibition is an attractive therapeutic approach for suppressing overexuberant inflammatory signaling, previously identified TLR4 antagonists have not shown any clinical benefit. Here, we identify disulfiram (DSF), an FDA-approved drug for alcoholism, as a specific inhibitor of TLR4-mediated inflammatory signaling. TLR4 cell surface expression, LPS sensing, dimerization and signaling depend on TLR4 binding to MD-2. DSF and other cysteine-reactive drugs, previously shown to block LPS-triggered inflammatory cell death (pyroptosis), inhibit TLR4 signaling by covalently modifying Cys133 of MD-2, a key conserved residue that mediates TLR4 sensing and signaling. DSF blocks LPS-triggered inflammatory cytokine, chemokine, and interferon production by macrophages in vitro. In the aggressive N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine mouse model of Parkinson’s disease (PD) in which TLR4 plays an important role, DSF markedly suppresses neuroinflammation and dopaminergic neuron loss, and restores motor function. Our findings identify a role for DSF in curbing TLR4-mediated inflammation and suggest that DSF and other drugs that target MD-2 might be useful for treating PD and other diseases in which inflammation contributes importantly to pathogenesis.

overall_design: To confirm the effectiveness of DSF to inhibit LPS activation of TLR4 signaling, iBMDMs pretreated or not with DSF and then challenged or not with LPS were subjected to RNA-seq.

first: Shenglin

last: Mei

first: Fan

last: Deng

first: Judy

last: Lieberman

first: Xing

last: Liu


title: Predicting gene level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework II

city: Pittsburgh

first: Rachel

middle: A.

last: Gottschalk

state: Pennsylvania

address: 200 Lothrop St., W1047 BST

department: Immunology

institute: University of Pittsburgh

summary:
To inhibit JAK2 upon IL-6 and IL-10-induced JAK-STAT signaling and quantify gene expression in bone marrow derived macrophages (BMDMs).
Bulk RNAseq was done on cytokine-stimulated BMDM with and without Fedratinib treatment in order to profile the JAK2-inhibited cytokine-induced response.

overall_design: We stimulated BMDM with IL-6 and IL-10  at 1 ng/ml at 0, 1 and 2 hours with or without 1 nM of Fedratinib

first: Neha

last: Cheemalavagu

first: Karsen

last: Shoger

first: Yuqi

last: Cao

first: Brandon

middle: A

last: Michalides

first: Samuel

last: Botta

first: James

middle: R

last: Faeder


title: Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory CD8+ T cell differentiation in vitro [RNA-Seq]

summary: Modulation of metabolic flux through pyruvate dehydrogenase complex (PDC) plays an important role in T cell activation and differentiation. PDC sits at the transition between glycolysis and the tricarboxylic acid cycle and is a major producer of acetyl-CoA, marking it as a potential metabolic and epigenetic node. To understand the role of pyruvate dehydrogenase complex in T cell differentiation, we generated mice deficient in T cell pyruvate dehydrogenase E1A (Pdha) subunit using a CD4-cre recombinase-based strategy. Herein, we show that genetic ablation of PDC activity in T cells (TPdh-/-) leads to marked perturbations in glycolysis, the tricarboxylic acid cycle, and OXPHOS. Due to depressed OXPHOS, TPdh-/- T cells became dependent upon substrate level phosphorylation via glycolysis.  Due to the block of PDC activity, histone acetylation was reduced, including H3K27, a critical site for CD8+ T cell memory differentiation. Transcriptional and functional profiling revealed abnormal CD8+ memory T cell differentiation in vitro. Collectively, our data indicate that PDC integrates the metabolome and epigenome in memory T cell differentiation. Targeting this metabolic and epigenetic node can have widespread ramifications on cellular function.

overall_design:
RNA-Seq
contributor: NISC Comparative Sequencing Program

first: T

last: Tarasenko

first: P

last: Banerjee

first: J

last: Gomez-Rodriguez

first: D

last: Gildea

first: S

last: Zhang

last: Wolfsberg

first: L

last: Jenkins

middle: J


title: Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory CD8+ T cell differentiation in vitro [ChIP-Seq]

first: Peter

last: McGuire

overall_design: In vitro differentiation of mouse memory T cells using IL-15.


title: Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish

city: Santiago

first: Carmen

middle: Gloria

last: Feijoo

state: Region metropolitana

address: Republica 330

department: Facultad de Ciencias de la vida

country: Chile

institute: Universidad Andres Bello

summary: The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins, and which exert non-overlapping functions. However, there is little information about ontogenetically distinct neutrophil populations. In this work, using a photoconvertible transgenic zebrafish line; Tg(mpx:Dendra2), we selectively label rostral blood island-derived and caudal hematopoietic tissue-derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single-cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury, both populations share a core transcriptional profile as well as subset-specific transcriptional signatures. Accordingly, both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly, caudal neutrophils respond heterogeneously. Collectively, our results reveal that co-existing neutrophils populations with ontogenically distinct origin display key functional differences.

overall_design: We photoconverted RBI-derived neutrophils in the head two times, at 34hpf and 44hpf, and performed caudal fin transections at 54hpf on the half of each group. Three hours later, we homogenized non-cut and cut embryos from each group and separately sorted red and green-fluorescent cells. The resulting four groups were analized by scRNAseq.

first: Juan

last: García-López

first: Alexandre

last: Grimaldi

first: Zelin

last: Chen

first: Claudio

last: Meneses

first: Karina

last: Bravo-Tello

first: Erica

last: Brescian

first: Alvaro

last: Banderas

first: Shawn

last: Burgess

first: Pedro

last: Hernández


title: Predicting gene level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework I

first: Rachel

last: Gottschalk

summary:
To link upstream IL-6 and IL-10-induced JAK-STAT signaling to downstream gene expression in bone marrow derived macrophages (BMDMs).
Bulk RNAseq was done on cytokine-stimulated BMDM in order to profile cytokine-induced response.

overall_design: We stimulated BMDM with six stimulation conditions (IL-6, IL-10 and in combination at 1 ng/ml and 10 ng/ml) at 1, 2 and 4 hours. Expression was compared to unstimulated BMDM.

first: Neha

last: Cheemalavagu

first: Karsen

last: Shoger

first: Yuqi

last: Cao

first: Brandon

last: Michalides

first: Samuel

last: Botta

first: James

last: Faeder


title: CCOGC canine Osteosarcoma tumor samples

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary: RNA-Seq of canine osteosarcoma tumor samples obtained from Canine Comparative Oncology and Genomics Consortium

overall_design: RNA-Seq of fresh frozen osteosarcoma tissues that had undergone a series of different therapies.

first: Jaime

last: Modiano


title: Regulation of transcriptional interference by the Swi/Snf complex [nanopore]

city: Berkeley

first: Elçin

last: Ünal

state: CA

address: 628 Barker Hall

institute: UC Berkeley

summary: Alternative transcription start sites regulate transcript isoform diversity and, in turn, often regulate translation levels for a given gene. Recently, a form of gene regulation was described in which transcriptional and translational interference are coordinated, resulting in transcript isoform-dependent changes in protein expression for affected genes. In this form of gene regulation, a long undecoded transcript isoform (LUTI) is transcribed from a gene-distal promoter, interfering with expression of the gene-proximal promoter. While transcriptional and chromatin features associated with LUTI expression have been described, the mechanism underlying LUTI-based transcriptional interference is not well-understood. Using an unbiased genetic approach followed by integrated genomic analysis, we have found that the Swi/Snf chromatin remodeling complex is required for co-transcriptional nucleosome remodeling that leads to LUTI-mediated repression. We uncovered twelve genes with tandem promoters that rely on Swi/Snf function for transcriptional interference during protein folding stress, including three LUTI-regulated genes. Our results provide evidence that, in addition to its canonical function in gene activation, the Swi/Snf complex directly represses promoters that are subject to transcriptional readthrough.

overall_design: Samples were grown as described in Morse et al., 2023. Cells were collected  from YPD media treated with 5 mM DTT in mid-log phase one hour after treatment. Library construction, sequencing and data processing are described in the methods section of our paper.

first: Kaitlin

last: Morse

first: Sarah

last: Swerdlow


title: Predicting gene level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework


title: Regulation of transcriptional interference by the Swi/Snf complex


title: Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory T cell differentiation in vitro [ATAC-Seq]

first: Peter

last: McGuire

summary: The chromatin landscape was assessed in effector and memory T-cells obtained from wildtype and pyruvate dehydrogenase knockout mouse. Disruption of the metabolic processes involving pyruvate dehydrogenase can affect T-cell differentiation through epigenetic and metabolic mechanisms.

overall_design:
Comparison of chromatin structure between wildtype and TPdh-/- (pyruvate dehydrogenase knockout) mice using ATAC-seq data
contributor: NISC Comparative Sequencing Program

first: T

last: Tarasenko

first: P

last: Banerjee

first: J

last: Gomez-Rodriguez

first: D

last: Gildea

first: S

last: Zhang

last: Wolfsberg

first: L

last: Jenkins


title: Regulation of transcriptional interference by the Swi/Snf complex [RNA-seq]

overall_design: Samples were grown as described in Morse et al. , 2023. Cells were collected in mid-log phase from YPD media. 3 biological replicates are included for each genotype


title: PfAP2-P DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages (ChIP-Seq II)

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Malarial parasite pathogenicity results from its ability to invade and remodel red blood cells (RBCs), expressing antigenic variant proteins for immune evasion and survival, and then to egress from the host cell.  These sequential processes require concerted actions of a large number of proteins during the intraerythrocytic developmental cycle (IDC), but the molecular basis of the required regulation is only partially understood. Here, we have characterized an essential Apicomplexan AP2 (ApiAP2) transcription factor (we refer to it as PfAP2-P; Master Regulator of Pathogenesis) that shows two peaks of expression during the IDC at 16- and 40-hour post invasion (h.p.i.). When expression of PfAP2-P at 40 h.p.i. was disrupted using an inducible gene knockout approach, ∆PfAP2-P parasites unable to form mature merozoites and egress from the host RBCs owing to strong down-regulation of several known egress- and invasion-associated genes, in addition to several novel hypothetical genes of thought to be involved in these key life cycle processes during the IDC. Disruption of PfAP2-P  expression at 16 h.p.i. results in transcriptional activation of virtually majority of silenced var genes observed at both bulk and single cell level. This is also reflected by significantly higher level of recognition of the exported proteins on the ∆PfAP2-P parasite-infected RBCs by pooled sera from malaria-exposed individuals from endemic region. In addition, over expression of many early gametocyte marker genes was also observed in ∆PfAP2-P parasites at both 40 h.p.i., and at 16 h.p.i. PfAP2-P directly regulates these genes by binding to their promoter region or indirectly through 14 other down-stream AP2 transcription factors. Taken together, we conclude that PfAP2-P is an upstream transcriptional regulator that participates in mutually exclusive expression pattern shown by the var family of genes and a critical determinant of parasite’s growth during the IDC.

overall_design: Chip was performed on AP2-P parasites at 40 hour post invasion and 16 hour post invasion using rabbit polyclonal anti H3K9me3 (RRID:AB_310620), rabbit polyclonal anti H3K9ac (RRID:AB_310544), rabbit polyclonal anti H3K4me3(RRID:AB_306649) antibodies . There are two biological replicates for each developmental stages. The input  served as the control.

first: Subudhi

last: Kumar

first: Pain

last: Arnab


title: Regulation of transcriptional interference by the Swi/Snf complex [Mnase-seq]

overall_design: Samples were grown as described in Morse et al., 2023. Cells were collected and fixed from YPD media that was untreated or treated with 5 mM DTT in late log phase. Two biological replicates are included for each genotype.


title: Regulation of transcriptional interference by the Swi/Snf complex [ChIP-seq]

overall_design: Samples were grown as described in Morse et al. , 2023. Cells were collected and fixed from YPD media that was untreated or treated with 5 mM DTT in late log phase. Chromatin immunoprecipitation was performed on Snf2-3V5 using anti-V5 agarose beads. Two biological replicates are included for each genotype.


title: An atlas of gene regulatory networks for T memory cells in youth and old age [RNA-seq]

city: Cincinnati

first: Joseph

last: Wayman

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

summary: We previously identified a population of IL-10-producing, T follicular helper-like cells ("Tfh10"), linked to suppressed vaccine responses in aged mice. Here, we applied scRNA-seq and scATAC-seq to characterize Tfh10 – and the full CD4+ memory T cell (CD4+TM) compartment – in young and old mice. Unprecedented scRNA-seq coverage of the CD4+TM compartment and parallel chromatin accessibility measurements (scATAC-seq) enabled identification of 13 CD4+TM populations, which we validated as a reference through comprehensive cross-comparison to aging cell atlases and scRNA-seq studies reporting Tfh10 in other contexts. In addition, we compared sc-resolved populations to flow-sorted CD4+TM populations (Treg, Tfh10 and "nonTfh, non-Treg IL-10-") subjected to bulk RNA-seq and bulk ATAC-seq. Beyond robust characterization of age- and cell-type-dependent transcriptional landscapes, we used integrative computational modeling to predict the underlying regulatory mechanisms: We inferred gene regulatory networks (GRNs) that describe transcription-factor control of gene expression in each T-cell population and how these circuits change with age. Furthermore, we integrated our data with prior, pan-cell scRNA-seq studies to identify intercellular-signaling networks driving age-dependent changes in CD4+TM. Our atlas of finely resolved CD4+TM subsets, GRNs and cell-cell communication networks is a critical resource for analysis of biologic processes operative in memory T cells in youth and old age. The resource presents new opportunities to manipulate regulatory circuits in CD4+TM, which, long-term, could improve immune responses in the elderly.

overall_design: CD4+ memory T cells were harvested from spleens of young (≤4 months) and old (≥18 months) mice and subject to scRNA-seq, scATAC-seq, bulk RNA-seq, or bulk ATAC-seq.

first: Alexander

last: Katko

first: Maha

last: Almanan

first: Artem

last: Barski

first: David

last: Hildeman

first: Emily

last: Miraldi


title: An atlas of gene regulatory networks for T memory cells in youth and old age [ATAC-seq]


title: Regulation of transcriptional interference by the Swi/Snf complex [TL-seq]

first: Elçin

last: Ünal

overall_design: Samples were grown as described in Morse et al., 2023. Cells were collected from YPD media that was untreated or treated with 5 mM DTT in mid-log phase. TL-seq libaries were prepared using the methods and pipeline described in Tresenrider et al., 2022. Two biological replicates are included for each genotype. Wild-type samples (SWI3) from untreated and DTT-treated cells that were not treated with Cap-Clip pyrophosphatase are included as controls for inefficient phosphatase activity in the library construction.

first: Kaitlin

last: Morse

first: Sarah

last: Swerdlow


title: An atlas of gene regulatory networks for T memory cells in youth and old age

overall_design: Refer to individual Series


title: An intracellular phosphorus-starvation signal activates the PhoB/PhoR two-component system in Salmonella enterica

city: Hershey

first: Mauricio

middle: Henriques

last: Pontes

state: PA

address: 500 University Drive

department: Pathology

institute: Penn State University

summary: Bacteria acquire P primarily as inorganic orthophosphate (Pi, PO43-). Once internalized, Pi is rapidly assimilated into biomass during the synthesis of ATP. Because Pi is essential, but excessive ATP is toxic, the acquisition of environmental Pi is tightly regulated. In the bacterium Salmonella enterica (Salmonella), growth in Pi-limiting environments activates the membrane sensor histidine kinase PhoR, leading to the phosphorylation of its cognate transcriptional regulator PhoB and subsequent transcription of genes involved in adaptations to low Pi. Pi limitation is thought to promote PhoR kinase activity by altering the conformation of a membrane signaling complex comprised by PhoR, the multicomponent Pi transporter system PstSACB and the regulatory protein PhoU. The identity of the low Pi signal and how it controls PhoR activity remain unknown. Here we characterize the PhoB-dependent and independent transcriptional changes elicited by Salmonella in response to P starvation, and identify PhoB-independent genes that are required for the utilization of several organic-P sources. We use this knowledge to identify the cellular compartment where the PhoR signaling complex senses the low Pi signal. We demonstrate that the PhoB and PhoR signal transduction proteins can be maintained in an inactive state even when Salmonella is grown in media lacking Pi. Our results establish that PhoR activity is controlled by by an intracellular signal resulting from P insufficiency.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Salmonella enterica 14028s and its ΔphoB::Kn derivative during growth in medium containing phosphate (Pi) or lacking a phosphorus source (P)

first: Roberto

last: Bruna

first: Christopher

last: Kendra

middle: H


title: Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer.

city: Boston

first: Stefano

last: Monti

state: Massachusetts

address: 72 East Concord Street,

institute: Boston University Chobanian & Avedisian School of Medicine

summary: Head and neck cancers are a complex malignancy comprising multiple anatomical sites, with cancer of the oral cavity ranking among the deadliest and most disfiguring cancers globally. Oral cancer (OC) constitutes a subset of head and neck cancer cases, presenting primarily as tobacco- and alcohol-associated oral squamous cell carcinoma (OSCC), with a 5-year survival rate of ~65%, partly due to the lack of early detection and effective treatments. OSCC arises from premalignant lesions (PMLs) in the oral cavity through a multi-step series of clinical and histopathological stages, including varying degrees of epithelial dysplasia. To gain insights into the molecular mechanisms associated with the progression of PMLs to OSCC, we profiled the whole transcriptome of 66 human PMLs comprising leukoplakia with dysplasia and hyperkeratosis non-reactive (HkNR) pathologies, alongside healthy controls and OSCC. Our data revealed that PMLs were enriched in gene signatures associated with cellular plasticity, such as partial EMT (p-EMT) phenotypes, and with immune response. Integrated analyses of the host transcriptome and microbiome further highlighted a significant association between differential microbial abundance and PML pathway activity, suggesting a contribution of the oral microbiome towards PML evolution to OSCC. Collectively, this study reveals molecular processes associated with PML progression that may help early diagnosis and disease interception at an early stage.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for oral pre-malignant lesions and cancer.

first: Mohammed

last: Muzamil Khan


title: Gastruloid-derived Primordial Germ Cell-like Cells (Gld-PGCLCs) develop dynamically within integrated tissues

city: London

first: Naomi

last: Moris

address: 1 Midland Way

institute: Francis Crick Institute

summary: Primordial Germ Cells (PGCs) are a rare population of cells specified early in embryonic development that give rise to gametes - sperm and egg cells. Current in vitro systems to derive PGC-like cells (PGCLCs) from pluripotent cells use large embryoid bodies, exposed to signalling cocktails, that do not recapitulate the native embryonic environment during PGC formation. Here we show that mouse gastruloids, three-dimensional in vitro models of gastrulation, generate a population of Gastruloid-derived PGC-like cells (Gld-PGCLCs) that resemble early PGCs in vivo. Importantly, the conserved organisation of mouse gastruloids leads to coordinated spatial and temporal localisation of Gld-PGCLCs relative to surrounding somatic cells, even in the absence of exogenous PGC-specific signalling or extraembryonic tissues. In gastruloids, self-organised interactions between cells and tissues, including the endodermal epithelium, enables the specification, migration, and subsequent maturation of a pool of Gld-PGCLCs. As such, mouse gastruloids represent a new source of PGCLCs in vitro and, due to their inherent co-development, serve as a novel model of dynamic PGC development within integrated tissue environments.

overall_design: To characterise gastruloid-derived primordial germ cell-like cells (Gld-PGCLCs) we generated mouse gastruloids and sorted populations of putative PGCLCs at 120h for single cell RNA-sequencing

middle: B

last: Cooke

last: Barrington

first: Peter

last: Baillie-Benson

first: Jennifer

last: Nichols


title: Selective modulation of gene expression in activated normal human peripheral blood mononuclear cells by store-operated calcium entry blocker BTP2

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

summary: Calcium is a critical signaling molecule in many cell types including immune cells. The calcium-release activated calcium channels (CRAC) responsible for store-operated calcium entry (SOCE) in immune cells are gated by STIM family members functioning as sensors of Ca2+ store content in the endoplasmic reticulum. We investigated the effect of SOCE blocker BTP2 on human peripheral blood mononuclear cells (PBMC) stimulated with the mitogen phytohemagglutinin (PHA).

overall_design: To investigate the effect of SOCE blocker BTP2 on human peripheral blood mononuclear cells (PBMC) stimulated with the mitogen phytohemagglutinin (PHA), we performed RNA sequencing (RNA-seq) to query gene expression at the whole transcriptome level and identified genes differentially expressed between PBMC activated with PHA and PBMC activated with PHA in the presence of BTP2.

first: Divya

last: Shankaranarayanan

first: Madhav

last: Mantri

first: Manikkam

last: Suthanthiran


title: Type I IFN Signaling Drives Responsiveness to Short Course Radiotherapy in a Murine Model of Rectal Cancer

city: Rochester

first: Scott

last: Gerber

state: NY

address: 601 Elmwood Ave

department: Microbiology and Immunology

institute: University of Rochester

summary: Specific cell types from orthotopic murine rectal tumors were sequenced to explore the effect that short course radiotherapy has on the immune response.

overall_design: MC38-luc tumor cells were orthotopically implanted in the rectum of C57BL6 female mice. Tumors were irradiated using a small animal irradiator from days 9-13 post tumor implantation. Tumors were treated with 5Gy radiation therapy for 5 consecutive daily fractions. Some mice were treated with anti-IFNAR blocking antibody. Tumors were harvested on day 14 and individual cell populations includining CD8 T cells (CD45+ CD8+), cancer associated fibroblasts (CD45-, CD31- Podoplanin+, PDGFRa+, Ly6c+), and tumor cells (GFP+)  were sorted and processed for RNA sequencing.

first: Taylor

last: Uccello


title: Modeling, dissecting, and subtyping of E-cadherin inactivation-associated diffuse-type gastric adenocarcinoma

city: Houston

first: Gengyi

last: Zou

state: Texas

institute: MD Anderson

summary: Diffuse-type gastric adenocarcinoma (DGAC) is lethal cancer that is often diagnosed late and resistant to therapeutics. Although hereditary DGAC is mainly characterized by mutations in the CDH1 gene that encodes E-cadherin, the impact of E-cadherin inactivation in DGAC tumorigenesis remains unclear. To address this, we established and characterized a CDH1 loss-associated DGAC model system with a human DGAC single-cell transcriptome. We genetically engineered murine gastric organoids (GOs; Cdh1 KO, KrasG12D, Trp53 KO [EKP]) that recapitulates human DGAC tumorigenesis. Cdh1 depletion is sufficient to 1. Single-cell transcriptomics of human DGAC datasets classified patients into three subtypes (DGAC1, 2, and 3). By transcriptional signature, EKP GOs belong to the DGAC1 subtype displaying CDH1 downregulation and epithelial-mesenchymal transition. Compared to DGAC2 and DGAC3, the DGAC1 subtype was characterized by T cell exhaustion, PILRA-CD99 enrichment, and potential sensitivity to PD1 inhibitors. Additionally, we identified the EZH2-mediated transcriptional circuit as a key regulon specifically activated in EKP and a therapeutic vulnerability. This study unravels the unexpected role of E-cadherin loss in cell lineage plasticity, transcriptional reprogramming, and immune evasion of DGAC and further stratifies DGAC patients by single-cell transcriptomics, providing novel insights into E-cadherin loss-associated DGAC tumorigenesis.

overall_design: Organoids from WT, KP, and EKP were collected 7 days after seeding and digested with 0.05% trypsin-EDTA at 37 ℃ for 30 min. After inactivating trypsin with 10% FBS DMEM, single-cell suspension was collected by passing through the 35 μm cell strainer. cDNA library was prepared with the 10x Genomics 3’ v2 kit, cDNA library was sequenced on an Illumina NovaSeq (Novogene) and mapped to GRCm38/mm10 genome and demultiplexed using Cellranger.

first: Yuanjian

last: Huang

first: Shengzhe

last: Zhang

first: Kyung-Pil

last: Ko

first: Bong

last: Kim

first: Jie

first: Sohee

last: Jun

first: Jae-Il

last: Park


title: An atlas of gene regulatory networks for T memory cells in youth and old age [scATAC-seq]

first: Joseph

last: Wayman

first: Alyssa

last: Thomas

first: Maha

last: Almanan

first: David

last: Hildeman

first: Emily

last: Miraldi


title: An atlas of gene regulatory networks for T memory cells in youth and old age [scRNA-seq]


title: DUX

city: Salt Lake City

first: Brad

last: Cairns

state: Utah

address: 2000 Cicle of Hope

department: Oncological Sciences

institute: University of Utah

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


title: RNA-sequencing in mESCs with overexpression of mCherry-tagged DUX and DUX domain derivatives

summary:
To investigate the requirement of DUX domains for target gene expression, we created clonal stable cell lines in Dux-/- mouse embryonic stem cells and expressed constructs for 12 hours with 0.25 ug/mL doxycycline
We then performed gene expression profiling analysis using data obtained from RNA-seq of 11 different cell lines at one time point

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mCherry-tagged DUX and DUX domain derivative constructs in mESCs

first: Christina

last: Smith


title: CUT&Tag for DUX recruitment,domain-influenced chormatin modifications, and a potential binding partner with a member of the SWI/SNF complex

summary:
In order to determine that CUT&Tag is similar to known DUX ChIP-seq, we performed CUT&Tag with a mCherry-tagged DUX (with the mCherry antibody). Once confirmed, we pewrformed CUT&Tag for other DUX derivatives with their mCherry tag
Then, we performed CUT&Tag for H3K9ac, which is known to globally increase in 2-cell-like cells, which occurs after DUX expression, and CUT&Tag for SMARCC1, a subunit of the SWI/SNF complex

overall_design: CUT&Tag sequencing in mCherry-tagged DUX and DUX domain derivative constructs in mESCs after 12 hours of doxycycline induction


title: The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions

city: La Jolla

first: Christopher

last: Dalldorf

address: 9500 Gilman Dr

department: Bioengineering

institute: UCSD

summary: Fit phenotypes are achieved through optimal transcriptomic allocation. Here, we performed a high-resolution, multi-scale study of the transcriptomic tradeoff between two key fitness phenotypes, stress response (fear) and growth (greed), in Escherichia coli. We introduced 12 RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and found that single mutations could result in large shifts in this fear vs. greed tradeoff likely through destabilizing the rpoB-rpoC interface. RpoS and GAD regulons drive the fear response while ribosomal proteins and the ppGpp regulon underlie greed. Growth rate selection pressure during ALE results in endpoint strains that universally have RNAP mutations, with synergistic mutations reflective of particular conditions. A phylogenetic analysis found the tradeoff in numerous bacteria species and one archaea species. The results suggest that the tradeoff represents a general principle of transcriptome allocation in bacteria where small genetic changes can result in large phenotypic adaptations to growth conditions.

overall_design: RNA-sequencing of RNAP single mutation strains using Qiagen RNA-protect bacteria reagant, Zymo Rsearch Quick-RNA MicroPrep Kit and Kapa Biosystems RNA HyperPrep

first: Kevin

last: Rychel

first: Richard

last: Szubin

first: Ying

last: Hefner

first: Arjun

last: Patel

first: Daniel

last: Zielinski

first: Bernhard

last: Palsson


title: DUX domain-dependent chromatin accessibility of DUX binding sites

summary:
To determine whether DUX domain binding to SMARCC1 influence chromatin reodeling at DUX binding sites, we performed ATAC-seq
We know DUX binding sites are open at the time of expression, but we do not know which domains are required to be present with the discovery of the C-terminal repeats and 14 amino acid tail

overall_design: After 12 hour expression of mCherry-tagged DUX derivatives, 30 minutes of transposition usina commercial Tn5 was followed by library preparation


title: Loss of MC1R signaling implicates TBX3 in pheomelanogenesis and melanoma predisposition

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

summary: 501mel cells engineered to express ectopically doxycyclin inducible TBX3 3xHA-tagged. Cells were seeded and treated with doxcyclin to achive expression comparable to endogeneous TBX3. 15x 15-cm dish worth of cells were collected for each replicate of ChIP-seq experiments.

overall_design: 4 samples

first: Sizhu

last: Lu

first: Colin

last: Goding


title: Genome-wide occupancy of CNBP and SMARCC2 in neuroblastoma cells.

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

summary: Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through integrated proteomics and validating studies, we discovered that CNBP physically interacted with SMARCC2 in NB cells. To investigate the mechanisms underlying the functions of CNBP and SMARCC2, we employed the Illumina Novaseq 6000 as a discovery platform to analyze the genome-wide occupancy of CNBP and SMARCC2 on target genes in human IMR-32 cells, while the results were further analyzed with CNBP-regulated target genes. The results showed that CNBP repressed the enrichment of SMARCC2 on 124 target genes, especially those involved in ribosome biogenesis, including BYSL, NOP58, and RRP9. Furthermore, we validated the ChIP-seq results by real-time PCR with high identity. Overall, our results provided fundamental information about the genomic enrichment of CNBP and SMARCC2 in human NB cells, and these findings will help us understand the pathogenesis of NB.

overall_design: Examination of genome-wide occupancy of two different transcriptional regulators in neuroblastoma cells.

first: Liduan

last: Zheng


title: Mechanism for the modifier effect of RCAN1 in neurodegeneration of Huntington’s disease in patient-derived neurons [ATAC-Seq]

city: Saint Louis

first: Youngmi

last: Oh

state: MO

address: 660 S. Euclid Avenue

department: Development department

institute: Washington University in St. Louis

summary: Genome-wide association studies have identified Genetic Modifiers of HD (GeM-HD) comprised of polymorphic gene variants associated with accelerated or delayed onset of Huntington’s disease (HD). However, GeM-HD genes that contribute to neurodegeneration in HD remain underexplored. Here, we used medium spiny neurons (MSNs) directly reprogrammed from fibroblasts of symptomatic HD patients (HD-MSNs), which recapitulate adult-onset neurodegenerative pathology of HD, to uncover genes whose reduced function alleviated HD-associated neurodegeneration. We identified RCAN1 whose knockdown (KD) robustly mitigated mutant HTT toxicity. RCAN1 KD enhanced chromatin accessibility of genes involved in longevity and autophagy through promoting Calcineurin and TFEB function. We reveal that G2 compounds, analogs of glibenclamide with autophagy enhancer activities, can mimic the RCAN1 KD-mediated neuroprotection by reducing the RCAN1-Calcineurin interaction, thereby promoting dephosphorylation and nuclear localization of TFEB. Our results indicate RCAN1 as a potential therapeutic target whose perturbation can increase neuronal resilience against neurodegeneration in HD.

overall_design: To delineate cellular events underlying HD-MSN degeneration, we compared the transcriptomes of HD-MSNs (four independent patients), HD-MSNs with RCAN1 KD (four independent patients), and HD-MSNs with CaN KD (four independent samples) by ATAC-seq (all with triple biological replicates, 36 samples total).

first: Seong Won

last: Lee

first: Young Mi

first: Andrew

middle: S

last: Yoo


title: single-cell RNA-sequencing reaveals VSMC function in aortic disease

city: Guangzhou

first: Tingting

last: zhang

address: zhongshan 2rd road,72

institute: Sun Yat-sen University

summary: the regulation of gene expression in the  murine determines the development of aortic disease.

overall_design: matching samples from murine aortic tissues

last: Zhang

first: Jiaguo

last: Zhou

first: Qingqing

last: Lei

first: Jie

last: He


title: Transcriptome analysis of embryonic mesenchyme

city: Brussels

first: Lila

last: Gannoun

address: Avenue Hippocrate 75

department: Institut de Duve

institute: Université Catholique de Louvain

summary: Purpose:  The aim of this study is to study the expression and function of axon guidance genes in the developing portal tract. Here, the RNA-Sequencing data were collected from purified embryonic mesenchyme at two developmental stages (E16 and E18).

overall_design: Three samples of E16 mesenchyme and three samples of E18 mesenchyme were analyzed in this study.

first: Frédéric

middle: P

last: Lemaigre

first: Catalina

last: De Schrevel

first: Axelle

last: Loriot


title: Allelic chromatin structure primes imprinted expression of Kcnk9 during neurogenesis

city: Cambridge

first: Daniel

last: Loftus

address: 16 Divinity Ave, Rm 4004

department: MCB

institute: Harvard University

summary: Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brain from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we show that on the maternal allele, an enhancer-promoter contact formed early in development primes the brain-specific potassium leak channel Kcnk9 for maternal expression prior to neurogenesis. In contrast, this enhancer-promoter contact is blocked by CTCF on the paternal allele, preventing paternal Kcnk9 activation. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.

overall_design: Region capture Hi-C of the Peg13-Kcnk9 imprinted locus in mESCs, induced neurons (iNs), and mouse brain, in biological duplicate.

first: Bongmin

last: Bae

first: Courtney

last: Whilden

first: Amanda

last: Whipple


title: Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis [miRNA-Seq]

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

institute: Tsinghua University

summary: MicroRNAs (miRNAs) play an important role in gene regulation. In Arabidopsis thaliana, mature miRNAs are processed from primary miRNA transcripts by Dicing complex, which contains DCL1, SE and HYL1 and forms nuclear dicing bodies (D-bodies) through SE phase separation. Here we report that Cyclophilin 71 (CYP71), a peptidyl-prolyl isomerase (PPIase), positively regulates miRNA processing. We show that CYP71 directly interacts with SE and enhances its phase separation, thereby promoting the formation of D-body and increasing the activity of Dicing complex. We further show that the PPIase activity is important for the function of CYP71 in miRNA production. Our findings reveal orchestration of miRNA processing by a cyclophilin protein and suggest the involvement of proline cis-trans isomerization, a structural mechanism, in SE phase separation and miRNA processing.

overall_design: To evaluate the impact of  CYP71 mutations on miRNA and miRNA target gene expression profile, we performed small RNA-seq and mRNA-seq in triplicate using 2-week-old Col-0, cyp71-2, cyp71-3 seedlings.

first: Gaozhan

last: Zhao

first: Jinrong

last: Niu

first: Zhuoyan

last: Hai

first: Tengfei

last: Li

first: Yan


title: Single cell gene expression, immune receptor and cell surface marker expression profiling of Spike-specfic splenic T and B cells of immunized mice

first: Huitian

last: Diao

state: MA

address: 40 Erie Street, Suite 110

institute: BioNTech US Inc.

summary: Spike-specific T and B cells from splenocytes of immunized mice were profiled with 10x sequencing for gene expression (Chromium Next Automated GEM 5’ v2 kit), cell surface marker (Chromium Automated 5’ Feature Barcode kit) and immune receptor (Chromium Automated Mouse BCR/TCR Amplification and Library Construction kit)

overall_design:
Splenocytes from immunized mice were FACS sorted with fluorescently-labelled Spike protein tetramer or Spike pMHC tetramer for antigen specific T and B cells for 10x single cell profiling

Please note that the processed data files generated from both *GEX and *CITE samples are linked to the corresponding *GEX sample records.

first: Joy

last: Xie


title: MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT

city: New Haven

first: Rafael

middle: de Cesaris

last: Araujo Tavares

state: Connecticut

address: 260 Whitney Ave

department: Chemistry

institute: Yale University

summary: The study aimed to characterize the mutational signatures produced by MarathonRT upon reverse transcription of modified cellular RNAs and use the signatures of validated modified rRNAs as training data for machine learning algorithms. Performance of the resulting trained algorithms was evaluated on a series of test RNAs in order to establish a general workflow for detection of RNA modifications

sample_organism:
Escherichia coli
Saccharomyces cerevisiae
Homo sapiens

overall_design:
Total RNA sequenced from human, bacterial and yeast cells; Mg libraries = untreated samples; Mn libraries = modified samples
PolyA-enriched RNA amplified and sequenced from human cells

Please note that the processed data generated from both *_Mg and *_Mn samples is linked to the corresponding *_Mg sample records.

last: Tavares

first: Gandhar

last: Mahadeshwar

first: Han

last: Wan

first: Anna

last: Pyle


title: Combination CDC-like kinase inhibition (CLK) and taxane therapy in CTNNB1-mutated endometrial cancer

city: Denver

first: Benjamin

last: Bitler

state: CO

department: OB-GYN

institute: The University of Colorado

summary: SM08502 is a novel pan CDC-like kinase (CLK) inhibitor that targets mRNA splicing and is optimized for Wnt pathway inhibition.  Previous evaluation of single agent CLK inhibition (SM04690) demonstrated inhibition of tumor progression and b-catenin/TCF transcriptional activity in CTNNB1-mutant endometrial cancer (EC).  In-vitro analysis of SM08502 similarly decreases Wnt transcriptional activity and cellular proliferation while increasing cellular apoptosis.  Examining transcriptomic analysis, SM08502 increases pathways involved in RNA metabolism and spliceosome. Examining alternative splicing (AS) events, SM08502 increased differential splicing compared to treatment with paclitaxel.  AS regulation is an important post-transcriptional mechanism associated with the oncogenic process in many cancers, including EC.

overall_design:
Endometrial cancer cell lines were treated with the cell viability 50% inhibitory concentration (IC50) of Paclitaxel and SM08502 for 24 hrs. Ishikawa (Paclitaxel 11 nM; SM08502 80 nM); Ishikawa-S33Y (Paclitaxel 6 nM; SM08502 85 nM); SNGM (Paclitaxel 11.7 nM; SM08502 350.7 nM); HEC265 (Paclitaxel 5.6 nM; SM08502 149 nM). Differential gene expression and alternative splicing were measured.
Please note that processed files for splicing analysis (rMATS) are for comparisons of samples, and therefore each sample has several processed files that are also shared with other samples as indicated in the corresponding sample description field.

first: Bradley

last: Corr

middle: G

first: Thomas

last: Danhorn

first: Elizabeth

last: Woodruff

first: Zachary

last: Watson


title: Idiopathic subglottic stenosis arises at the interface of host and pathogen

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

summary: Cellular characterization of proximal airway scar in idiopathic subglottic stenosis

overall_design: 7 iSGS patients mucosal scar compared to 3 matched healthy  airway mucosal specimens

first: Alexander

last: Gelbard


title: PfAP2-P DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages (scRNA-seq)

city: Thuwal

first: AMIT

last: SUBUDHI

address: Level4, Builiding, 2, KAUST

institute: King Abdullah University of Science and Technology

summary: Malarial parasite pathogenicity results from its ability to invade and remodel red blood cells (RBCs), expressing antigenic variant proteins for immune evasion and survival, and then to egress from the host cell. These sequential processes require concerted actions of a large number of proteins during the intraerythrocytic developmental cycle (IDC), but the molecular basis of the required regulation is only partially understood. Here, we have characterized an essential Apicomplexan AP2 (ApiAP2) transcription factor (we refer to it as PfAP2-P; Pathogenesis) that shows two peaks of expression during the IDC at 16- and 40-hour post invasion (h.p.i.). When expression of PfAP2-P at 40 h.p.i. was disrupted using an inducible gene knockout approach, ∆PfAP2-P parasites unable to form mature merozoites and egress from the host RBCs owing to strong down-regulation of several known egress- and invasion-associated genes, in addition to several novel hypothetical genes of thought to be involved in these key life cycle processes during the IDC. Disruption of PfAP2-P expression at 16 h.p.i. results in transcriptional activation of virtually majority of silenced var genes observed at both bulk and single cell level. This is also reflected by significantly higher level of recognition of the exported proteins on the ∆PfAP2-P parasite-infected RBCs by pooled sera from malaria-exposed individuals from endemic region. In addition, over-expression of many early gametocyte marker genes was also observed in ∆PfAP2-P parasites at both 40 h.p.i., and at 16 h.p.i. PfAP2-P directly regulates these genes by binding to their promoter region or indirectly through 14 other down-stream AP2 transcription factors. Taken together, we conclude that PfAP2-P is an upstream transcriptional regulator that participates in mutually exclusive expression pattern shown by the var family of genes and a critical determinant of parasite’s growth during the IDC.

overall_design: Single-cell RNA-seq was conducted on parasites from two stages i.e. 16 h.p.i. and 40 h.p.i. Conditional knockout of PfAP2-P was carried out by adding 10nM of Rapamycin to the culture and as a control same volume of DMSO was added to the culture. For 40 h.p.i. parasites, DMSO (control) or Rapamycin (to induce PfAP2-P knockout) was added to culture at 16 h.p.i. in the same cycle of sample collection. For 16 h.p.i. parasites, DMSO (control) or Rapamycin (to induce PfAP2-MRP knockout) was added to cultures at 35 h.p.i. in cycle 0 and parasites were collected at 16 h.p.i. in cycle 1.

first: Amit

last: Subudhi

first: Rohit

last: Satyam

first: Luke

last: Esau

first: Ishaan

last: Gupta

first: Arnab

last: Pain


title: PfAP2-P DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages

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

overall_design: Refer to individual Series


title: PfAP2-P DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages (RNA-seq)

overall_design: RNAseq was performed on control (DMSO +) and △PfAP2-P (Rapamycin +) parasites collected at 16 hour post-invasion and 40 housr post invasion. For each time point 3 biological replicates were used giving a total of 6 samples per time point.

first: Subudhi

last: Kumar

first: Green

last: Judith

first: Holder

last: Tony

first: Pain

last: Arnab


title: PfAP2-P DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages (ChIP-Seq I)

overall_design: Chip was performed on AP2-P HA tagged parasites at 40 hour post invasion and 16 hour post invasion using anti-rat HA antibodies (3F10 clone). There are two biological replicates for each developmental stages. The input and the IgG antibodies based immunoprecipitaion served as the control.

middle: K

first: Yogesh

last: Otswal

first: Steven

last: Abel

first: Wolfgang

last: Fischle

first: Karine

last: Leroch


title: Expression profiles of circular RNA in A549 cells infected by Influenza virus

city: hangzhou

first: Hu

last: boli

state: zhejiang

address: Yuhangtang Road No.866

institute: Zijingang Campus of Zhejiang University

summary: Circular RNAs (circRNAs) participate in regulating many biological processes. However, their roles in influenza A virus (IAV) pathogenicity are largely unknown. Here, we analyzed the expression profile of circRNAs  in the H1N1-infected cells by high-throughput sequencing

overall_design: Expression profiles of circRNAs in A549 cells infected by A/Puerto Rico/8/34 (H1N1)  were generated by deep sequencing,in triplicate, using Illumina Hiseq 3000.

first: Tianqi

last: Yu

first: Zixiao

last: Zhang

first: Boli

last: Hu

first: Jinyan

last: Gu

first: Jiyong

last: Zhou


title: Transcriptomes of Wild Type tomato and slstop1 under -Al/+Al treatment

city: Beijing

first: lei

last: zhang

address: Yuanmingyuan West Rd. No.2, Beijing, China

department: College of Horticulture

institute: China Agricultural University

summary:
Purpose: Find SlSTOP1 regulated genes
Methods: Total RNA was extracted from 20 days old wild-type tomato and slstop1 mutant plants treated with 0 and 60 μM Al solutions (pH 4.7). Three biological replicated samples were collected form each treatment and sequenced.
Results:A total of 83.7 GB clean data was obtained by transcriptome sequencing. The clean data of each sample was more than 6.30 GB, and the percentage of q30 base was more than 93.82%.
Conclusions: By RNA-seq analysis, we find potential SlSTOP1-regulated genes

overall_design: mRNA profiles of 20-day old wild type (WT) and slstop1 mutant.

first: Lei

first: Ruyue

last: Bai

first: Yang-Dong

last: Guo


title: Gene-expression profiling in pancreatic cancer cells treated with macrophage conditioned media and etomoxir

city: Zaragoza

first: Patricia

last: Sancho

state: Aragón

address: P. Isabel la Católica 1-3

department: Traslational Research Unit

institute: Hospital Miguel Servet IIS Aragón

summary: The study aims to show that a metabolic shift is a precondition for the initiation of an invasive/metastatic program in pancreatic cancer. Paracrine cues and metabolic stress (mimicked in vitro by treatment with macrophage-conditioned media and low dose etomoxir) regularly found in the metastasis-promoting tumor stroma consistently induced transcriptional changes resulting in the acquisition of migratory and invasive abilities.

overall_design: Samples from primary cultures corresponding to 3 different patient-derived xenografts either untreated (CONT, used as reference for each Pdx) or treated for 48h with macrophage conditioned media (MCM) or low-dose etomoxir (ETO), in duplicate.

first: Beatriz

last: Parejo-Alonso

first: Meng-Lay

last: Lin

first: Christopher

last: Heeschen


title: TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes [ATAC-seq]

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

institute: University of Pennsylvania

summary:
Purpose: To characterize epigenomic heterogeneity in GSI-responsive and -resistant T-ALL cells
Method: We generated GSI-resistant T-ALL DND41 cells and profiled their epigenome using single-cell RNA sequencing.
Result: We report here the presence of resistant-like subpopulation in drug naïve DND41 T-ALL cells.
Conclusion: While other popular scRNA-seq clustering algorithms failed, TooManyPeaks, a suite of clustering and visualization algorithm developed in our lab, could identify rare resistant-like DND41 T-ALL cells.

overall_design: Single-cell ATAC-seq was performed on cells acquiring resistance to a gamma secretase inhibitor (GSI) after long-term treatment of Notch-mutated T-cell acute lymphoblastic leukemia (T-ALL) DND41 cells.

first: Yeqiao


title: TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes [ChIP-seq]

summary:
Purpose: To investigate the impact of GSI resistance on epigenome of Notch-mutated T-ALL
Methods: We generated scATAC-seq and H3K27ac ChIP-seq in parental and GSI-resistant cells
Results: Using TooManyPeaks, a novel algorithm for scATAC-seq analysis, we identified subpopulation of epigenetically resistant-like parental cell.

overall_design: ChIP-seq of H3K27ac was used to characterize enhancer activity in parental and resistant NOTCH1-mutated T-ALL DND-41 cells


title: RNA-Seq and ChIP-Seq analysis of genes involved in regulation of BFU-E self-renewal

city: Cold Spring Harbor

first: Lingbo

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: RNA-Seq was utilized to monitor changes of gene expression profile of BFU-E cultured with DMSO, compound OB or PD; ChIP-Seq was utilized to identify binding sites of CREB in BFU-E

overall_design: BFU-E cultured with DMSO, compound OB or PD; examination of CREB binding in BFU-E

first: Gaurang

last: Trivedi


title: CRSPR/Cas9 gene knockout screen identifies colorectal cancer dependency on cryptic open reading frames

status: Public on Aug 06 2023

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street,  Unit 1410

department: Bioinformatics & Comp Biology

institute: UT MD Anderson Cancer Center

summary: Emerging evidence suggests that the cryptic translation beyond the annotated translatome may yield proteins with important function. However, the role and function mechanism of these cryptic ORFs in complex diseases such as cancer remain largely unknown. To fill this gap, we combined  ribosome profiling and CRISPR/Cas9 screen to systematically identify the colorectal cancer (CRC) dependency on cryptic ORFs.

overall_design: CRISPR/Cas9 knockout screen and ribosome profiling to systematically discover nocanonical open reading frame encoded in long noncoding RNAs (lncRNAs) and explored their critical roles in colorectal cancer progression. RNA-Seq analysis the differernt expressed genes after SMMIP kockout or SMC1A knockdown. ChIP-Seq analysis SMC1A binding sites on genome.

first: Caishang

last: Zheng

first: Yanjun

last: Wei


title: Neuronal γ-secretase regulates lipid metabolism, linking cholesterol to synaptic dysfunction in Alzheimer's disease

city: Stanford

first: Sofia

last: Essayan-Perez

state: CA

address: 265 Campus Drive

department: Molecular and Cellular Physiology

institute: Stanford University

summary: Presenilin mutations that alter γ-secretase activity cause familial Alzheimer's disease (AD), whereas ApoE4, an apolipoprotein for cholesterol transport, predisposes to sporadic AD. Both sporadic and familial AD feature synaptic dysfunction. Whether γ-secretase is involved in cholesterol metabolism and whether such involvement impacts synaptic function remains unknown. Here, we show that in human neurons, chronic pharmacological or genetic suppression of γ-secretase increases synapse numbers but decreases synaptic transmission by lowering the presynaptic release probability without altering dendritic or axonal arborizations. In search of a mechanism underlying these synaptic impairments, we discovered that chronic γ-secretase suppression robustly decreases cholesterol levels in neurons but not in glia, which in turn stimulates neuron-specific cholesterol-synthesis gene expression. Suppression of cholesterol levels by HMG-CoA reductase inhibitors (statins) impaired synaptic function similar to γ-secretase inhibition. Thus, γ-secretase enables synaptic function by maintaining cholesterol levels, whereas the chronic suppression of γ-secretase impairs synapses by lowering cholesterol levels.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Differential gene expression analysis of bulk RNA-seq data for human iN cells (generated by Ngn2 overexpression) and mouse glia treated with the gamma-secretase inhibitors DAPT (40 µM) or LY411575 (2.5 µM), relative to DMSO-treated controls (0.5%).

first: Thomas

middle: C

last: Südhof


title: Effect of LL-2 conditional medium on bone marrow-derived macrophages

city: Chengdu

first: Ziqi

last: Zhang

state: Sichuan

address: No. 17, Block 3, Southern Renmin Road

department: National Clinical Research Center for Geriatrics,

institute: West China Hospital, Sichuan University

summary: To investigate the effect on LL-2 conditional medium on bone marrow-derived macrophages, equal volum of LL-2 conditional medium and fresh RPMI 1640 was used to culture bone marrow-derived macrophages for 24 hours. The cells were then lysed for RNA-seq.

overall_design: Primary bone marrow-derived macrophages in 6 wells were divided into two group. Three wells were added with RPMI 1640 medium, while the other three wells were added with equal volum of LL-2 conditional medium and RPMI 1640 medium. Twenty four hours later, the cells were lysed for RNA-seq.

first: Yuexin

first: Xiuyue


title: Extrachromosomal circular SUZ12 amplicon dictates retinoblastoma progression through reprogramming H3K27 methylation [CUT&Tag]

status: Public on Aug 05 2023

city: Shanghai

first: Ludi

last: Yang

state: Shanghai

address: ZhiZaoju road，833，Shanghai, China

institute: Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine

summary: Extrachromosomal circular DNA (eccDNA) is double-stranded circular DNA that is derived from but independent of chromosomal DNA. Owing to its nonchromosomal inheritance, eccDNA facilitates the amplification of oncogenes and expedites the process of genome evolution in tumor. However, the role of eccDNA in RB remains enigmatic. Herein, we identified a set of SUZ12-containing eccDNAs in RB. Through multiomics analyses, we demonstrated that SUZ12 contributes to elevated levels of H3K27me3 modification and subsequently inhibits the transcription of KLF4 during the oncogenic progression of retinoblastoma. Conclusively, our study unveiled a novel SUZ12-containing eccDNA/H3K27me3 oncogenic mechanism where eccDNA dictates retinoblastoma progression through regulating transcription levels of linear DNA.

overall_design: Knockdown of SUZ12 in retinoblastoma cells affects its H3K27me3 modification

first: Peiwei

last: Chai

first: Xianqun

last: Fan