title: The FISHGASTRO study:  gene expression profiles in human colonic biopsies following a 6 month fish intervention

first: Guido

last: Hooiveld

summary:
Gene expression profiles in human colonic biopsies following a 6 month fish intervention highlights the importance of interactions between diet and mucosal immunoregulation: the FISHGASTRO study.
Data from population based studies indicate a strong association between risk of colon cancer and lifestyle, including diet. There is an increasing body of evidence to suggest that high fish intake may be protective. N-3 polyunsaturated fatty acids, highly abundant in oily fish such as salmon, have been the focus of attention and several molecular mechanisms have been proposed to explain their anti-neoplastic activity. Other nutrients such as vitamin D and selenium (also found in lean fish) are well recognised as protective agents against many cancers, including colon cancer. The FISHGASTRO human intervention study was carried out to assess the impact of two types of fish, salmon and cod, on already established markers of gastrointestinal health and to search for novel biomarkers of cancer risk based on post-genomic technology.

Keywords: Expression profiling by array

overall_design: In a parallel controlled feeding trial, colon samples were collected from apparently healthy human subjects at baseline and after 6 months consumption of either extra cod or salmon (both: 300g per week), which was given in addition to their regular diet. Biopsies were put immediately into RNAlater (Qiagen), and total RNA was isolated from the samples using the RNeasy Plus Mini kit (Qiagen). Total RNA (350 ng) was was labeled using a one-cycle cDNA labeling kit (MessageAmpTM II-Biotin Enhanced Kit, Ambion, Inc.) and hybridized to Affymetrix NuGO_Hs1a52018 arrays.

first: Gosia

last: Majsak-Newman

first: Gerda

middle: K

last: Pot

last: Seers

first: Joanne

middle: F

last: Doleman

first: Linda

last: Harvey

first: Anouk

last: Geelen

first: Ellen

last: Kampman

first: Elizabeth

last: Lund


title: NiV and HeV virus like particles (VLPs) were used on HEK293T cells to determine transcriptomics profile

status: Public on Feb 01 2025

city: ITHACA

first: Hector

last: Aguilar-Carreno

state: New York

address: T8016A Veterinary Research Tower

department: Microbiology and Immunology

country: USA

institute: Cornell University

summary: To delineate cellular processes involved in NiV and HeV VLPs, we have employed whole genome microarray expression profiling as a discovery platform to identify the upregulated and downregulated genes. Total RNA was collected from transfected cells and untransfected controls. Cy3 labeled cRNA is used for hybridization platform Agilent Human 4 x 44K gene expression array.

overall_design: Time-course based transfections were performed at 2h and 19h post-incubation time-points. These VLP treated cells were compared to untreated HEK293T cells. Five replicates were performed for each condition.

middle: C

last: Aguilar

first: Joshua

middle: N

last: Adkins


title: Long-term maintenanance of patient-specific characteristics in tumoroids from six cancer indications

status: Public on Jan 31 2025

city: Frederick

first: Pradip

last: Shahi Thakuri

state: Maryland

address: 7305 Executive Way

department: Cell Biology

institute: Thermo Fisher Scientific

type: Expression profiling by high throughput sequencing

summary: Tumoroids, sometimes referred to as cancer organoids, are patient-derived cancer cells grown as 3D, self-organized multicellular structures that maintain key characteristics (e.g., genotype, gene expression levels) of the tumors from which they originated. These models have emerged as valuable tools for studying tumor biology, cytotoxicity, and the response of patient-derived cells to cancer therapies. However, the establishment and maintenance of tumoroids have historically been challenging, labor-intensive, and highly variable from lab to lab, hindering their widespread use. Here, we established patient-derived colorectal cancer tumoroid lines in OncoPro Tumoroid Culture Medium and performed RNA profiling of single cells from primary dissociated tumors and the corresponding tumoroids to compare the transcriptomic concordance in primary and OncoPro-derived samples.

overall_design: Dissociated tumor cells obtained from Discovery Life Sciences (DLS) and tumoroid lines at different passages after culture in OncoPro Tumoroid Culture Medium were used for single cell RNA sequencing experiments.

first: Colin

last: Paul

first: Chris

last: Yankaskas

first: Brittany

last: Balhouse

first: Shyanne

last: Salen

first: Amber

last: Bullock

first: Sylvia

last: Beam

first: Anthony

last: Chatman

first: Sybelle

last: Djikeng

first: Xiaoyu Jenny

last: Yang

first: Garrett

last: Wong

first: Isha

last: Dey

first: Spencer

last: Holmes

first: Abigail

last: Dockey

first: Lindsay

last: Bailey-Steinitz

first: Lina

last: Zheng

first: Weizhong

last: Li

first: Vivek

last: Chandra

first: Jakhan

last: Nguyen

first: Jason

last: Sharp

first: Erik

last: Willems

first: Mark

last: Kennedy

first: Matthew

last: Dallas

first: David

last: Kuninger


title: EWS-FLI1 in embryonic hMSCs induces DNA damage and Ewing sarcoma tumorigenesis [ChIP-seq]

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Ewing sarcoma (ES) is an aggressive bone and soft tissue neoplasm, unique to humans, characterized by EWSR1/ETS rearrangements and whose cellular origin remains unclear. Expression of EWS-FLI1 in pediatric human mesenchymal stem cells (hMSCs) induced a transcriptional profile more resembling ES than its expression in adult hMSCs, but did not confer tumorigenic capacity. We have isolated human mesenchymal stem-like cells (hMSLCs) from experimental human embryonic stem cell (hESC)-derived teratomas. EWS-FLI1 expression in hMSLCs results in the acquisition of an ES signature through its preferential binding to microsatellites of intergenic and intronic regions. In hMSLCs, EWS-FLI1 directly regulates BRCA1 expression, although oncogene-expressing cells show defects in DNA damage repair (DDR). Xenografting in mice of EWS-FLI1-transduced hMSLCs resulted in the formation of tumors expressing characteristic ES markers. In summary, EWS-FLI1 enforces an aberrant transcriptome and endows in vivo transforming capacity when expressed in an undifferentiated early embryonic hMSC. Our approach represents an innovative experimental method for understanding critical aspects of the biology of developmental tumors, from leukemia to sarcomas, in which few (even single) genetic alterations are able to transform a fetal stem cell.

overall_design: human Mesenchymal Stem Like Cells (hMSLCs) line 1 was infected with flag-tagged EWS-FLI1 or with control lentivirus

first: Hernández-Muñoz

last: Inmaculada


title: cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [Bulk RNA-seq]

city: Pittsburgh

first: Michael

last: Tsang

state: PA

address: 3501 Fifth Ave. BST3-5062

institute: University of Pittsburgh

summary: Cardiac regeneration involves interplay of complex interactions between many different cell types, including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress-response, myofibril assembly, proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this, we determined that cited4a, a p300/CBP transcriptional co-activator, is induced after injury in mature cardiomyocyte population. Moreover, loss-of-cited4a mutants showed increased dedifferentiation, proliferation and accelerated heart regeneration. Thus, suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration.

overall_design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 days post amputation (dpa). Total RNA was extracted from ventricles was used for RNA-seq experiments.

first: Rachel

last: Forman-Rubinksky


title: Corticosteroid premedication and the antitumor effect of immune checkpoint blockade in murine hepatocellular carcinoma models

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: This study aims to investigate whether corticosteroid premedication may compromise antitumor efficacy of dual immune checkpoint inhibitors (anti-PD-1 + anti-CTLA4), a regimen that may cause significant irAEs.

overall_design: We profiled the immune-related genes from hepatocellular carcinoma mouse model.

first: Ying-Chun

last: Shen

first: Ann-Lii

last: Cheng


title: EWS-FLI1 in embryonic hMSCs induces DNA damage and Ewing sarcoma tumorigenesis [Spatial_transcriptomics]

overall_design: Two different samples from mice inoculated with human mesenchymal stem cells infected with EWS-FLI1, one of which corresponded to a soft mass in the abdominal cavity and the other to a lung metastasis, were analyzed by spatial transcriptomics.


title: EWS-FLI1 Expression in Human Embryonic Mesenchymal Stem Cells Leads to Defective DNA Damage Repair and Ewing Sarcoma

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

overall_design: Refer to individual Series


title: Single cell gene expression from the kidneys of calcium oxalate (CaOx) nephrocalcinosis mice model.

city: Wuhan

first: Chen

last: Duan

address: Donghu Road 169

country: China

institute: Zhongnan hospital of Wuhan University

summary: We used single cell RNA sequencing (scRNA-seq) to identify changes in cellular compositions and their transcriptomic expressions in kidney tissues of calcium oxalate (CaOx) nephrocalcinosis mouse model and normal mouse kidney tissues.

overall_design: Male C57BL/6 J mice aged 6 to 8 weeks were used in this experiment. To establish the mouse model of CaOx nephrocalcinosis, mice were treated with GLY (100 mg/kg/d) by intraperitoneal injection for 7 days. Single cell suspensions from kidneys of these mice were used for analysis.

first: Haoran

last: Liu

first: Xiangyang

last: Yao

first: Bo

first: Hua

last: Xu


title: CREB regulates Th17 cell development and function.

city: San Diego

first: Ezra

last: Wiater

state: CA

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

summary: Forskolin treatment upregulates several genes involved in Th17 development and function

overall_design: Following 4 days of Th17 cell differentiation, cells were treated with forskolin or vehicle for 1 hour

first: Jeniffer

last: Hernandez

first: Marc

last: Montminy


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

city: St. Louis

first: Mati

middle: Tesfaye

last: Nemera

state: Missouri

address: 660 S Euclid Ave

department: Neuroscience

institute: Washington University in St. Louis School of Medicine

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

overall_design: MERFISH

first: James

middle: R

last: Moore

middle: T

first: Rinaldo

middle: D

last: D'Souza

first: Nicole

last: Hamagami

first: Adam

middle: W

last: Clemens

first: Diana

last: Beard

first: Alaina

last: Urman

first: Victoria

last: Mendoza

first: Yasmin

last: Razia

first: Travis

last: Law

first: John

last: Edwards

first: Harrison

last: Gabel


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

overall_design: INTACT-isolated cortical and PV nuclei were profiled by ChIP-seq.


title: Transcriptome-wide RNA and genome-wide DNA G-Quadruplex mediates alternative transcripts

city: Guangzhou

first: Huichuan

last: Yu

state: Guangdong

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

summary: We demonstrate that G4-DNA and G4-RNA may present splicing sites and alternative transcription starting positions on a transcriptome-wide and genome-wide scale by showing widespread effect on alternative transcripts in response to the established intracellular G4 binding ligands PDS.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Examination of transcripts following PDS treatment in HCT116 and rat NP cells.

first: Xiaolin

last: Wang

first: Yanxin

last: Luo


title: Effects of gene expression changes by Ephexin1 deficiency in HCT116 cells

city: Gwangju

first: Jeeho

last: Kim

address: Biotechnology Bldg. Rm210 309 Pilmundaero, Dong-gu

country: South Korea

institute: Chosun Univ.

summary:
To investigate Ephexin1-induced gene changes in colon cells, we established HCT116 cell line knocked down by Ephexin1-shRNA.
We then performed gene expression profiling analysis using the data obtained from RNA-seq of shControl and shEphexin1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for shControl and shEphexin1 in HCT116 cells.

first: Hojin

last: You


title: HoxBlinc lncRNA reprograms CTCF-independent TADs to drive leukemic transcription and HSC dysregulation in NUP98 fusion transformed leukemia

city: Hershey

first: Suming

last: Huang

address: 500 University Dr.

department: Pediatrics

institute: Penn State College of Medicine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


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

first: Mati

last: Nemera

platform_organism:
Mus musculus
synthetic construct


title: Transcriptomics insight into the metabolism of the toxic producing Microcystis aeruginosa

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur


title: Single-nuclei RNA sequencing of the locus coeruleus and pericoerulear brain regions

city: Seattle

first: Li

last: Li

state: WA

address: 1959 NE Pacific St J181-Health Sciences

department: Anesthesiology & Pain Medicine

institute: University of Washington

summary:
As the primary source of norepinephrine (NE) in the brain, the locus coeruleus (LC) regulates both arousal and stress responses, but how neuromodulatory inputs contribute to LC modulation remains incompletely understood. In this study, we isolated a network of transcriptionally diverse inhibitory pericoerulear (peri-LC) GABAergic neurons that integrate distant stimuli and modulate modes of LC firing. To define the peri-LC anatomy, we used viral tracing, single-nuclei and high-resolution spatial RNA transcriptomics to molecularly characterize both LC and peri-LC cell types. We complemented this approach with techniques in electrophysiology, photometry, optogenetics, and chemogenetics to probe the function of peri-LC neurons in behaving mice. These findings indicate that LC and peri-LC neurons comprise transcriptionally heterogenous neuronal groups which integrate diverse inputs to influence behavioral arousal states and avoidance.
We used snRNAseq to characterize the peri-LC and LC brain regions. Our dataset contains 30,838 cells, of which 12,278 are neurons.

overall_design: We microdissect the LC and peri-LC brain regions in wild type adult male and female mice, dissociated the nuclei, captured single nuclei transcriptomes via Chromium technology developed by 10X Genomics, and generated cDNA for sequencing.

first: Luskin

last: Andrew

first: Bruchas

last: Michael


title: Sex dimorphism in the bone marrow niche regulates hematopoietic engraftment via sexspecific Kdm5c-Cxcl12 signaling

status: Public on Jan 30 2025

city: San Antonio

first: Pinpin

last: Sui

state: TX

address: 8403 Floyd Curl Dr., STRF

department: Molecular Medicine

institute: UT health San Antonio

summary: The bone marrow (BM) niche is critical in regulating hematopoiesis, and sexual dimorphism in hematopoiesis and immunocompetence is observed in both mice and humans. Beyond hormonal influences, the mechanisms underlying sexual differences in the BM niche and their impact on hematopoiesis are not well understood. Here, we show that male mice exhibit a higher abundance of leptin-receptor-expressing mesenchymal stromal cells (LepR-MSCs) compared to female mice. Through sex-mismatched co-culture and BM transplantation experiments, we find that the male BM niche provides superior support for in vitro colony formation and in vivo hematopoietic engraftment. Notably, the co-transplantation of male stromal cells significantly enhances engraftment in female recipients. Single-cell RNA sequencing reveals sex-specific differences in cellular composition and gene expression profiles within BM stromal cells, with MSCs being the predominant population, particularly in the male BM stroma. Mechanistically, we identify lower expression of the X-linked lysine H3K4 demethylase, Kdm5c, in male MSCs, leading to increased levels of Cxcl12. In a mouse model with MSC-specific Kdm5c knockout, the reduction of Kdm5c in female MSCs enhances MSC quantity and function, ultimately improving engraftment to the male level. This suggests that Kdm5c may play a role in driving sexual dimorphism in the BM niche and hematopoietic regeneration. Our study unveils a sex-dependent mechanism governing BM niche regulation and its impact on hematopoietic engraftment. The finding offers potential implications for enhancing BM transplantation efficacy in clinical settings by harnessing the resource of male MSCs or targeting Kdm5c.

overall_design: Single cell RNA sequencing for bone marrow stromal cells from male and female mice.

first: Ying

last: Liang

first: Xiaojing

last: Cui

first: Bowen

last: Yan


title: ZBTB24 is a conserved multifaceted transcription factor at genes and centromeres that governs the DNA methylation state and expression of satellite repeats [RNA-Seq]

first: Guillaume

last: Velasco

address: 35 rue Hélène Brion

department: UMR7216 Epigenetics and Cell Fate

institute: Université Paris Cité

summary: ZBTB24 has emerged as a key player in DNA methylation, immunity and development. To explore these multiple facets of ZBTB24 functions, we performed and integrated multi-omics  analyses in mouse and human cellular systems relevant  for the physiopathological features of the ICF2 syndrome, a rare genetic disease caused by ZBTB24 mutations.

overall_design: We compared trancriptomic profiles by RNA-seq in human and mouse cells wild-type or mutant for ZBTB24. For mESCs, the study was conducted during the mESCs cell-state transition : in mESCs maintained in 2i conditions (2i) and after 3 days of differentiation (d3).

first: Velasco

last: Guillaume

first: Grillo

last: Giacomo


title: ZBTB24 is a conserved multifaceted transcription factor at genes and centromeres that governs the DNA methylation state and expression of satellite repeats [RRBS]

type: Methylation profiling by high throughput sequencing

summary: ZBTB24 has emerged as a key player in DNA methylation, immunity and development. To explore these multiple facets of ZBTB24 functions, we performed and integrated multi-omics  analyses in mouse and human cellular systems relevant for the physiopathological features of the ICF2 syndrome, a rare genetic disease caused by ZBTB24 mutations.

overall_design: DNA methylation profiles were performed and compared by Reduced representation bisulfite sequencing (RRBS) in mESCs cells wild-type or mutant for ZBTB24. The study was conducted during the mESCs cell-state transition : in mESCs maintained in 2i conditions (2i) and after 3 days of differentiation (d3).

first: Dahlet

last: Thomas

first: Dumas

first: Weber


title: Transcriptome profile of EZR_KO cells

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: To analyze gene expression differences between cells EZR_KO cells compared to wt MEF cells

overall_design: Total RNA was extracted from n=4 for each conditions.


title: ZBTB24 is a conserved multifaceted transcription factor at genes and centromeres that governs the DNA methylation state and expression of satellite repeats [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ZBTB2 protein in human and mouse cells wild-type. For mESCs, the study was conducted during the mESCs cell-state transition : in mESCs maintained in 2i conditions (2i) and after 3 days of differentiation (d3).


title: ZBTB24 is a conserved multifaceted transcription factor at genes and centromeres that governs the DNA methylation state and expression of satellite repeats


title: CpG island methylator phenotype classification improves risk assessment in pediatric T-cell Acute Lymphoblastic Leukemia [methylation array]

status: Public on Jan 29 2025

city: Umeå

first: Sofie

last: Degerman

state: Sweden

address: NUS, Blg 6M, 2nd floor

department: Medical Biosciensces

country: Sweden

institute: Umeå University

type: Methylation profiling by genome tiling array

summary: Current intensive treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has substantial side-effects, highlighting a need for novel biomarkers to improve risk stratification. Canonical biomarkers such as genetics and immunophenotype are largely not used in pediatric T-ALL stratification. This study aimed to validate the prognostic relevance of DNA methylation CpG island methylator phenotype (CIMP) risk stratification in two pediatric T-ALL patient cohorts: the Nordic NOPHO ALL2008 T-ALL study cohort (n=192) and the Dutch DCOG ALL-10/ALL-11 validation cohorts (n=156). Both cohorts showed that combining CIMP classification at diagnosis with measurable residual disease (MRD) at treatment day 29 or 33 significantly improved outcome prediction. The poor prognosis subgroup, characterized by CIMP low/D29 or D33 MRD≥0.1%, showed a cumulative incidence of relapse (pCIR5yr) of 29.0% and 23%, and overall survival (pOS5yr) of 59.7% and 65.4%, in NOPHO and DCOG, respectively. Conversely, a good prognosis subgroup was also identified representing CIMP high/D29 or D33 MRD<0.1% with pCIR5yr of 0% and 3.4%, and pOS5yr of 98.2% and 94.8%, in NOPHO and DCOG, respectively. For NOPHO, MRD was also evaluated on D15, and the relapse prediction accuracy of CIMP/D29 MRD (0.79) and CIMP/D15 MRD (0.75) classification was comparable, indicating potential for earlier stratification. The evaluation of the biology behind the CIMP subgroups revealed associations with transcriptome profiles, genomic aberrations, and mitotic history, suggesting distinct routes for leukemia development. In conclusion, integrating MRD assessment with the novel CIMP biomarker has the potential to improve risk stratification in pediatric T-ALL and guide future therapeutic decisions.

overall_design:
DNA methylation profiling of primary pediatric (> 1-year-old and < 18-years-old) T-ALL samples taken at diagnosis (n = 128), and cell-sorted CD34+ and CD3+ cells and a fresh frozen lymph node as control samples (n = 3), analyzed on Illumina EPIC v1.0 DNA methylation arrays (Illumina, CA, USA). T-ALL samples analyzed by Illumina 450K DNA methylation arrays (Illumina, CA, USA) (n = 64) are available in GSE69954 (GSM1713872 T-ALL Sample 85 was excluded due to mislabeling). For the validation DCOG cohort, n = 156 samples (≥1 and <18 years-old) stored in the Princess Máxima biobank were analyzed using Illumina EPICv.2.0 arrays (Illumina, CA, USA).
***Submitters state that raw *.idat files will not be submitted to a repository because the patients providing the samples were not consented for raw data deposition****

first: Fernanda

middle: S

last: Hackenhaar

first: Nina

last: Refhagen

first: Melanie

last: Hagleitner

first: Frank

last: van Leeuwen

first: Hanne

middle: V

last: Marquart

first: Hans

middle: O

last: Madsen

first: Mattias

last: Landfors

first: Pia

last: Osterman

first: Kjeld

last: Schmiegelow

first: Trond

last: Flaegstad

first: Ólafur

last: Jónsson

first: Jukka

last: Kanerva

first: Jonas

last: Abrahamsson

first: Mats

last: Heyman

first: Ulrika

last: Nyström

first: Magnus

last: Hultdin


title: CpG island methylator phenotype classification improves risk assessment in pediatric T-cell Acute Lymphoblastic Leukemia [RNA-seq]

first: Sofie

last: Degerman

overall_design:
Gene expression profiling of primary pediatric (> 1-year-old and < 18-years-old) T-ALL samples taken at diagnosis (n = 108), and cell-sorted CD34+ and CD3+ cells and a fresh frozen lymph node as control samples (n = 3).
***Submitters state that raw data files will not be submitted to a repository because the patients providing the samples were not consented for raw data deposition****


title: An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [smllRNA-seq]

status: Public on Jan 28 2025

city: Columbus

first: Yi-Hui

last: Wang

state: OH

address: 1060 Carmack Road

department: Biological Chemistry and Pharmacology

institute: The Ohio State University

type: Non-coding RNA profiling by high throughput sequencing

summary: In all three domains of life, genes with related functions can be organized into specific genomic regions known as gene clusters. In eukaryotes, histone, piRNA, and rDNA (ribosomal DNA) clusters are among the most notable clusters which play fundamental roles in chromatin formation, genome integrity, and translation, respectively. These clusters have long been thought to be regulated by distinct transcriptional mechanisms. In this study, using C. elegans as a model system we identify ATTF-6, a member of the AT-hook family, as a key factor for the expression of histone, piRNA, and 5S rDNA-SL1 (spliced leader 1) clusters. ATTF-6 forms distinct nuclear foci at both piRNA and 5S rDNA-SL1 clusters. Loss of ATTF-6 leads to a depletion of histone mRNAs and SL1 transcripts. Additionally, we demonstrate that ATTF-6 is required for the recruitment of USTC (Upstream Sequence Transcription Complex) to piRNA clusters, which is necessary for piRNA production. Collectively, our findings reveal a unifying role for an AT-hook transcription factor in promoting the expression of fundamental gene clusters.

overall_design: Small RNA expression of control , attf-6 depleted, and attf-6 binding site deletion strains by small RNA sequencing

first: Hannah

middle: L

last: Hertz

first: Benjamin

last: Pastore

first: Wen

last: Tang


title: An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [mRNA-Seq]

overall_design: Gene expression analysis of wild type and attf-6 depleted C. elegans by mRNA sequencing


title: Fluo-Cast-Bright: A Deep Learning Pipeline for the Non-Invasive Prediction of Chromatin Structure and Developmental Potential in Live Oocytes

city: Athens

first: Claudia

last: Baumann

state: GA

address: 501 DW Brooks Drive

department: College of Veterinary Medicine - Physiology and Pharmacology

institute: University of Georgia

summary: In mammalian oocytes, large-scale chromatin organization regulates transcription, nuclear architecture, and maintenance of chromosome stability in preparation for meiosis onset. Pre-ovulatory oocytes with distinct chromatin configuration exhibit profound differences in metabolic and transcriptional profiles that ultimately determine meiotic competence and developmental potential. Here, we developed a deep learning pipeline for the non-invasive prediction of chromatin structure and developmental potential in live mouse oocytes. Our Fluorescence prediction and Classification on Bright-field (Fluo-Cast-Bright) pipeline achieved 91.3% accuracy in the classification of chromatin state in fixed oocytes and 85.7% accuracy in live oocytes. Importantly, transcriptome analysis following non-invasive selection revealed that meiotically competent oocytes exhibit a higher expression of transcripts associated with RNA and protein nuclear export, maternal mRNA deadenylation, histone modifications, chromatin remodeling and signaling pathways regulating microtubule dynamics during the metaphase-I to metaphase-II transition. Our pipeline provides fast and non-invasive selection of meiotically competent oocytes for downstream research and clinical applications.

overall_design: Methods: Oocyte collection was carried out on non-primed day 20 female mice.  Collected cells are maintained in minimal essential medium (MEM) supplemented with 3mg/ml bovine serum albumin (Sigma Aldrich, St. Louis, MO) and milrinone (Sigma; 1 μg/ml) to prevent meiotic resumption. These oocytes are separated into different wells with one oocyte in each well and imaged one by one under the confocal microscope. The 3D bright-field images of each oocyte are then processed by the Fluo-Cast-Bright pipeline and classified into NSN and SN oocytes and prepared for RNA-seq. Allowing for the non-invasive separation of NSN and SN oocytes. A total of 30 oocytes (15 NSN and 15 SN) were sequenced and analyzed in two replicates. Results: Transcriptomics analyses revealed that meiotically competent oocytes exhibit a higher expression of transcripts associated with RNA and protein nuclear export, maternal mRNA deadenylation, histone modifications, chromatin remodeling and signaling pathways regulating microtubule dynamics during the metaphase-I to metaphase-II transition. Our pipeline provides fast and non-invasive selection of meiotically competent oocytes for downstream research and clinical applications.

first: Xiangyu

last: Zhang

first: Rabindranath

last: De La Fuente


title: A cis-regulatory element controls HDAC9 expression to fine-tune inflammasome-dependent chronic inflammation

city: Munich

first: Rainer

last: Malik

address: Feodor-Lynen-Str. 17

department: Institute for Stroke and Dementia Research

country: Germany

institute: Klinikum der Universität München

summary: Transcriptomic profiling of BMDMs from HDAC9 mutant mice.

overall_design: Bone marrow-derived macrophages (BMDM) were generated as established by flushing the bone marrow from femurs and tibiae with ice-cold PBS, resuspending in PBS by repeated pipetting and filtering through a 40 µm cell strainer (BD Biosciences). After centrifugation of the cell suspension at 500 g for 10 min, the pellet was resuspended in culture medium (RPMI 1640 containing 10% FCS, 15% L929-cell-conditioned medium (LCM) and 100 µl/ml gentamycin) and plated on 15 cm untreated culture plates (Greiner). 15 % fresh LCM was added again on day 1 and 2 of culturing. For the stimulation experiments, differentiated macrophages were harvested by gentle scraping, transferred onto untreated 6-well or 12-well plates (Greiner) on Day 7 of culturing and left in LCM-free medium for 24 hours, allowing cells to adhere. Cells were then stimulated in FCS-free medium with LPS or left untreated.

first: Yaw

last: Asare

first: Federica

last: Tosato

first: Martin

last: Dichgans


title: An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters [ChIP-Seq]

overall_design: ATTF-6 genome binding loci analysis using attf-6::Flag-IP vs. untagged-IP by ChIP-seq


title: Massively parallel reporter assays investigate shared genetic variants of eight psychiatric disorders

city: Chapel Hill

first: Hyejung

last: Won

address: 116 Manning Drive, CB# 7250

institute: University of North Carolina at Chapel Hill

summary: A meta-genome-wide association study encompassing eight psychiatric disorders has shed light on the genetic architecture of pleiotropy. However, mechanisms underlying pleiotropic effects of these variants remain to be investigated. We conducted a massively parallel reporter assay to decipher the regulatory logic of variants with disease-specific and pleiotropic effects. Pleiotropic variants differ from disease-specific variants by manifesting chromatin accessibility that extends across diverse cell types in the neuronal lineage, and altering motifs for transcription factors with higher connectivity in protein-protein interaction (PPI) networks. Next, we mapped pleiotropic and disease-specific variants to putative target genes, which may offer insights into potential mechanisms of pleiotropy. Compared with disease-specific genes, pleiotropic genes demonstrate associations with generic biological pathways, widespread temporal dynamics during neuronal lineage, and higher connectivity in PPI networks. Collectively, variants exert pleiotropic effects by regulating genes involved in global biological functions.

overall_design: Massively parallel reporter assay (MPRA) on risk variants of eight psychiatric disorders in human neural progenitors (HNP)

first: Sool

last: Lee

first: Jessica

last: McAfee


title: Photoreceptor-induced LHL4 protects the photosystem II monomer in Chlamydomonas reinhardtii

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: Photosynthesis, the fundamental process using light energy to convert carbon dioxide to organic matter, is vital for life on Earth. It relies on capturing light through light-harvesting complexes (LHC) in photosystem I (PSI) and PSII and on the conversion of light energy into chemical energy. Composition and organization of PSI and PSII core complexes are well conserved across evolution. PSII is particularly sensitive to photodamage but benefits from a large diversity of photoprotective mechanisms, finely tuned to handle the dynamic and ever-changing light conditions. Light Harvesting Complex protein family members (LHC and LHC-like families) have acquired a dual function during evolution. Members of the LHC antenna complexes of PS capture light energy, whereas others dissipate excess energy that cannot be harnessed for photosynthesis. This process mainly occurs through nonphotochemical quenching (NPQ). In this work, we focus on the Light Harvesting complex-Like 4 (LHL4) protein, a LHC-like protein induced by ultraviolet-B (UV-B) and blue light through UV Resistance locus 8 (UVR8) and phototropin photoreceptor-activated signaling pathways in the model green microalgae Chlamydomonas reinhardtii. We demonstrate that alongside established NPQ effectors, LHL4 plays a key role in photoprotection, preventing singlet oxygen accumulation in PSII and promoting cell survival upon light stress. LHL4 protective function is distinct from that of NPQ-related proteins, as LHL4 specifically and uniquely binds to the transient monomeric form of the core PSII complex, safeguarding its integrity. LHL4 characterization expands our understanding of the interplay between light harvesting and photoprotection mechanisms upon light stress in photosynthetic microalgae.

overall_design: mRNA profiles generated by deep sequencing from triplicate of Chlamydomonas reinhardtii (CC5325) WT, uvr8, CrCo (CO), and CrBlz3 (Hy5) cells grown under continuous light (20 µmol photons m-2 s-1) and exposed for 1 h  (+) or not (-) to UV (0.2 mW cm-2)

first: Roman

last: Ulm

first: Emilie

last: Demarsy

first: Marie

last: Dannay

first: Guillaume

last: Allorent


title: Zika virus modulates human skin cells to increase its transmission success

city: Hannover

first: Karsten

last: Cirksena

state: Lower Saxony

address: Bünteweg 2

department: Institute of Biochemistry

institute: University of Veterinary Medicine Hannover

summary: Gene expression in human dermal fibroblasts was analysed 10 and 24 hours post infection with ZIKA virus, to identify processes involved in the production of metabolites that influence Mosquito host-seeking behavior. Cluster analysis revealed one cluster of transcripts affected by infection with ZIKV and two clusters of transcripts affected by the course of time independent from ZIKV infection. Enrichment analysis among transcripts affected by ZIKA virus pointed enrichment of transcripts involved in antiviral defence mechanisms and lipoprotein metabolic processes.

overall_design: Human dermal fibroblasts were infected with ZIKA virus. Gene expression profiling analysis with data obtained from RNA-seq was performed 10 and 24 hours post infection.

first: Noushin

last: Emami

first: Gisa

last: Gerold

first: Oliver

last: Dittrich-Breiholz

first: Annasara

last: Lenman


title: Identification of cold tumor induction–related markers in pancreatic cancer and the clinical implication of PCDH7

status: Public on Jan 25 2025

city: Fukuoka

first: Yuki

last: Mochida

address: 3-1-1 Maidashi

department: Graduate School of Medical Sciences

country: Japan

institute: Kyushu University

summary:
Purpose: Pancreatic ductal adenocarcinoma (PDAC) is considered a “cold” tumor because the tumor immune microenviron- ment (TIME) exhibits poor intratumoral T-cell infiltration. This study aimed to identify the marker genes associated with induction of cold TIME in PDAC cells.
Methods: We orthotopically transplanted 10 primary cultures of PDAC derived from KrasG12D/+; Trp53R172H/+; Pdx-1- Cre (KPC) mice into immunocompetent mice and evaluated TIME by immunohistochemistry (IHC) staining of CD8. We divided primary cultures into two groups: cold TIME group with low CD8+ T-cell infiltration and a hot TIME group with high infiltration. RNA sequencing was performed to identify specific genes in the cold TIME group, and single-cell RNA sequencing (scRNA-seq) data was used for validation. IHC was performed to evaluate expressions in human PDAC samples.
Results: We identified six genes specific in PDAC cells to the cold TIME group by RNA sequencing; these were defined as “cold tumor induction–related genes”. Human PDAC scRNA-seq data revealed that cold tumor induction–related genes were significantly and negatively correlated with the number of CD8+ T-cells (p = 0.0341). These genes included protocad- herin 7 (PCDH7). High expression of PCDH7 significantly and negatively correlated with the number of CD8+ T-cells in scRNA-seq (p = 0.0474) and IHC (p = 0.0110) data using human PDAC samples. PCDH7 was an independent factor for poor prognosis in PDAC (overall survival: hazard ratio = 2.07, p = 0.0367).
Conclusion: PCDH7 is a prognostic marker associated with CD8+ T-cell infiltration for PDAC patients.

overall_design: RNA sequencing of murine PDAC cell lines inducing low or high infiltration of CD8+ T cells

first: Kenoki

last: Ohuchida


title: Epigenome-wide DNA methylation profiling in septic and non-septic patients with similar infections: Potential use as sepsis biomarkers

status: Public on Jan 24 2025

city: Valencia

first: Jose Luis

last: Garcia-Gimenez

address: Avinguda Blasco Ibáñez, 15

department: Physiology

institute: University of Valencia

summary:
Sepsis is a life-threatening condition caused by a dysregulated immune response to infection, leading to organ failure. Despite its significant global burden, the underlying mechanisms of immune dysfunction in sepsis remain incompletely understood.
This study explores the role of DNA methylation in white blood cells in sepsis pathogenesis by assessing a prospective case-control study comparing DNA methylation profiles between patients with community-acquired sepsis and matched controls with similar infections who did not develop sepsis. Blood samples were collected within 24 hours of hospital admission, and DNA methylation was analyzed using Illumina MethylationEPIC 850 v2 arrays and bisulfite pyrosequencing.
The discovery cohort (n=32) identified 4,640 differentially methylated positions (DMPs), with notable hypomethylation in immune-related genes. Functional enrichment analysis revealed significant involvement of these genes in immune processes, including neutrophil activation and monocyte differentiation. Key findings highlighted hypomethylation of SERPINA1, AZU1, MPO, and SLX4, which was validated in an independent cohort (n=28).
Correlation analyses demonstrated significant associations between the methylation levels of these genes and clinical severity markers, such as SOFA score and procalcitonin levels. Notably, SLX4 hypomethylation showed the highest predictive value for poor prognosis (AUC 0.821), while SERPINA1 hypomethylation exhibited strong diagnostic potential for sepsis (AUC 0.858).
Our findings suggest that DNA methylation changes, particularly in immune-related genes, could serve as valuable biomarkers for diagnosing sepsis and predicting patient outcomes. Further research is warranted to confirm their clinical utility and explore potential therapeutic targets.

overall_design: We investigated DNA methylation in whole blood from patients with community-acquired sepsis and matched controls to identify epigenetic biomarkers. A total of 32 samples (16 sepsis, 16 controls) were analyzed using Infinium MethylationEPIC v2.0 Beadchip arrays. Differentially methylated positions and regions were identified, and selected genes were validated with bisulfite pyrosequencing.

first: Ian

last: López-Cruz

first: Jose

last: García-Giménez

first: Manuel

last: Madrazo

first: Judit

last: Garcia-Guallarte

first: Laura

last: Piles

first: Federico

last: Pallardó

first: Arturo

last: Artero


title: Macrophage migration inhibitory factor in inflammasome formation and macrophage recruitment in cervical cell carcinoma

city: taiyuan

first: qianqian

last: zhang

state: shanxi

address: 99 Longcheng Street, Xiaodian District

department: Department of Obstetrics and Gynecology

institute: Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital,

summary: The present study aimed to explore the role of macrophage migration inhibitory factors in cervical squamous cell carcinoma (CSCC) recurrence and metastasis.

overall_design: Western blotting, reverse transcription quantitative PCR, cell-counting kit 8 assay, flow cytometry, and ELISA were used to investigate the effects of MIF on CSCC progression and formation of inflammasomes. Transcriptome and proteome sequencing were combined to screen for key effector proteins of MIF. Moreover, in vitro co-culture experiments, Transwell assays, and flow cytometry were used to evaluate the roles of MIF and TSC22 domain family protein 3 (TSC22D3) as inflammatory tumor-promoting factors in macrophage recruitment and polarization induction.

first: mengxin

last: wang

first: suhui

last: wu


title: SPT5 regulates RNA polymerase II stability via Cullin 3–ARMC5 recognition [RNA-Seq]

city: Chicago

last: Aoi

state: IL

address: 303 E Superior St. SQBRC 7-300

department: Biochemistry & Molecular Genetics

institute: Northwestern University

summary: The stability of RNA polymerase II (Pol II) is tightly regulated during transcriptional elongation for proper control of gene expression. Our recent studies revealed that promoter-proximal Pol II is destabilized via the ubiquitin E3 ligase cullin 3 (CUL3) upon loss of transcription elongation factor SPT5. Here, we investigate how CUL3 recognizes chromatin-bound Pol II as a substrate. Using an unbiased proteomic screening approach, we identify armadillo repeat-containing 5 (ARMC5) as a CUL3 adaptor required for VCP/p97-dependent degradation of SPT5-depleted, chromatin-bound Pol II. Genome-wide analyses indicate that ARMC5 targets promoter-proximal Pol II in a BTB domain–dependent manner. Further biochemical analysis demonstrates that interaction between ARMC5 and Pol II requires the transcriptional cyclin-dependent kinase 9 (CDK9), supporting a phospho-dependent degradation model. We propose that defective, promoter-proximal Pol II that lacks SPT5 is rapidly eliminated from chromatin in a noncanonical early termination pathway that requires CDK9-dependent interaction with the CUL3-ARMC5 ubiquitin ligase complex.

overall_design: To understand the function of ARMC5 in promoter-proximal Pol II stability, cells treated with ARMC5 shRNA knockdown were used to analyze ChIP-seq for Pol II and ARMC5 and RNA-seq for gene expression.

first: Ali

last: Shilatifard


title: SPT5 regulates RNA polymerase II stability via Cullin 3–ARMC5 recognition [ChIP-seq]


title: Canonical and non-canonical PRC1 differentially contribute to the regulation of neural stem cell fate

city: Dresden

first: Mareike

last: Albert

address: Fetscherstr. 105

department: Center for Regenerative Therapies TU Dresden

institute: TUD Dresden University of Technology

summary:
Neocortex development is characterized by sequential phases of neural progenitor cell (NPC) expansion, neurogenesis and gliogenesis. Polycomb-mediated epigenetic mechanisms are known to play important roles in regulating the lineage potential of NPCs during development. The composition of Polycomb Repressive Complex 1 (PRC1) is highly diverse in mammals and was hypothesized to contribute to context-specific regulation of cell fate. Here, we have performed side-by-side comparison of the role of canonical PRC1.2/1.4 and non-canonical PRC1.3/1.5, all of which are expressed in the developing neocortex, in NSC proliferation and differentiation. We found that the deletion of Pcgf2/4 in NSCs led to a strong reduction in proliferation and to altered lineage fate, both during the neurogenic and gliogenic phase, whereas Pcgf3/5 played a minor role. Mechanistically, genes encoding stem cell and neurogenic factors were bound by PRC1 and differentially expressed upon Pcgf2/4 deletion. Thus, rather than different PRC1 sub-complexes contributing to different phases of neural development, we found that canonical PRC1 played a more significant role in NSC regulation during proliferative, neurogenic and gliogenic phases compared to non-canonical PRC1.
Here, we analyzed gene expression changes upon ablation of Pcgf2/4 in mouse NSCs after four days of neural differentiation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse NSCs (isolated from Pcgf2F/F; Pcgf4F/F; Nes::CreERT2/+ mice) treated with Ethanol (Ctrl) or with 1 μM OH-Tamoxifen in EtOH to induce deletion of Pcgf2/4 (KO) combined with a four day differentiation of the mNSC towards neural fate.

first: Janine

last: Hoffmann

first: Theresa

middle: M

last: Schütze


title: Systematic identification of Y-chromosome gene functions in mouse spermatogenesis [bulk]

city: London

first: Jeremie

last: Subrini

address: 1 Midland road

country: United Kingdom

institute: The Francis Crick Intitute

summary: The mammalian Y chromosome is essential for male fertility, but how individual Y genes regulate spermatogenesis is poorly understood. To resolve this question, we generate a deletion series of the mouse Y chromosome, creating thirteen Y-deletant mouse models and conducting exhaustive reproductive phenotyping. Eight Y genes, including several that are deeply conserved and exhibit testis-specific expression, are dispensable for spermatogenesis. For others, we uncover novel functions, including a role for Uty in establishment and differentiation of spermatogonia, and for Zfy2 in ensuring meiotic pairing and reciprocal recombination between the sex chromosomes. We also generate the first mouse equivalent of the human infertility AZFa deletion, revealing cumulative detrimental effects of Y-gene loss on spermatogenesis. We use single nuclei RNAseq to identify candidate mechanisms by which Y genes regulate the germ cell transcriptome and reveal an unexpected impact of Y genes on testis supporting cells. Our study represents a paradigm for the complete functional dissection of a mammalian Y chromosome and advances our knowledge of human infertility and Y-chromosome evolution.

overall_design: To interrogate how Y genes impact the testis transcriptome, we performed bulk RNAseq on adult testes from 13 Y-KOs. Total RNA was extracted from 4 biological replicates (different animals) for each genotype. The transcriptome landscape of each Y-KO genotype was compared to that of controls.


title: The differentiation state of small intestinal organoid models influences prediction of drug-induced toxicity

status: Public on Jan 23 2025

city: South San Francisco

first: Julia

last: Co

state: California

address: 1 DNA Way

institute: Genentech

summary: Drug-induced intestinal toxicity (GIT) is a frequent dose-limiting adverse event that can impact patient compliance and treatment outcomes. In vivo, there are proliferative and differentiated cell types critical to maintaining intestinal homeostasis. Traditional in vitro models using transformed cell lines do not capture this cellular complexity, and often fail to predict intestinal toxicity. Primary tissue-derived intestinal organoids, on the other hand, are a scalable Complex in vitro Model (CIVM) that recapitulates major intestinal cell lineages and function. Intestinal organoid toxicity assays have been shown to correlate with clinical incidence of drug-induced diarrhea, however existing studies do not consider how differentiation state of the organoids impact assay readouts and predictivity. We employed distinct proliferative and differentiated organoid models of the small intestine to assess whether differentiation state alone can alter toxicity responses to small molecule compounds in cell viability assays. In doing so, we identified several examples of small molecules which elicit differential toxicity in proliferative and differentiated organoid models. This proof of concept highlights the need to consider which cell types are present in CIVMs, their differentiation state, and how this alters interpretation of toxicity assays.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for small intestine (duodenum)-derived organoids grown in proliferative or differentiated conditions

first: Jessica

middle: A

last: Klein

last: Heidmann

first: Tomomi

last: Kiyota

first: Aaron

last: Fullerton

first: Kimberly

last: Homan

middle: Y


title: Systematic identification of Y-chromosome gene functions in mouse spermatogenesis [10x]

overall_design: To gain deeper molecular insights into each spermatogenic defect, we performed single nuclei RNA sequencing on Eif2s3y-KO, Uty-KO, AZFa-KO, Zfy2-KO, and Zfy1&2-DKO males. P10 testes from Eif2s3y and Uty-KOs were used to enrich for spermatogonia, since this was where the phenotypes manifested, and adult testes were used for Zfy1, Zfy2, Zfy1&2, and AZFa-KOs to capture all cell types.


title: Dynamics and regulatory roles of RNA m6A methylation in unbalanced genomes

city: Beijing

first: Lin

last: Sun

address: Xinjiekouwai Street

institute: Beijing Normal University

summary: N6-methyladenosine (m6A) in eukaryotic RNA is critical for RNA metabolism, gene expression regulation, and the development of organisms. Aberrant expression of m6A components appears in a variety of human diseases. RNA m6A modification in Drosophila has proven to be involved in sex determination regulated by Sxl and may affect X chromosome expression through the MSL complex. The dosage-related effects under the condition of genomic imbalance (i.e., aneuploidy) are related to various epigenetic regulatory mechanisms. We investigated the roles of RNA m6A modification in unbalanced genomes using aneuploid Drosophila.

overall_design: m6A methylated RNA immunoprecipitation sequencing (MeRIP-Seq) for wildtype female, wildtype male, trisomy 2L female, trisomy 2L male, and metafemale Drosophila.

first: Shuai

last: Zhang


title: Investigate the effect of high-glucose treatment in mouse endothelial cell

city: Los Angeles

first: Yao Wei

last: Lu

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

summary: Freshly isolated murine skin endothelial cells were treated with high glucose and control with normal glucose.

overall_design: Mouse skin endothelial cells were treated with normal glucose (5 mmol/L) or high glucose (20 mmol/L) medium for 48 hours before harvesting to process for RNA-sequencing.

first: Sudarshan

last: Bhattacharjee

first: Jianing

last: Gao

first: Hong

last: Chen


title: Identification of FSH-regulated and estrous stage-specific transcriptional networks in mouse ovaries

status: Public on Jan 22 2025

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Follicle-stimulating hormone (FSH) acts by binding to FSHRs on ovarian granulosa cells to produce estradiol. FSH is essential for female fertility because mice lacking FSH (Fshb KO) are anestrus, and infertile. Although several in vitro and ex vivo cell culture approaches combined with pharmacological hormone treatments were used to identify FSH-regulated genes, how FSH orchestrates ovarian gene networks in vivo has not been investigated. Similarly, whether FSH-regulated genes display estrus stage-specific expression changes has also not been studied. Here, we functionally rescued Fshb null mice with a well-established gonadotrope-targeted HFSHB transgene-mediated in vivo genetic rescue approach and performed RNA-Seq analysis on ovarian RNAs obtained from FSH-intact (WT), FSH-deficient (Fshb KO) and FSH-rescue (HFSHB+ rescue) mice. By comparing WT vs Fshb KO and Fshb KO vs Fshb KO HFSHB+ ovarian gene expression datasets, we identified bona-fide FSH-responsive genes in vivo in mouse ovaries. Cross interrogation of WT vs Fshb KO and Fshb KO vs Fshb KO HFSHB+ data sets further allowed us to identify several transcription factors and RNA-binding proteins specifically in  FSH - regulated genes. In an independent set of experiments, we performed RNA-Seq analysis on ovarian RNAs obtained from mice in diestrus (DE), proestrus (PE) and estrus (E) stages and identified estrus stage-specific ovarian gene expression patterns. Interestingly, many of the FSH-regulated transcription factors themselves were estrus-stage specifically expressed. We found that ESR2 and GATA6, two known FSH-responsive granulosa cell-specific transcription factors and their target genes are reciprocally regulated with distinct patterns of expression in estrus stages. Thus, our in vivo genetic models and RNA-Seq analyses identify FSH-regulated ovarian genes in specific estrus stages that are under transcriptional and post-transcriptional control.

overall_design: RNA-seq samples from WT, Fshb (+/-), Fshb (-/-), Fshb (-/-) HFshb (+/+) and WT cycling mice staged in DE, P, and E stages of estrus cycle.

first: Kathryn

last: Walters

first: Amber

last: Baldwin

first: Zhenghui

last: Liu

first: Mark

last: Larsen

first: T

last: Kumar


title: Transcriptional analysis of murine biliary atresia identifies macrophage heterogeneity and subset-specific macrophage functions

first: Deborah

last: Winter

address: 240 E. Huron Street, M300

summary: Macrophages play an important role in disease progression of pediatric cholestatic liver disease, particularly biliary atresia (BA); however, the restorative versus pathogenic role for precise macrophage subsets remains poorly defined. We aimed to distinguish the transcriptional profiles and roles of defined macrophage subset(s) in murine BA. Ly6c+ macrophages demonstrated the greatest increase in numbers and percent of total macrophages in murine BA versus saline controls whereas MHCII+ macrophages decreased. Transcriptional changes in murine BA MHCII+ macrophages included reduced expression of the Kupffer cell gene signature, lower expression of genes involved in homeostatic processes, and increased expression of genes involved in inflammatory processes. Ly6c+ macrophages in murine BA showed increased expression for Hif1a and other genes involved in the cellular response to hypoxia. Among all subsets, the number of Ly6c+ macrophages exhibited the strongest correlation with severity of histologic liver injury by Ishak score. Our data identify specific pathways upregulated in Ly6c vs MHCII+ macrophage subsets in murine BA. Transcriptional similarities between murine BA and human cholestatic macrophages may enable translation of future mechanistic studies to new macrophage subset-specific therapies.

overall_design: Bulk RNA-seq of 4 sorted hepatic macrophage populations in RRV mouse model of biliary atresia with saline-treated control.

first: Sarah

last: Taylor


title: Genome-wide binding sites of HOXC4 in brown adipocytes

first: Ting

last: Yang

state: Beijing

address: 10 Xitoutiao, Youanmen Wai, Fengtai District, Beijing, China

institute: Capital Medical University

summary: We found that overexpression of HOXC4 in mature adipocytes enhances thermogenesis. To investigate the binding sites of HOXC4 in the genome of brown adipocytes, we performed HOXC4 ChIP-seq experiments on differentiated primary brown adipocytes, which overexpressed HOXC4.

overall_design: The binding sites of HOXC4 on the genome of brown adipocytes

first: Mengxi

last: Jiang


title: Dysfunctional b-cell autophagy induces b-cell stress and enhances islet immunogenicity

status: Public on Jan 21 2025

city: Indianapolis

first: Matthew

last: Austin

state: Indiana

address: 1210 Waterway Blvd., Suite 4000

institute: Indiana University School of Medicine

summary: We knocked out the critical autophagy enzyme, ATG7, in the β-cells of mice (ATG7Δβ-cell) then monitored blood glucose to assess the phenotype induced by this KO model. We found that all ATG7Δβ-cell mice developed diabetes between 11-15 weeks of age. We isolated islets from ATG7Δβ-cell and littermate control mice several weeks prior to diabetes development (7-10 weeks of age) and performed bulk islet mRNA sequencing. The purpose of this experiment was  to understand the islet biological process pathways altered by dysfunctional β-cell autophagy in the ATG7Δβ-cell model.

overall_design: RNA-seq profiling of ATG7Δβ-cell and littermate control islets several weeks prior to diabetes development.

first: Charanya

last: Muralidharan

first: Justin

middle: J

last: Crowder

first: Amelia

last: Linnemann


title: FBXO31-mediated Ubiquitination of OGT Maintains O-GlcNAcylation Homeostasis to Restrain Endometrial Malignancy

city: Changsha

first: zhang

address: Xiangya road

institute: Xiangya hospital

summary: CRISPR screen and biochemical characterization reveal that tumor suppressor F-box only protein 31 (FBXO31) regulates O-GlcNAcylation homeostasis in EC by ubiquitinating the O-GlcNAc transferase OGT.

overall_design: The human GeCKO v2 library was transduced into 293T cells by lentivirus at a multiplicity of infection of 0.3. Cells were selected with puromycin for 7 days followed by fluorescence-activated cell sorting (FACS) based on their O-GlcNAcylation staining intensities. An unsorted sample was used to assess sgRNA library coverage, and the sorted RL2 high population was subjected to genomic DNA extraction. The inserted sgRNA library was amplified by two steps of PCR for next-generation sequencing. Each screen was performed twice.


title: Full-Length Transcriptome Analysis of Male and Female Gonads in Japanese Eel (Anguilla japonica)

status: Public on Jan 20 2025

city: Xiamen

first: Tiansheng

address: No. 43, Yindou Road, Jimei District, Fisheries College of Jimei University

institute: Jimei University

summary: Background: The Japanese eel (Anguilla japonica) holds significant economic value in East Asia, but limitations in understanding its reproductive biology have hindered advancements in artificial breeding techniques. Previous research has primarily focused on conserved sex differentiation genes, offering limited insights into the broader molecular mechanisms driving gonadal development and sexual dimorphism. To address these limitations, this study aims to investigate key genes and pathways involved in gonadal development through a comprehensive transcriptomic analysis of male and female eel gonads. Results: PacBio Iso-Seq and Illumina RNA-Seq technologies were combined to conduct a full-length transcriptome analysis of male and female Japanese eel gonads at a post-differentiation, pre-maturation stage. A total of 24661 unigenes were identified in ovaries and 15023 in testes, along with genomic regulatory elements such as transcription factors, simple sequence repeats, and long non-coding RNAs. Additionally, 1,210 differentially expressed genes were detected. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed significant pathways involved in cell cycle regulation, metabolic processes, apoptosis, and hormone activity. Notably, several reproductive-related genes, including bambi, ccnb1, cdc20, gdf9, prlh, ccdc39, chrebp, tspo, syce3, and ngb, demonstrated significant dimorphic expression in eel gonads. Conclusions: This study provides valuable insights into the molecular mechanisms of gonadal differentiation and sexual dimorphism in Japanese eels. The findings expand the genetic resources available for the eel breeding industry and could facilitate the development of improved artificial breeding techniques focused on reproductive development.

overall_design: In this experiment, we investigated sexual dimorphism and gonadal development in aquaculture-reared Japanese eels (Anguilla japonica) at the silver eel stage, where gonads had differentiated but remained immature without hormone induction. Ovarian tissues from three females and testicular tissues from three males were collected, forming two groups with three biological replicates each. Six RNA libraries were constructed and sequenced using Illumina RNA-seq for gene expression analysis, with PacBio Iso-seq data serving as a reference for transcript validation.

first: Jingjie

last: Liang

first: Jiangling

last: Li

first: Yuewen


title: Muscarinic agonism restores degenerated salivary glands through a calcium-ATP metabolic axis

city: San Francisco

last: Knox

address: 513 Parnassus Ave

department: Cell Tissue Biology

institute: University of California San Francisco

summary: Chronic damage to tissues and organs is deemed irreversible. This has led to a focus on the development of regenerative therapies that replace tissues. Here, we break with this dogma by demonstrating that the chronically injured degenerating salivary gland can be functionally and structurally restored through a nerve-associated mechanism. Extensive disruption of the chronically injured secretory acinar-nerve niche can be reversed by muscarinic agonism, with the tissue maintaining a homeostatic-like state months after treatment ends. In addition, the proportion of de-differentiated acinar cell types that appear with chronic damage are greatly reduced by muscarinic stimulation, suggesting recovery of cells critical for function. This reversal is due, in part, to re-balancing a calcium-dependent metabolic pathway that enables cell replacement. Finally, we show that radiation damaged hair follicles also benefit from muscarinic stimulation through a similar mechanism. Thus, these data challenge the concept that chronic damage is irreversible and provide a new avenue for the development of restorative treatments, a paradigm shift that can be explored more broadly.

overall_design: To irreversible degeneration that lead to a permanent loss in organ function, we performed transcriptomic analysis of SGs at 30-, 60-, and 90-days post-IR via bulk RNA-sequencing

first: Jianlong


title: Changes in the transcriptome of Azospirillum brasilense, sp7 in response to ethylene

city: Knoxville

first: Brad

last: Binder

state: Tennessee

address: 309 Ken and Blaire Mossman Bldg.

department: Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee

summary: The goal of this study was to determine the effects of ethylene on Azospirillum brasilense strain Sp7 and to deliniate the signal transduction pathway involved in these responses. One main focus was to determine the role of the ethylene receptor, AzoEtr1, in these responses. Since this is a plant-associated bacterium and plants produce ethylene, we evaluated the role of this pathway in mediating the ability of A. brasilense to associate with plants.

overall_design: Cells were grown in liquid minimal media for A. brasilense (MMAB) with sodium nitrate for 12h. They were then treated for 4h with 0.1 ppm ethylene or ethylene-free air (controls) prior to RNA extraction and analysis. Three replicates of each conditions were obtained. But, one air sample (Air Rep 3) did not cluster with the other 2 replicates in PCA analysis and was removed from further analysis.

first: Gladys

last: Alexandre

first: Eric

last: Brenya

last: Carlew


title: GPR55 in the tumor microenvironment of pancreatic cancer controls tumorigenesis

city: Graz

first: Rudolf

last: Schicho

address: Neue Stiftingtalstraße 6

country: Austria

institute: Medical University of Graz

summary: The G protein-coupled receptor 55 (GPR55) is part of an expanded endocannabinoid system (ECS), and plays a pro-tumorigenic role in different cancer models, including pancreatic cancer. Next to cancer cells, various cells of the immune tumor microenvironment (TME) express receptors of the ECS that critically determine tumor growth. The role of GPR55 in cancer cells has been widely described, but its role in the immune TME is not well understood. We, therefore, intended to uncover the role of GPR55 in tumor immunity in a model of pancreatic ductal adenocarcinoma (PDAC). To this end, a KPCY tumor cell line from murine PDAC, or GPR55-overexpressing KPCY cells (KPCY55) were subcutaneously injected into wildtype (WT) and GPR55 knockout (KO) mice, and immune cell populations were evaluated by flow cytometry. Deficiency of GPR55 in the TME led to reduced tumor weight and volume, and altered the immune cell composition of tumors, favoring an anti-tumorigenic environment by increasing the number of CD3+ T cells, particularly CD8+ T cells, and the expression of PD-L1 on macrophages. RNA-seq pathway analysis revealed higher T cell activity in KPCY55 tumors of GPR55 KO vs. WT mice. In addition, tumors from GPR55 KO mice displayed increased levels of T cell chemokines Cxcl9 and Cxcl10. Migration of T cells from GPR55 KO mice towards CXCL9 was increased in comparison to T cells from WT mice, suggesting that a CXCR3/CXCL9 axis was involved in T cell influx into tumors of GPR55 KO mice. Notably, anti-PD-1 immunotherapy increased tumor burden in WT mice, while this effect was absent in the GPR55 KO mice. Our study indicates that GPR55 in TME cells may drive tumor growth by suppressing T cell functions, such as migration, in a model of PDAC, making it an interesting target for immunotherapies.

overall_design: KPCY55 (mouse pancreatic adenocarcinoma cells overexpressing GPR55) were subcutaneously injected into GPR55 WT or KO mice to study the influence of GPR55 on the tumor microenvironment in pancreatic cancer. After 29 days, the tumors were collected for bulk RNA-seq, and differential gene expression was performed.

first: Thomas

last: Bärnthaler

first: Dušica

last: Ristić


title: SUMOylation inhibition potentiates the glucocorticoid receptor to program growth arrest of acute lymphoblastic leukemia cells (ATAC-seq)

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: Glucocorticoids (GCs) are a crucial component of effective treatment for acute lymphoblastic leukemia (ALL). GCs exert their functions through the glucocorticoid receptor (GR), a ligand-activated transcription factor (TF). Chromatin occupancy, chromatin-protein networks and gene programmes of GR are regulated by SUMOylation, which has therapeutic implications in other hematomalignancies. To unravel the GR-SUMO crosstalk in ALL, we induced a hypoSUMOylated state in NALM6 ALL cells with a SUMOylation inhibitor (ML-792). Genome-wide profiling of GR and SUMO binding and chromatin accessibility revealed that hypoSUMOylation augmented GR chromatin occupancy and altered chromatin openness upon dexamethasone (Dex) exposure. Association with transcriptome data indicated that on the novel binding sites GR predominantly suppressed target gene expression. Chromatin-proteomic analyses identified a substantial number of shared TFs and coregulators associated with chromatin-bound GR and SUMO. The chromatin-protein network of GR contained several TFs with corresponding binding motifs found on GR-adjacent chromatin sites, implying their simultaneous presence on chromatin. Cell cycle and proliferation analyses indicated that hypoSUMOylation potentiated Dex-induced cell cycle arrest and suppressed NALM6 cell proliferation, complementing the significant expression changes of cell cycle-related genes in our transcriptome data. Our work provides a valuable resource of GR chromatin partners and implies potential for targeting SUMOylation to increase sensitivity to GCs in ALL.

overall_design: Examination of chromatin accessibility by ATAC-seq from NALM6 cells treated with or without Dex in the presence or absence of SUMOylation inhibitor ML792 (SUMOi). All sequencing was done with Illumina NextSeq 500.

first: Emma

last: Valima

first: Jorma

last: Palvimo


title: SUMOylation inhibition potentiates the glucocorticoid receptor to program growth arrest of acute lymphoblastic leukemia cells (RNA-seq)

overall_design: Gene expression profiling by RNA-seq from NALM6 cells treated with or without Dex in the presence or absence of SUMOylation inhibitor ML-792 (SUMOi). All sequencing was done with Illumina NextSeq 500.


title: Changes in circulating miRNA expression in right heart remodeling due to pulmonary hypertension

status: Public on Jan 18 2025

city: Luzhou

first: Huiling

last: Cai

address: Longmatan District, Luzhou City, Sichuan Province

institute: Southwest Medical University

summary: Clinical practice currently faces a significant shortfall in specific biomarkers needed for diagnosing right ventricular (RV) remodeling in patients with pulmonary hypertension (PH). MiRNAs are crucial regulators of cardiovascular development, influencing processes like angiogenesis, cardiomyocyte differentiation, cell cycle, cardiac electrical activity, and cardiomyocyte growth. Furthermore, circulating miRNAs are cell-or tissue-specific, relatively stable in serum, and resistant to degradation factors. These properties make serum miRNAs possible promising biomarkers for predictive diagnosis of cardiovascular disease (CVD). This study systematically screened and identified candidate serum miRNAs as potential diagnostic biomarkers for RV remodeling in PH patients.

overall_design: Serum samples from Sprague - Dawley rats surviving 4 weeks after Pulmonary artery banding (PAB) and sham surgery were subjected to miRNA high-throughput sequencing and analyzed for differences.

first: Cheng

last: Yu

first: Xiuchuan

first: Xuenan

last: Wang

first: Yongjian

last: Yang

first: Cong

last: Lan


title: SUMOylation inhibition potentiates the glucocorticoid receptor to program growth arrest of acute lymphoblastic leukemia cells

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

overall_design: Refer to individual Series


title: Age-associated microglial transcriptome leads to diminished immunogenicity and dysregulation of MCT4 and P2RY12/P2RY13 related functions

status: Public on Jan 17 2025

city: Stockholm

first: Martin

last: Skandik

address: Nobels vag 13

institute: Karolinska Institutet

summary: The aging process is marked by a time-dependent deterioration in cellular functions, particularly the immune and neural systems. Understanding the phenotype acquisition of microglia, the sentinel immune cells of the brain, is crucial for understanding the nature of age-related neurological diseases. However, the specific phenotype adopted by microglia during aging remains a subject of debate and is contingent on the chosen experimental model. To address these unresolved questions, we employed a novel and highly controlled approach utilizing long-term cultivated BV-2 microglia, exempted of additional external stimuli. Our findings revealed that aged microglial cells, in comparison to their younger counterparts, acquire a distinct gene expression profile, primarily characterized by alterations in microglial immune response. Indeed, pro-inflammatory stimulated aged and young BV-2 microglia exhibited similar transcriptomic profiles, yet the response intensity to stimulus was markedly muted in the aged microglia. Functional neurotoxic assays confirmed diminished neuronal death in coculture with aged, activated microglia, underscoring a compromised immune response. Furthermore, a subsequent comparative analysis of aged BV-2 microglia with established transcriptomic microglial datasets from aged mice and humans identified 13 overlapping genes, laying the foundation for identifying core microglial aging signature. Particularly noteworthy were SLC16A3 and P2RY13, which consistently exhibited upregulation and downregulation, respectively, across all datasets. Additionally, four other genes—CAPG, LGALS3BP, NRIP1, and P2RY12—were found to share regulatory patterns in response to both aging and extrinsic activation. In-depth investigation focused on SLC16A3, encoding the high-affinity lactate transporter MCT4, revealed disruptions in extracellular acidification rate and lactate concentration with age. Microglial purine sensing and motility capacities, regulated by P2RY12/P2RY13, displayed age-related alterations. Remarkably, protein analysis in human brain tissue validated the observed upregulation of MCT4 and downregulation of P2RY12 in aged microglia. In conclusion, our study unveils a distinct phenotype in aged microglia characterized by compromised immune responsiveness. Through the integration of in vitro cultured BV-2 microglia with primary microglia datasets, we identify critical molecular determinants of microglial cellular aging confirmed in human aged brain tissue. This comprehensive approach offers potential insights for understanding and potentially reprogramming aged microglia, with implications for combating age-related neurological disorders.

overall_design: RNA-Seq profiling of in vitro young and aged BV-2 microglia untreated or treated with lipopolysaccharide (LPS) for 6 hours

last: Škandík

first: Bertrand

last: Joseph


title: Identifying THAP1 target genes in HEK-293T cells

city: Cambridge

first: Richard

last: Timms

address: Cambridge Biomedical Campus, Hills Road

department: CITIID, Department of Medicine

institute: University of Cambridge

summary: The 26S proteasome is a multi-catalytic protease that serves as the endpoint for protein degradation via the ubiquitin-proteasome system. Proteasome function requires the concerted activity of 33 distinct gene products, but how the expression of proteasome subunits is regulated in mammalian cells remains poorly understood. Leveraging coessentiality data from the DepMap project, here we characterize an essential role for the Dystonia gene THAP1 in maintaining the basal expression of PSMB5. PSMB5 insufficiency resulting from loss of THAP1 leads to defects in proteasome assembly, impaired proteostasis and cell death. The toxicity associated with loss of THAP1 can be rescued upon exogenous expression of PSMB5, explaining the molecular basis for their coessentiality. Leveraging a fluorescent reporter knocked-in to the endogenous PSMB5 locus, we define the transcriptional targets of THAP1 through RNA-seq analysis and perform a deep mutational scan to systematically assess the function of thousands of single amino acid THAP1 variants. Altogether, these data identify THAP1 as a new regulator of proteasome function and suggest that aberrant proteostasis may contribute to the pathogenesis of THAP1 Dystonias.

overall_design: We generated THAP1 knockout cells through CRISPR/Cas9-mediated gene disruption and peformed RNA-seq analysis

first: Dylan

middle: E

last: Ramage


title: Ticam2 ablation facilitates monocyte exhaustion recovery after sepsis

city: Blacksburg

first: Blake

middle: Alexander

last: Caldwell

state: VA

address: 149 Life Sciences I Building, 970 Washington Street SW

department: Biological Sciences

institute: Virginia Tech

summary: Sepsis is a leading cause of death worldwide, with most patient mortality stemming from lingering immunosuppression in sepsis survivors. This is due in part to immune dysfunction stemming from monocyte exhaustion, a phenotype of reduced antigen presentation, altered CD14/CD16 inflammatory subtypes, and disrupted cytokine production. Whereas previous research demonstrated improved sepsis survival in Ticam2-/- mice, the contribution of TICAM2 signaling to long-term exhaustion memory was unknown. Using a cecal slurry injection sepsis model, we monitored the establishment and recovery of monocyte exhaustion in Ticam2-/- mice. Like wild-type controls, Ticam2-/- monocytes develop an exhaustion phenotype defined by CD38high; CX3CR1low; MHCIIlow cell surface expression 48 hours after sepsis onset. Time course analysis of sepsis patient blood samples revealed a similar effect in human monocytes, which steadily transition into a CD38high; CX3CR1low; HLA-DRlow state within four days of hospital admittance. To determine the impact of TICAM2 ablation on innate epigenetic memory in sepsis, we measured genome-wide DNA methylation in bone marrow monocytes and found that Ticam2-/- cells exhibit a unique profile of altered methylation at CEBPE binding sites and regulatory features for key immune genes such as Dmkn and Btg1. Finally, after one week of sepsis recovery, we profiled bone marrow and splenic reservoir monocytes in Ticam2-/- mice and found that, in contrast to the persistent exhaustion observed in wild-type monocytes, Ticam2-/- monocytes largely resembled healthy controls. Thus, in addition to improving survival during the inflammatory phase of sepsis progression, TICAM2 ablation facilitates the resolution of monocyte exhaustion in sepsis survivors.

overall_design: Genome-wide DNA methylation profiling was performed using Infinium Mouse Methylation BeadChip arrays. Based on variability observed in previous studies, a minimum of 5 biological replicates were collected for control and experimental day 7 mice. From discussions with the sesame analysis pipeline author, it was determined that n = 4 was sufficiently powered to detect differences in 5mC as low as 5% for in vivo bone marrow monocytes. All experiments were performed on at least two separate days and with mice from at least 3 separate litters. Mice were randomly split between cecal slurry injection and PBS control injection groups by researchers uninvolved with downstream analyses.

first: Susanti

last: Ie

first: Liwu

last: Li


title: Metabolic dependency mapping identifies Peroxiredoxin 1 as a driver of resistance to ATM inhibition

status: Public on Jan 19 2025

city: Bethesda

first: Urbain

last: Weyemi

state: Maryland

address: Bldg. 37,  Rm 4016A, 37 Convent Dr.

department: Developmental Therapeutics Branch

institute: National Institute of Health

summary: Metabolic pathways fuel tumor progression and resistance to stress conditions including chemotherapeutic drugs, such as DNA damage response (DDR) inhibitors. Yet, significant gaps persist in how metabolic pathways confer resistance to DDR inhibition in cancer cells. Here, we employed a metabolism-focused CRISPR knockout screen and identified genetic vulnerabilities to DDR inhibitors. We unveiled Peroxiredoxin 1 (PRDX1) as a synthetic lethality partner with Ataxia Telangiectasia Mutated (ATM) kinase. Tumor cells depleted of PRDX1 displayed heightened sensitivity to ATM inhibition in vitro and in mice in a manner dependent on p53 status. Mechanistically, we discovered that the ribosomal protein RPL32 undergoes redox modification on active cysteine residues 91 and 96 upon ATM inhibition, promoting p53 stability and altered cell fitness. Our findings reveal a new pathway whereby RPL32 senses stress and induces p53 activation impairing tumor cell survival.

overall_design: To investigate the effect of ATM kinase inhibition on PRDX1 deficient cells, we established A549 cell line in which PRDX1 gene has been knocked out by CRISPR/Cas9 and NCIH1299 cell line in which PRDX1 gene has been knocked down by shRNA. We then performed gene expression profiling analysis using data from RNA-seq of the established cell lines (A549_sgControl, A549_sgPRDX1, NCIH1299_shCT and NCIH1299_shPRDX1) with/without ATM inhibition treatment. Comparative gene expression profiling analysis was done by comparing the RNA-seq data from those four cell lines with/without ATM inhibition treatment.

first: Haojian

first: Yunjie

last: Xiao


title: Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety

city: yangzhou

first: Liu

middle: zi

last: yu

address: shuangqiao

institute: Yangzhou University


title: Lagging strand detection with SDL-TOPO protocol

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

summary: SDL-TOPO protocol was applied for the detection of lagging-strand in replicating budding yeast strain. Genomic DNA was extracted from cdc9 mutant strain, and served for library preparation with SDL-TOPO. To see the sensitivity of SDL-TOPO for the detection of lagging strand, various amounts of genomic DNA were used for the library preparation: 75 ng, 25 ng, 7.5 ng, 2.5 ng, 750 pg, 250 pg, 75 pg, and 25 pg. The prepared libraries were sequenced on Illumina iSeq100 with paired-end mode of 150x2. Only read 1 was served for mapping with bowtie2 against reference sequence sacSer3. The mapped reads were separated strand specifically, and read depths were visualized. The strand-biased mapping patterens were observed for libraries prepared from each amount of input DNA.

overall_design: To detect lagging strand DNA fragment, cdc9 mutant cells were used. Genomic DNA extracted from the strain was firstly denatured, and served for library preparation with SDL-TOPO protocol. Since SDL-TOPO can generate sequencing library from single-stranded DNA, any types of DNA can be converted to sequencing library.  Because leading strand and template genomic DNA are too long to be amplified with indexing PCR, only library molecules originated from lagging strand can be amplified and indexed.


title: Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells

city: New York

first: John

last: Blair

state: NY

address: 101 6th Avenue

institute: New York Genome center

summary: Cell signaling plays a critical role in neurodevelopment, regulating cellular behavior and fate. While multimodal single-cell sequencing technologies are rapidly advancing, scalable and flexible profiling of cell signaling states alongside other molecular modalities remains challenging. Here we present Phospho-seq, an integrated approach that aims to quantify cytoplasmic and nuclear proteins, including those with post-translational modifications, and to connect their activity with cis-regulatory elements and transcriptional targets. We utilize a simplified benchtop antibody conjugation method to create large custom neuro-focused antibody panels for simultaneous protein and scATAC-seq profiling on whole cells, alongside both experimental and computational strategies to incorporate transcriptomic measurements. We apply our workflow to cell lines, induced pluripotent stem cells, and months-old retinal and brain organoids to demonstrate its broad applicability. We show that Phospho-seq can provide insights into cellular states and trajectories, shed light on gene regulatory relationships, and help explore the causes and effects of diverse cell signaling in neurodevelopment.

overall_design:
Phospho-seq Pilot: A mixed population of iPS cells and K562 Cells. The K562 cells consist of two populations, One treated with 50 ng/ml EGF for 15 mins and one treated with 500 nM PX-866 for four hours. The cells were harvested and prepared according to the Phospho-seq protocol and stained with ADTs and HTOs.
Phospho-seq Benchmark: A mixed population of HEK and K562 cells were processed according to Phospho-seq protocol and stained with ADTs and HTOs
Phospho-seq Benchmark_2: a mixed population of K562 cells treated with 50 ng/ml EGF and 500 nm PX-866 processed with the Phospho-seq protocol,stained with a pRPS6 ADT and a flourescent pRPS6 antibody and FACS sorted into quartile bins, where each population was satined with HTOs and run through the 10x Genomics scATAC-seq Protocol
ASAP-seq Benchmark_2: a mixed population of K562 cells treated with 50 ng/ml EGF and 500 nm PX-866 processed with the ASAP-seq protocol,stained with a pRPS6 ADT and a flourescent pRPS6 antibody and FACS sorted into quartile bins, where each population was satined with HTOs and run through the 10x Genomics scATAC-seq Protocol
Phospho-seq RetOrg: 34 week-old retinal organoids dissociated and processed with the Phospho-seq protocol, stained with ADTs and HTOs
Phospho-multi: 18 and 24 week-old retinal organoids processed according to the Phospho-seq Multi protocol, stained with ADTs and constructed libraries using the 10x Genomics scATAC+scRNA kit
Phospho-seq BrainOrg: 3-month old brain organoids dissociated and processed with the Phospho-seq protocol, stained with ADTs and HTOs
Bridge-Multi: 3-month old brain organoids dissociated and processed with the according to the 10x Genomics scRNA and scATAC-seq kit
Organoid RNA-seq reference: 3-month old brain organoids dissociated and stained with HTOs  and processed with the 10x Genomics 3' v3.1 scRNA-seq processing protocol

first: Austin

last: Hartman

first: Fides

last: Zenk

first: Phillip

last: Wahle

first: Giovanna

last: Brancati

first: Carol

last: Dalgarno

first: Barbara

last: Treutlein

first: Rahul

last: Satija


title: A comparison of methylome data produced with tPBAT and sPBAT library preparation protocols.

summary: Genomic DNA extracted from IMR-90 cells were subjected to library preparations with tPBAT and sPBAT protocols. Sequencing was done with HiSeq X Ten platform and reads obtained were mapped with our own pipeline. The methylome data produced were compared. There is a little differences between the two datasets, which indicate sPBAT developped here is comparable with tPBAT protocol.

first: Yukiko

last: Shibata

first: Miki

first: Kazune

last: Inatomi

first: Yutaka

last: Suzuki

first: Takashi

last: Ito


title: SUMOylation inhibition potentiates the glucocorticoid receptor to program growth arrest of acute lymphoblastic leukemia cells (ChIP-seq)

first: Ville

last: Paakinaho

overall_design: Examination of GR and SUMO2 chromatin binding by ChIP-seq from NALM6 cells treated with or without Dex in the presence or absence of SUMOylation inhibitor ML792 (SUMOi). All sequencing was done with Illumina NextSeq 500.

first: Emma

last: Valima

first: Jorma

last: Palvimo


title: Altering the redox status of Chlamydia trachomatis directly impacts its developmental  cycles progression

status: Public on Jan 16 2025

city: Omaha

first: Vandana

last: Singh

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology, Microbiology, and Immunology

institute: University of Nebraska Medical Center

summary: RNAseq analysis was performed for ahpc Knockdown strain of Chlamydia trachomatis in the unindcued (-aTc) or induced (+aTc) at 14 hpi to monitor transcriptional changes.

overall_design: The transformants of ahpC KD were infected into HeLa cells. At 10 hpi, the constructs were induced or not with 1 nM aTc.  RNA samples were prepared from ahpC-KD-infected cells at 14 hpi. 20 μg RNA samples were treated with DNase to remove DNA contamination by using DNA-free Turbo kit (Thermo) according to the manusfacturer’s instruction. Ribosomal RNA was depleted from samples using the MICROBEnrich (Thermo) and MICROBExpress kits (Thermo) following the manufacturer’s instructions. RNA samples were processed for sequencing by the UNMC Genomics Core Facility.

first: Scot

middle: P

last: Ouellette


title: The RNA interactomes of Imp and Syp reveal temporal RNA regulatory network in Drosophila brain development

city: Oxford

first: Jeffrey

last: Lee

address: Dorothy Hodgkin Road

institute: University of Oxford

summary: The temporal patterning of neural stem cells is a powerful mechanism to generate neural diversity. In Drosophila, the progression of post-embryonic neurogenesis is driven by RNA-binding proteins Imp (IGF2BP) and Syp (SYNCRIP), however how they achieve their function is not well understood, since little is known about their RNA targets in the brain. Here, we present comprehensive RNA interactomes of Imp and Syp at different time points during larval brain development. Imp and Syp target highly overlapping sets of mRNAs whose encoded proteins impact fate specification, stem cell maintenance and tumourigenesis. Within these transcripts, Imp and Syp footprints exhibit limited overlap, instead we show their binding sites have co-evolved, suggesting a combinatorial or cooperative mode of regulation rather than competitive binding. Further, we identify RNAs dynamically interacting with Imp/Syp across development, consisting of existing and potentially new candidates of the neurogenesis program, and loss of Imp or Syp disrupts expression of key transcripts denotative of early or late-born neurons. Together, our findings highlight a post-transcriptional regulatory network that influences temporal order, and our study is a valuable resource for future studies finely-dissecting molecular mechanisms of neuronal fate specifications.

overall_design: iCLIP of Imp and Syp in developing Drosophila nervous system at 24, 48 and 96 hours after larval hatching. 2-3 replicates each for immunoprecipitate and size-mated input samples.

first: Niles

last: Huang

first: Tamsin

last: Samuels

first: Ilan

last: Davis


title: Potential off-targets investigation of a lead antisense oligonucleotides targeting ABCA4 c.768G>T in retinal organoids

city: Nijmegen

first: Dyah

middle: Winiarty

last: Karjosukarso

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboudumc

summary: Stargardt disease type 1 (STGD1) is a progressive retinal disorder caused by bi-allelic variants in the ABCA4 gene. More than 2,400 unique ABCA4 variants have been described, a significant proportion of which affects pre-mRNA splicing. A recurrent variant at the exon-intron junction of exon 6, c.768G>T causes a 35 nt elongation of exon 6 that leads to premature termination of protein synthesis. Testing of antisense oligonucleotides (AON) in photoreceptor precursor cells and retinal organoids allowed the selection of a lead candidate AON that performed the best in rescuing the splicing defect caused by ABCA4 c.768G>T. Total transcriptomics analysis was performed to investigate the potential off-targets of this AON.

overall_design: Retinal organoids were treated with 10 uM of the lead candidate AON or its sense oligonucleotidesfor 10 days. RNA was isolated from these materials and subsequently subjected to total RNA-seq with rRNA depletion. Two independent biological replicates were included in the analysis

first: Rob

last: Collin

first: Sander

last: Bervoets

first: Lonneke

last: Duijkers

first: Femke

last: Bukkems


title: Discrete vulnerability to pharmacological CDK2 inhibition is governed by heterogeneity of the cancer cell cycle

city: Buffalo

first: Jianxin

last: Wang

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

summary: Cyclin dependent kinase 2 (CDK2) regulate cell cycle and is an emerging target for cancer therapy.  There are relatively small numbers of tumor models that exhibit strong dependence on CDK2 and undergo G1 cell cycle arrest following CDK2 inhibition. The expression of P16INK4A and cyclin E1 determines this sensitivity to CDK2 inhibition. The co-expression of these genes occurs in breast cancer patients highlighting their clinical significance as predictive biomarkers for CDK2-targeted therapies.  In cancer models that are genetically independent of CDK2; pharmacological inhibitors suppress cell proliferation by inducing 4N cell cycle arrest and increasing the expressions of phospho-CDK1 (Y15) and cyclin B1.   CRISPR screens identifiy CDK2 loss as a mediator of resistance to INX-315. Furthermore, CDK2 deletion reverses the G2/M block induced by CDK2 inhibitors and restores cell proliferation. Complementary drug screens define multiple means to cooperate with CDK2 inhibition beyond G1/S. These include the depletion of mitotic regulators as well as CDK4/6 inhibitors cooperate with CDK2 inhibition in multiple phases of the cell cycle.  Overall, this study underscores two fundamentally distinct features of response to CDK2 inhibitors that are conditioned by tumor context and could serve as the basis for differential therapeutic strategies in a wide range of cancers.

overall_design:
MB157-WT, MB157-RBdel, MCF7 and HCC1806 were seeded in 6 well dish at a denisty of 100,000 cells/well. Following 24 hours, the cells were treated with 0.1% DMSO and INX-315 (100 nM). The tretments were done in triplicates. The cells were exposed to the INX-315 for 48 hours and RNA was extracted using Qiagen RNeasy plus kit.

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company will not provide the raw data files
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first: Vishnu

last: Kumarasamy

first: Michelle

last: Roti

first: Yin

last: Wan

first: Adam

last: Dommer

first: Hanna

last: Rosenheck

first: Sivasankar

last: Putta

first: Alec

last: Trub

first: John

last: Bisi

first: Jay

last: Strum

first: Patrick

last: Roberts

first: Seth

last: Rubin

first: Costakis

last: Frangou

first: Karen

last: McLean

first: Erik

last: Knudsen

first: Agnieszka

middle: K

last: Witkiewicz


title: Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Hypertranscription occurs at targets of oncogene transcription factors in aggressive human cancers. However, detection relies on mRNAs which are heavily processed and have variable half-lives, and on accurate cell number estimations. Here we apply FFPE-CUTAC on slides and curls to quantify hypertranscription at regulatory elements and replication-coupled histone genes.

overall_design: We used FFPE-CUTAC, a modification of the CUT&Tag chromatin profiling strategy, whereby antibody-targeted controlled integration of DNA sequencing adapters at sites of paused RNA Polymerase II or between nucleosomes flanking open chromatin sites produces libraries for paired-end sequencing from Formalin-Fixed Paraffin-Embedded (FFPE) sections.

first: Steven

middle: G

first: Ronald

last: Paranal

first: Jacob

last: Greene

first: Zachary

middle: R

last: Russell

first: Frank

last: Szulzewsky

first: Sita

last: Kugel

first: Eric

middle: C

last: Holland

first: Kami

last: Ahmad

first: Ye

last: Zheng