title: Immune profiling of murine cardiac leukocytes identifies Trem2 as a novel mediator of hypertensive heart failure

city: Nashville

first: Charles

middle: Duncan

last: Smart

address: 2201 West End Ave

department: Molecular Physiology and Biophysics

institute: Vanderbilt University

summary: Heart failure with preserved ejection fraction (HFpEF) is characterized by diastolic dysfunction, microvascular dysfunction and myocardial fibrosis with recent evidence implicating the immune system in orchestrating cardiac remodeling. Here, we show the mouse model of deoxycorticosterone acetate (DOCA)-salt hypertension induces key elements of HFpEF, including diastolic dysfunction, exercise intolerance, and pulmonary congestion in the setting of preserved ejection fraction. CITE-Seq analysis of cardiac immune cells reveals an altered abundance and/or transcriptional signature in multiple cell types, most notably cardiac macrophages. The DOCA-salt model results in differential expression of several known and novel genes in cardiac macrophages, including upregulation of Trem2, which was also recently implicated in obesity and atherosclerosis. The role of macrophage Trem2 in cardiac remodeling, however, is unknown. We found that mice with genetic deletion of Trem2 exhibit increased cardiac hypertrophy and decreased cardiac capillary density after DOCA-salt treatment compared to wild-type controls, and Trem2-deficient macrophages have impaired expression of pro-angiogenic gene programs. Furthermore, we found that plasma levels of soluble TREM2 are elevated in human heart failure. Together, our data suggest a novel cardioprotective role for macrophage Trem2 in cardiac remodeling and heart failure and provide an atlas for the identification of additional targets that can lead to improved diagnostic and therapeutic strategies for HFpEF.

overall_design: Cardiac immune cells were isolated by mechanical and enzymatic digestion (Liberase TM), enriched with microbeads to CD45, stained with hashtags and extracellular antibodies, flow sorted on live single immune cells and loaded onto the 10X controller for single cell sequencing.

first: Daniel

last: Fehrenbach

first: Jean

middle: W

last: Wassenar

first: Vineet

last: Agarwal

first: Debra

last: Dixon

first: Niki

last: Fortune

first: Mattew

last: Cottam

first: Alyssa

last: Hasty

first: Anna

last: Hemnes

first: Amanda

last: Doran

first: Deepak

last: Gupta

first: Meena

middle: S

last: Madhur


title: TF ChIP-seq from HepG2 (ENCSR539PMH)

status: Public on Apr 30 2023

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR238XDV)


title: TF ChIP-seq from WTC11 (ENCSR962BEI)

summary:
ChIP-Seq on WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR231NMZ)


title: TF ChIP-seq from HepG2 (ENCSR237OGW)


title: TF ChIP-seq from HepG2 (ENCSR537FDJ)


title: TF ChIP-seq from WTC11 (ENCSR229QAN)


title: TF ChIP-seq from K562 (ENCSR229KXQ)

summary:
ChIP-Seq on K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from glutamatergic neuron (ENCSR950CIR)

summary:
eGFP-FOSL1 ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR225UTR)


title: TF ChIP-seq from HepG2 (ENCSR957LTN)


title: TF ChIP-seq from HepG2 (ENCSR523RGJ)


title: TF ChIP-seq from K562 (ENCSR955LXM)


title: TF ChIP-seq from HepG2 (ENCSR512JVC)


title: TF ChIP-seq from WTC11 (ENCSR513WUJ)


title: TF ChIP-seq from K562 (ENCSR516SWI)


title: TF ChIP-seq from WTC11 (ENCSR508NBY)

summary:
eGFP-TOX4 ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR216GKQ)


title: TF ChIP-seq from WTC11 (ENCSR214RUE)


title: TF ChIP-seq from WTC11 (ENCSR943MQH)


title: TF ChIP-seq from HepG2 (ENCSR946BKU)


title: TF ChIP-seq from HepG2 (ENCSR211BDR)


title: TF ChIP-seq from WTC11 (ENCSR507RVF)


title: TF ChIP-seq from HepG2 (ENCSR507BRS)


title: TF ChIP-seq from HepG2 (ENCSR941WVJ)


title: TF ChIP-seq from HepG2 (ENCSR505ELD)


title: TF ChIP-seq from K562 (ENCSR940PYZ)


title: TF ChIP-seq from HepG2 (ENCSR204ZIN)


title: TF ChIP-seq from K562 (ENCSR498JCG)


title: TF ChIP-seq from HepG2 (ENCSR203UQM)


title: TF ChIP-seq from K562 (ENCSR225OGU)


title: TF ChIP-seq from HepG2 (ENCSR202OLE)


title: TF ChIP-seq from HepG2 (ENCSR494HMS)


title: TF ChIP-seq from K562 (ENCSR942XQI)

summary:
eGFP-RAD21 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR938SDM)


title: TF ChIP-seq from K562 (ENCSR201DCF)


title: TF ChIP-seq from K562 (ENCSR493JTJ)


title: TF ChIP-seq from WTC11 (ENCSR203PCF)


title: TF ChIP-seq from HepG2 (ENCSR200AWS)


title: TF ChIP-seq from HepG2 (ENCSR932BNN)


title: TF ChIP-seq from HepG2 (ENCSR210DDA)


title: TF ChIP-seq from WTC11 (ENCSR199PXS)


title: TF ChIP-seq from HepG2 (ENCSR929KSH)


title: TF ChIP-seq from HepG2 (ENCSR482SWD)


title: TF ChIP-seq from HepG2 (ENCSR478ZYO)


title: TF ChIP-seq from WTC11 (ENCSR934WOF)


title: TF ChIP-seq from WTC11 (ENCSR928BPP)


title: TF ChIP-seq from HepG2 (ENCSR478SKI)


title: TF ChIP-seq from HEK293 (ENCSR186JMM)

summary:
ChIP-Seq on HEK293

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR199MFT)


title: TF ChIP-seq from K562 (ENCSR926TAH)


title: TF ChIP-seq from K562 (ENCSR475ZGL)


title: TF ChIP-seq from HepG2 (ENCSR924KZA)


title: TF ChIP-seq from K562 (ENCSR924JOW)


title: TF ChIP-seq from WTC11 (ENCSR473ASI)


title: TF ChIP-seq from HepG2 (ENCSR178SXA)


title: TF ChIP-seq from HepG2 (ENCSR917SSX)


title: TF ChIP-seq from K562 (ENCSR166BAY)


title: TF ChIP-seq from HepG2 (ENCSR175MIA)


title: TF ChIP-seq from K562 (ENCSR471WXT)


title: TF ChIP-seq from WTC11 (ENCSR454GVT)


title: TF ChIP-seq from HepG2 (ENCSR165EGX)


title: TF ChIP-seq from HepG2 (ENCSR727IJD)


title: TF ChIP-seq from HepG2 (ENCSR913KJZ)


title: TF ChIP-seq from HepG2 (ENCSR912NEF)


title: TF ChIP-seq from WTC11 (ENCSR722OTA)


title: TF ChIP-seq from HepG2 (ENCSR443YTB)


title: TF ChIP-seq from K562 (ENCSR163VTS)


title: TF ChIP-seq from HepG2 (ENCSR722IIB)


title: TF ChIP-seq from WTC11 (ENCSR910UQX)


title: TF ChIP-seq from HepG2 (ENCSR440OJH)


title: TF ChIP-seq from K562 (ENCSR436CZV)


title: TF ChIP-seq from HepG2 (ENCSR907PAR)


title: TF ChIP-seq from HepG2 (ENCSR163PYB)


title: TF ChIP-seq from glutamatergic neuron (ENCSR431UCR)

summary:
eGFP-ID3 ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR155IXY)


title: TF ChIP-seq from K562 (ENCSR906CWK)

summary:
eGFP-ZFPM2 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR715EIP)


title: TF ChIP-seq from HepG2 (ENCSR720ODW)


title: TF ChIP-seq from K562 (ENCSR153DWR)


title: TF ChIP-seq from HepG2 (ENCSR430BKC)


title: TF ChIP-seq from WTC11 (ENCSR156JWW)


title: TF ChIP-seq from K562 (ENCSR901VIE)


title: TF ChIP-seq from WTC11 (ENCSR150LGS)


title: TF ChIP-seq from HepG2 (ENCSR898XQZ)


title: TF ChIP-seq from WTC11 (ENCSR700LFA)


title: TF ChIP-seq from HepG2 (ENCSR148FHD)


title: TF ChIP-seq from HepG2 (ENCSR888QFJ)


title: TF ChIP-seq from K562 (ENCSR427XYP)


title: TF ChIP-seq from HepG2 (ENCSR893BAO)


title: TF ChIP-seq from WTC11 (ENCSR713KVZ)


title: TF ChIP-seq from WTC11 (ENCSR426WZU)

summary:
EGR1 ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from WTC11 (ENCSR146UIC)


title: TF ChIP-seq from HepG2 (ENCSR699ZES)


title: TF ChIP-seq from WTC11 (ENCSR887VJM)


title: TF ChIP-seq from HepG2 (ENCSR141XJW)


title: TF ChIP-seq from WTC11 (ENCSR879YNX)


title: TF ChIP-seq from HepG2 (ENCSR421ADK)


title: TF ChIP-seq from HepG2 (ENCSR697CNF)


title: TF ChIP-seq from K562 (ENCSR696URR)


title: TF ChIP-seq from K562 (ENCSR140GLO)


title: TF ChIP-seq from HepG2 (ENCSR423TVD)


title: TF ChIP-seq from HepG2 (ENCSR879RGN)


title: TF ChIP-seq from HepG2 (ENCSR693TYT)


title: TF ChIP-seq from HepG2 (ENCSR692RKS)


title: TF ChIP-seq from HepG2 (ENCSR136QQF)


title: TF ChIP-seq from HEK293 (ENCSR418XXL)


title: TF ChIP-seq from HepG2 (ENCSR689JMY)


title: TF ChIP-seq from HepG2 (ENCSR875FZN)


title: TF ChIP-seq from HepG2 (ENCSR410LFU)


title: TF ChIP-seq from HepG2 (ENCSR136EQX)


title: TF ChIP-seq from K562 (ENCSR409PXW)


title: TF ChIP-seq from K562 (ENCSR133DMU)


title: TF ChIP-seq from HepG2 (ENCSR685GGQ)


title: TF ChIP-seq from HepG2 (ENCSR407MQT)


title: TF ChIP-seq from HepG2 (ENCSR409DYM)


title: TF ChIP-seq from HepG2 (ENCSR871EQD)


title: TF ChIP-seq from K562 (ENCSR124YFA)


title: TF ChIP-seq from WTC11 (ENCSR866VOW)


title: TF ChIP-seq from HepG2 (ENCSR125MLR)


title: TF ChIP-seq from HEK293 (ENCSR865HXK)


title: TF ChIP-seq from HepG2 (ENCSR864WKA)


title: TF ChIP-seq from HepG2 (ENCSR397EOT)


title: TF ChIP-seq from HepG2 (ENCSR860ONE)


title: TF ChIP-seq from HepG2 (ENCSR392TWV)


title: TF ChIP-seq from K562 (ENCSR676KDJ)

summary:
eGFP-ARID4B ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR672OHP)


title: TF ChIP-seq from HepG2 (ENCSR117XJA)


title: TF ChIP-seq from HepG2 (ENCSR124QQJ)


title: TF ChIP-seq from K562 (ENCSR392JVX)


title: TF ChIP-seq from WTC11 (ENCSR859ZAC)


title: TF ChIP-seq from WTC11 (ENCSR115QIT)


title: TF ChIP-seq from HepG2 (ENCSR384YOP)


title: TF ChIP-seq from HepG2 (ENCSR853BYT)


title: TF ChIP-seq from dorsolateral prefrontal cortex (ENCSR384DBJ)

summary:
CTCF TF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR850YDX)


title: TF ChIP-seq from WTC11 (ENCSR381IES)


title: TF ChIP-seq from HepG2 (ENCSR655QNQ)


title: TF ChIP-seq from HepG2 (ENCSR377GZS)


title: TF ChIP-seq from K562 (ENCSR652OGX)


title: TF ChIP-seq from HepG2 (ENCSR115LFG)


title: TF ChIP-seq from HepG2 (ENCSR110GQV)


title: TF ChIP-seq from WTC11 (ENCSR373ZOY)


title: TF ChIP-seq from HepG2 (ENCSR656RTA)


title: TF ChIP-seq from HEK293 (ENCSR847PFO)


title: TF ChIP-seq from K562 (ENCSR645ZWR)


title: TF ChIP-seq from HepG2 (ENCSR102YQB)


title: TF ChIP-seq from MCF-7 (ENCSR848QXX)

summary:
eGFP-TSC22D1 ChIP-seq on human MCF-7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR124XCX)


title: TF ChIP-seq from WTC11 (ENCSR092DCD)


title: TF ChIP-seq from WTC11 (ENCSR373KKV)


title: TF ChIP-seq from K562 (ENCSR372IML)


title: TF ChIP-seq from HepG2 (ENCSR095JQV)


title: TF ChIP-seq from K562 (ENCSR091IQZ)

summary:
eGFP-DMBX1 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR846FMR)


title: TF ChIP-seq from K562 (ENCSR368GJN)


title: TF ChIP-seq from HepG2 (ENCSR642PQK)


title: TF ChIP-seq from WTC11 (ENCSR640STN)


title: TF ChIP-seq from K562 (ENCSR845GGY)


title: TF ChIP-seq from glutamatergic neuron (ENCSR364POR)


title: TF ChIP-seq from HepG2 (ENCSR088LFR)


title: TF ChIP-seq from WTC11 (ENCSR634WRC)


title: TF ChIP-seq from K562 (ENCSR085XDP)


title: TF ChIP-seq from K562 (ENCSR841GLE)


title: TF ChIP-seq from K562 (ENCSR361UTL)


title: TF ChIP-seq from K562 (ENCSR084WHZ)


title: TF ChIP-seq from K562 (ENCSR360ECJ)


title: TF ChIP-seq from HepG2 (ENCSR081VFY)


title: TF ChIP-seq from K562 (ENCSR628DJK)


title: TF ChIP-seq from HepG2 (ENCSR634GEO)


title: TF ChIP-seq from WTC11 (ENCSR352RXE)


title: TF ChIP-seq from MCF-7 (ENCSR079SHZ)

summary:
eGFP-OTX1 ChIP-seq on human MCF-7

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR827ZGB)


title: TF ChIP-seq from HepG2 (ENCSR810DBO)


title: TF ChIP-seq from K562 (ENCSR626HJW)


title: TF ChIP-seq from WTC11 (ENCSR350LBJ)


title: TF ChIP-seq from HepG2 (ENCSR823QTA)


title: TF ChIP-seq from HepG2 (ENCSR613YQN)


title: TF ChIP-seq from HepG2 (ENCSR620ZUC)


title: TF ChIP-seq from HepG2 (ENCSR073OBD)


title: TF ChIP-seq from HepG2 (ENCSR808FZR)


title: TF ChIP-seq from WTC11 (ENCSR349FYX)


title: TF ChIP-seq from WTC11 (ENCSR804OBA)


title: TF ChIP-seq from HepG2 (ENCSR605JAI)


title: TF ChIP-seq from K562 (ENCSR609ZLF)


title: TF ChIP-seq from WTC11 (ENCSR836SPL)


title: TF ChIP-seq from K562 (ENCSR068QXO)


title: TF ChIP-seq from HEK293 (ENCSR600SMN)


title: TF ChIP-seq from K562 (ENCSR338UQU)


title: TF ChIP-seq from WTC11 (ENCSR063FUV)


title: TF ChIP-seq from HepG2 (ENCSR062TDX)


title: TF ChIP-seq from HepG2 (ENCSR828TVO)


title: TF ChIP-seq from HepG2 (ENCSR329RRQ)


title: TF ChIP-seq from K562 (ENCSR809JSD)


title: TF ChIP-seq from HepG2 (ENCSR803PAI)


title: TF ChIP-seq from K562 (ENCSR800KMQ)


title: TF ChIP-seq from HepG2 (ENCSR318GET)


title: TF ChIP-seq from K562 (ENCSR799URB)


title: TF ChIP-seq from HepG2 (ENCSR591MYB)


title: TF ChIP-seq from HepG2 (ENCSR056SXR)


title: TF ChIP-seq from WTC11 (ENCSR795KRU)


title: TF ChIP-seq from WTC11 (ENCSR048PPE)


title: TF ChIP-seq from HepG2 (ENCSR590BHJ)


title: TF ChIP-seq from HEK293 (ENCSR294SAK)


title: TF ChIP-seq from HepG2 (ENCSR308LFD)


title: TF ChIP-seq from HepG2 (ENCSR782WWY)


title: TF ChIP-seq from WTC11 (ENCSR583CGO)


title: TF ChIP-seq from WTC11 (ENCSR285HHZ)


title: TF ChIP-seq from K562 (ENCSR044UJJ)

summary:
eGFP-ATF4 ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from WTC11 (ENCSR579RFH)


title: TF ChIP-seq from HepG2 (ENCSR775EOB)


title: TF ChIP-seq from HepG2 (ENCSR037LQB)


title: TF ChIP-seq from WTC11 (ENCSR284SMX)


title: TF ChIP-seq from WTC11 (ENCSR572DUR)

summary:
eGFP-FOS ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from WTC11 (ENCSR592ZQB)


title: TF ChIP-seq from HepG2 (ENCSR039IQA)

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR765VDK)


title: TF ChIP-seq from WTC11 (ENCSR760GZL)

summary:
ChIP-Seq on WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HepG2 (ENCSR282ZLP)


title: TF ChIP-seq from WTC11 (ENCSR032DGZ)


title: TF ChIP-seq from K562 (ENCSR279IMD)

summary:
ChIP-Seq on K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from WTC11 (ENCSR034IND)


title: TF ChIP-seq from K562 (ENCSR784IMK)


title: TF ChIP-seq from K562 (ENCSR755CRA)


title: TF ChIP-seq from WTC11 (ENCSR753PPY)


title: TF ChIP-seq from WTC11 (ENCSR029OPK)


title: TF ChIP-seq from WTC11 (ENCSR264OKN)


title: TF ChIP-seq from K562 (ENCSR269BSA)


title: TF ChIP-seq from K562 (ENCSR568ZXG)


title: TF ChIP-seq from glutamatergic neuron (ENCSR749BFL)


title: TF ChIP-seq from WTC11 (ENCSR564TIP)


title: TF ChIP-seq from HepG2 (ENCSR747MFU)


title: TF ChIP-seq from WTC11 (ENCSR261EBV)


title: TF ChIP-seq from WTC11 (ENCSR744RAS)

summary:
eGFP-GRHL2 ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from K562 (ENCSR015KAM)


title: TF ChIP-seq from HepG2 (ENCSR560HRJ)


title: TF ChIP-seq from HepG2 (ENCSR569GKR)


title: TF ChIP-seq from HepG2 (ENCSR031WWM)


title: TF ChIP-seq from HepG2 (ENCSR250LJG)


title: TF ChIP-seq from WTC11 (ENCSR561YGS)


title: TF ChIP-seq from WTC11 (ENCSR546PDE)


title: TF ChIP-seq from K562 (ENCSR014ARU)


title: TF ChIP-seq from HepG2 (ENCSR267TGY)


title: TF ChIP-seq from K562 (ENCSR744GHR)


title: TF ChIP-seq from WTC11 (ENCSR029TLS)


title: TF ChIP-seq from HepG2 (ENCSR545ADB)


title: TF ChIP-seq from K562 (ENCSR013UDY)


title: TF ChIP-seq from WTC11 (ENCSR245QUM)


title: TF ChIP-seq from HepG2 (ENCSR263YXJ)


title: TF ChIP-seq from K562 (ENCSR028WJI)


title: TF ChIP-seq from K562 (ENCSR744CXJ)


title: TF ChIP-seq from K562 (ENCSR058DRG)


title: TF ChIP-seq from HepG2 (ENCSR553ZJQ)


title: The KEAP1-NRF2 pathway regulates TFEB/TFE3-dependent lysosomal biogenesis

city: Melbourne

first: Andrew

last: Cox

state: Victoria

address: 305 Grattan St

country: Australia

institute: PeterMacCallum Cancer Centre

type: Expression profiling by high throughput sequencing

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

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Refer to individual Series


title: TF ChIP-seq from K562 (ENCSR249VFB)


title: T cell stimulation of resolved and non lesional epidermis- psoriasis patients

city: besancon

first: irène

last: gallais sérézal

address: boulevard stalingrad

country: France

institute: CHU Besançon

summary: Biopsies were stimulated with OKT3 16 hours, epidermis was separated from dermis, RNA was purified and nanostring analysis was performed on a custom panel of transcripts.

overall_design: 13 patients were included

first: I

middle: G

last: Sérézal

first: Y

last: El Mahi


title: TF ChIP-seq from WTC11 (ENCSR248QBT)


title: The KEAP1-NRF2 pathway regulates TFEB/TFE3-dependent lysosomal biogenesis [RNA-seq: HepG2 cells sitfebtfe3]

summary: Under homeostatic conditions, NRF2 is repressed by Kelch-like ECH-associated protein 1 (KEAP1). Here, we demonstrate that Keap1 deficiency induces Nrf2 activation and post-developmental lethality in zebrafish larvae. Loss of viability is preceded by severe liver abnormalities characterized by an accumulation of lysosomes. Mechanistically, we demonstrate that loss of Keap1 promotes aberrant activation of transcription factor EB (TFEB)/transcription factor binding to IGHM Enhancer 3 (TFE3)-dependent lysosomal biogenesis. Importantly, we find that NRF2-dependent regulation of lysosomal biogenesis is cell autonomous and evolutionarily conserved.

overall_design: HepG2 cells were transduced with lentiCRISPRv2 containing guides for either sgAAVS168, KEAP1 (sequence 1 or 2) and transfected with siRNAs targeting a non-targeting control or TFEB and TFE3.

first: Athena

middle: J

last: Ong

first: Kristin

last: Brown


title: Single Nucleus RNA sequencing of the mouse placental junctional zone

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: To characterise the transcriptome of mouse placental junctional zone cells in Control litters (deletion of the maternally-inherited and silent Igf2 allele, with normal Igf2 levels in whole litters) in UE litters (dams carried offspring with a deletion of the paternally-inherited Igf2 allele in the placental endocrine cells with diminished Igf2 production from the endocrine cells in whole litters), we performed single nucleus RNA sequencing on the placenta Junctional zone 8 Control placentas (offspring sex: 4M:4F) and 8 UE placentas (offspring sex: 4M:4F) in 2 batches each.

overall_design: The placental junctional zone was dissected from 8 Control and 8 UE litters and stored at -80ºC. Single nucleus suspensions were made, pooling together 2x 4 junctional zones from Control litters (offspring sex: 2M, 2F) and 2x 4 junctional zones from UE litters (offspring sex: 2M, 2F), totalling 4 different samples. Suspensions were FACS sorted for DRAQ5 positive events. Single nucleus RNA sequencing libraries were generated using the 10X Chromium single cell 3' reagents.

first: Jorge

last: Lopez-Tello

first: Ionel

last: Sandovici

first: Georgina

middle: K

last: Dowsett

first: Giles

last: Yeo

middle: Y

first: Miguel

last: Constancia

middle: N

last: Sferuzzi-Perri


title: CCL24 regulates biliary inflammation and fibrosis in primary sclerosing cholangitis

city: Jerusalem

first: Yuval

last: Nevo

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University of Jerusalem

summary: CCL24 is a profibrotic, proinflammatory chemokine expressed in several chronic fibrotic diseases. In the liver, CCL24 plays a role in fibrosis and inflammation and blocking CCL24 led to reduced liver injury in experimental models. We studied the role of CCL24 in primary sclerosing cholangitis (PSC) and evaluated the potential therapeutic effect of blocking CCL24 in this disease. Mdr2-/- mice demonstrated CCL24 expression in liver macrophages and were used as a relevant experimental PSC model. CCL24 neutralizing monoclonal antibody, CM-101, significantly improved inflammation, fibrosis and cholestasis-related markers in the biliary area. Moreover, using spatial transcriptomics we observed reduced proliferation and senescence of cholangiocytes following CCL24 neutralization. Next, we demonstrated that CCL24 expression was elevated under profibrotic conditions in primary human cholangiocytes and macrophages and it induced proliferation of primary human hepatic stellate cells and cholangiocytes, which was attenuated following CCL24 inhibition. Correspondingly, CCL24 was found to be highly expressed in liver biopsies of PSC patients. CCL24 serum levels correlated with Enhanced Liver Fibrosis score, most notably in patients with high alkaline phosphatase levels. These results suggest that blocking CCL24 may have a therapeutic effect in PSC patients via reduced liver inflammation, fibrosis and cholestasis.

overall_design: Levels of chemokines and chemokine receptors were compared between liver cells populations. A single liver lobe sample from Mdr-2 KO mouse.

first: Raanan

last: Greenman

first: Michal

last: Segal-Salt

first: Neta

last: Barashi

first: Ophir

last: Hay


title: The KEAP1-NRF2 pathway regulates TFEB/TFE3-dependent lysosomal biogenesis [RNA-seq: HepG2 cells KeapKO]

first: Andrew

last: Cox

overall_design: HepG2 cells were transduced with lentiCRISPRv2 containing guides for either sgAAVS168, KEAP1 (sequence 1 or 2).


title: Gene expression profile in the atrial fibrillation patient right atrial appendages

city: Akita

first: Yosuke

last: Okamoto

address: 1-1-1 Hondo

department: Cell Physiology

country: Japan

institute: Akita University Graduate School of Medicine

summary: Atrial fibrillation (AF) is the most frequent persistent arrhythmia, and many genes have been reported as a causal gene candidate for AF. However, most transcriptome analyses of AF have limited to the atrial samples and have not evaluated by multiple cardiac regions. In this study, we analyzed the expression levels of protein-coding and long noncoding RNAs (lncRNAs) in six different cardiac regions by RNA-seq. Surprisingly, the most changed region in gene expression by the presence of AF was the pulmonary vein (PV), not the atria. Upon analysis of these significant genes, the ion channel-related gene set was significantly enriched. In addition, cancer-related lncRNAs was up-regulated in PV in AF. A Co-expression network analysis could detect the functional gene clusters. In particular, the functional coupling between the lncRNA FOXCUT and transcription factor FOXC1 are known to be involved in process of the epithelial-mesenchymal transition in cancer tissues. Thus, they may also play an aggravating role in the pathogenesis of AF. In the least, this study suggests that (1) RNA alteration is most intense in PVs and (2) post-acquired gene regulation, such as the FOXCUT-FOXC1 axis, may contribute to the progression of AF.

overall_design: High-througput sequence was demonstrated with NovaSeq 6000 (Illumina). First, extracted RNAs were purified by poly(A) capture. Resultant mRNAs were then fragmented and reverse-transcribed into single-stranded complementary DNAs (cDNAs). Subsequently, cDNAs were double-stranded by a DNA polymerase. During the polymerase reactions, deoxy UTP (dUTP) were mixed in nucleotide materials. Both ends of double-stranded DNA (ds DNA) were ligated to a 13 bp adapter sequence. Next, the ds DNAs were subjected to PCR amplification for the multi-sized DNA library preparation. NovaSeq Control software v1.4.0 analyzed the sequencing runs and tag sequences classified each read in the raw sequencing data. A total of 4 RNA-seq data were used for human right atrial appendages. fastp software (version 0.12.4) was used for Read quality control and adapter removal. Reads were aligned using STAR software (version 2.7.0a).

first: Wataru

last: Igarashi

first: Daichi

last: Takagi

first: Daigo

last: Okada


title: Gene expression profile in the atrial fibrillation patient hearts across seven heart regions

overall_design: High-througput sequence was demonstrated with NovaSeq 6000 (Illumina). First, extracted RNAs were purified by poly(A) capture. Resultant mRNAs were then fragmented and reverse-transcribed into single-stranded complementary DNAs (cDNAs). Subsequently, cDNAs were double-stranded by a DNA polymerase. During the polymerase reactions, deoxy UTP (dUTP) were mixed in nucleotide materials. Both ends of double-stranded DNA (ds DNA) were ligated to a 13 bp adapter sequence. Next, the ds DNAs were subjected to PCR amplification for the multi-sized DNA library preparation. NovaSeq Control software v1.4.0 analyzed the sequencing runs and tag sequences classified each read in the raw sequencing data. A total of 21 RNA-seq data were used for three samples each of sinoatrial node (SAN), left atrium (LA), right atrium (RA), left ventriclle (LV), right ventricle (RV), pulmonary vein (PV), and left atrial appendage (LAA), LV, pulmonary vein (PV). fastp software (version 0.12.4) was used for Read quality control and adapter removal. Reads were aligned using STAR software (version 2.7.0a).

first: Miho

last: Oka

first: Toshiro

last: Io


title: Hematopoiesis and cell growth are differentially regulated by TAL1 isoforms

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

institute: HUJI

summary: T-cell acute lymphoblastic leukemia (T-ALL) protein 1 (TAL1) is a central transcription factor in hematopoiesis. The timing and level of TAL1 expression orchestrate the differentiation to specialized blood cells and its overexpression is the most common cause of T-ALL. Here we studied the two protein isoforms of TAL1, short and long, that are generated by the use of alternative promoters as well as by alternative splicing. We analyzed the expression of each isoform by deleting an enhancer or insulator, or by opening chromatin at the enhancer location. Our results show that each enhancer promotes expression from a specific TAL1 promoter. Expression from a specific promoter gives rise to a unique 5’ UTR with differential regulation of translation. In addition, the enhancers regulate TAL1 exon 3 alternative splicing by altering the chromatin at its location. Furthermore, our results indicate that TAL1-short binds more strongly to TAL1 E-protein partners and function as a stronger transcription factor than TAL1-long. Specifically TAL1-short has a unique transcription signature promoting apoptosis. Finally, expressing both isoforms in mice bone marrow, we found that while overexpression of both isoforms prevents lymphoid differentiation, expression of TAL-short alone reduced survival capability of hematopoietic stem cells. Furthermore, we found that TAL1-short promoted erythropoiesis and reduced cell survival in the AML cell line K562. While TAL1 and its partners are considered promising therapeutic targets in the treatment of T-ALL, our results show that TAL1-short could act as a tumor suppressor and suggest that altering TAL1 isoform’s ratio could be a preferred therapeutic approach.

overall_design: We silenced endogenous TAL1 by stably transfecting Jurkat cells with inducible TAL1 shRNA targeting its 3’ UTR, and by that targeting only the endogenous mRNA. We continued by transfecting either empty vector, TAL1-short or TAL1-long and monitored total mRNA amount of the targets.

first: Aveksha

last: Sharma

first: Shani

last: Mistriel-Zerbib

first: Rauf

middle: A

last: Najar

first: Maayan

last: Salton


title: TF ChIP-seq from K562 (ENCSR011WGT)

first: ENCODE

last: DCC


title: Comparison between sinus rhythm and atrial fibrillation samples from eight different cardiac regions


title: Gene expression analysis of mouse brain.

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

summary: Inbred mouse strains differ in their innate anxiety levels. We used RNA-sequencing to identify gene expression differences in hippocampus and frontal cortex of six mouse strains.

overall_design: Mice were singly housed for one week before dissections and killed by cervical dislocation between 8 a.m. and 11 a.m. Dissections were performed on a Petri dish filled with ice. FCx included 2 mm of the anterior part of the cortex. The Hpc was dissected whole. Samples were directly frozen in liquid nitrogen and stored in -80°C. We extracted total RNA with TriReagent according to the manufacturer’s instructions and verified its quality by the Agilent Bioanalyzer Small RNA Analysis and RNA 6000 Nano Kits. Ribo-depleted RNA was sequenced with Illumina High-Seq 2000.


title: Chromatin opening by p53 is confined by Trim24 in a histone methylation-dependent manner [ChIP-seq]

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

institute: SAiGENCI

summary: Chromatin modifications are thought to provide additional context dependence for sequence-based gene activation. Binding sites of the transcription factor (TF) and important tumor suppressor p53 are unusually diverse with regards to their chromatin accessibility and histone modifications, suggesting different modes of binding. Here, we show that the ability of p53 to open chromatin and activate its target genes upon DNA damage is locally restricted by its cofactor Trim24. The histone-binding domains of Trim24 limit the role of p53 at closed chromatin but not at accessible chromatin where Trim24 is blocked by histone 3 methylation at lysine 4. In turn p53 regulates gene expression as a function of the naïve chromatin state prior to activation.   These findings establish a set of p53 response genes in closed chromatin that are Trim24-regulated and illustrate how histone modification sensing cofactors bridge local chromatin state and TF potency.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of p53 and Trim24 function in cell lines including mouse embryonic stem cells. Includes p53 ChIPseq in WT mouse ESCs in untreated/p53activated conditions (duplicates), p53 ChIPseq in DNMT-triple KO and parental line mouse ESCs (triplicates), p53 ChIPseq in Trim24-degron tagged mouse ESC lines under Trim24degraded/untreated/p53activated/p53activated;Trim24degraded conditions (duplicates), p53 ChIPseq in p53-degron tagged mouse ESC lines under p53untreated/p53-activated conditions (duplicates), p53 ChIPseq human HMEC cells in untreated/p53activated conditions. Includes Trim24 ChIPseq in WT mouse ESCs in untreated/p53activated conditions (duplicates), Trim24 ChIPseq in p53-degron tagged mouse ESC lines under p53degraded/untreated conditions (duplicates). Includes addback-FlagNLS-Tagged-mutant Trim24 ChIPseq in Trim24-KO mouse ESCs for WT-Trim24/Nterminal-Trim24/Ndeletion-Trim24/PHDmutant-Trim24/ING1-PHDmutant-Trim24/TAF3-PHDmutant-Trim24 in p53-activated conditions (duplicates). Includes H3K23ac ChIPseq in WT mouse ESCs (duplicates). Includes H3K27ac ChIPseq in p53-degron tagged mouse ESC lines under p53degraded/p53untreated/p53-activated conditions (duplicates). Also includes matched IgG ChIPseq control datasets (duplicates) in all cases.  All conditions to activate p53 or degrade degron tagged alleles performed for 4 hours.

first: Murat

last: Iskar

first: Dirk

last: Schübeler


title: Chromatin opening by p53 is confined by Trim24 in a histone methylation-dependent manner [RNA-seq]

overall_design: Examination of p53 and Trim24 function in cell lines including mouse embryonic stem cells. Includes RNAseq in WT mouse ESCs in untreated/p53activated conditions (duplicates), RNAseq in Trim24-degron tagged mouse ESC lines under Trim24degraded/untreated conditions (triplicates), RNAseq in Trim24-degron tagged mouse ESC lines under p53activated/p53activated;Trim24degraded conditions at multiple timepoints of 2/4/8/12 hours (triplicates). All conditions to activate p53 or degrade degron tagged alleles performed for 4 hours unless specified in a timecourse series.


title: Genome-wide essential gene identification for lysenin-induced cell death using CRISPR/CAS9 screening system

city: Shinjuku-ku

first: Aya

last: Mizuike

state: Tokyo

address: 1-23-1 Toyama

department: Quality Assurance, Radiation Safety and Information System

institute: National Institute of Infectious Diseases

summary: Isolation of genes whose knockout conferring resistance to lysenin-Induced cell death

overall_design: A genome-wide CRISPR/CAS9 knockout screen in HeLa cells was performed to identify factors involved in the regulation of sphingomyelin biosynthesis, delivery, or distribution by exploiting lysenin sensitivity. Lentivirus-based GeCKO v2 pooled library, which is delivered as two half-libraries (A and B), was used. Two independent sgRNAs-expressing cell libraries (A-1, A-2, B-1, B-2) were prepared by transducing the lentivirus libraries, and cells were then treated with lysenin three times. The sgRNAs integrated into the cellular genomes of the surviving cells were amplified by PCR and analyzed with high-throughput sequencing. For untreated controls, cells in each cell library were kept subcultured for the same period as lysenin-treated cells. sgRNA profiles of control and lysenin-treated HeLa cell were generated by next-generation sequencing, using Illumina MiniSeq, in biological duplicates.

first: Toshiyuki

last: Yamaji

first: Kentaro

last: Hanada


title: ETV4 mediates dosage-dependent prostate tumor initiation and cooperates with p53 loss to generate prostate cancer

status: Public on Apr 29 2023

city: New York City

first: Dan

last: Li

state: NY

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

summary: Comparision of single cell transcriptome of prostate cells of T2,EYFP; T2,ETV4WT; T2,ETV4AAA and T2,ETV4AAA,p53L/L mice at 2 weeks and 4 months after TAM treatment

overall_design: Alive prostate cells of TMPRSS2-CreERT2;Rosa26-CAG-LSL-EYFP, TMPRSS2-CreERT2;Rosa26-CAG-LSL-ETV4WT, TMPRSS2-CreERT2;Rosa26-CAG-LSL-ETV4AAA and TMPRSS2-CreERT2;Rosa26-CAG-LSL-ETV4AAA;Trp53L/L mice at 2 weeks and 4 months after tamoxifen treatment were isolated by Fluorescence-activated cell sorting (FACS) according to DAPI and analyzed using scRNAseq.

first: Yu

last: Chen


title: The KEAP1-NRF2 pathway regulates TFEB/TFE3-dependent lysosomal biogenesis [RNA-seq: 7dpf_larvae]

first: Andrew

last: Cox

overall_design: Zebrafish embryos were injected with CRISPR/Cas9 targetting genes at the single-cell stage. RNA was extracted and sequenced at 7dpf.

first: Athena

last: Ong

first: Kristin

last: Brown


title: Transcriptome profiling of lungs from young and aged hamster

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

institute: Inserm 1052

summary: Older age is one of the strongest risk factors for COVID-19 morbidity and mortality. Here, we sought to determine whether age-associated cellular senescence contributes to the severity of COVID-19 by studying the well-established golden hamster model of SARS-CoV-2-driven lung disease. We found that aged hamsters (22 months of age) accumulate senescent cells in the lungs and that the senolytic drug ABT-263 depletes these cells at baseline and during a SARS-CoV-2 infection. Relative to young hamsters (2 months of age), aged hamsters had a greater viral load during the acute phase of infection and displayed higher levels of sequelae during the post-acute phase. Interestingly, early treatment with ABT-263 was associated with a significantly lower pulmonary viral load, an effect associated with lower angiotensin converting enzyme 2, the receptor for SARS-CoV-2, and an amelioration of COVID-19-like lung disease in aged (but not young) animals. ABT-263 treatment of aged animals was also associated with lower pulmonary and systemic levels of senescence-associated secretory phenotype factors. Furthermore, early removal of senescent cells reduced the longer-term pulmonary inflammation. These data demonstrate the causative role of age-associated pre-existing senescent cells on the pathologic severity of experimental COVID-19.

overall_design: Transcriptome analysis has been performed on lung tissue derived from 3 independent Aged (22 months old) Hamster and  4 independent Young Hamster (2 months old)

first: François

last: Trottein

first: David

last: Bernard

first: Jean-Michel

last: Flaman


title: Multi-parametric analysis of human livers reveals variation in intrahepatic inflammation across phases of chronic hepatitis B infection

status: Public on Apr 28 2023

city: Rotterdam

first: Andre

last: Boonstra

state: Zuid-Holland

address: Wytemaweg 80

department: Gastroenterology & Hepatology

country: Netherlands

institute: Erasmus MC

summary: Chronic HBV is clinically categorized into 4 phases by a combination of serum HBV DNA levels, HBeAg status and alanine aminotransferase (ALT): immunotolerant (IT), immune-active (IA), inactive carrier (IC) and HBeAg-negative hepatitis (ENEG). Immune and virological measurements in the blood have proven useful but are insufficient to explain the interrelation between the immune system and the virus since immune dynamics differ in the blood and liver. Furthermore, the inflammatory response in the liver and parenchymal cells cannot be fully captured in blood.

overall_design: Immunological composition and transcriptional profiles of core needle liver-biopsies in chronic HBV phases were compared to those of healthy controls by multiplex immunofluorescence and RNA-sequencing (n = 37 and 78, respectively) analyses.

first: Noe

middle: R

last: Montanari

first: Ricardo

last: Ramírez

first: Abhishek

last: Aggarwal

first: Nick

last: van Buuren

first: Michael

last: Doukas

first: Christina

last: Moon

first: Scott

last: Turner

first: Lauri

last: Diehl

first: Li

first: Jose

middle: D

last: Debes

first: Becket

last: Feierbach


title: The KEAP1-NRF2 pathway regulates TFEB/TFE3-dependent lysosomal biogenesis [RNA-seq: 7dpf_liver]

first: Andrew

last: Cox

overall_design: Zebrafish embryos were injected with CRISPR/Cas9 targetting genes at the single-cell stage. Livers were dissected into TRIzol for RNA extraction and sequencing at 7dpf.

first: Athena

last: Ong

first: Kristin


title: The LncRNA Fendrr Regulates Lung Development via its Triplex Forming Site the Expression of Fibrosis Genes

city: Frankfurt am Main

first: Phillip

last: Grote

state: Hessen

address: Paul-Ehrlich-Str. 42-44

department: Genome Regulation

country: Germany

institute: Georg-Speyer-Haus

summary: Long non-coding RNAs are a very versatile class of molecules that have important roles in regulating a cells function, including regulating other genes on the transcriptional level. One of these mechanisms is that RNA can directly interact with DNA by recruiting additional components such as proteins to these sites via a RNA:dsDNA triplex formation. We genetically deleted the triplex forming sequence from the lncRNA Fendrr in mice and find that this FendrrBox is partially required for Fendrr function. we We find that the loss of the triplex forming site in developing lungs causes a dysregulation of gene programs, associated with lung fibrosis. Deregulated genes that contain a FendrrBox binding element in their promoter are regulated by Wnt signaling, together with Fendrr, implicating that Fendrr acts in concert with Wnt signaling to regulate lung fibrosis.

overall_design: Examination of  Fendrr triplex-forming box  function in vivo and ex vivo in mouse lung

first: Tamer

last: Ali

first: Sandra

last: Rogala


title: Multiple pals gene modules control a balance between immunity and development in Caenorhabditis elegans [RNA-Seq 2]

city: La Jolla

first: Emily

last: Troemel

state: California

address: 4202 Bonner Hall, 9500 Gilman #0349

department: Cell and Developmental Biology

institute: University of California, San Diego

summary: The immune system continually battles against pathogen-induced pressures, which often leads to the evolutionary expansion of immune gene families in a species-specific manner. For example, the pals gene family expanded to 39 members in the Caenorhabditis elegans genome, in comparison to a single mammalian pals ortholog. Our previous studies have revealed that two members of this family, pals-22 and pals-25, act as antagonistic paralogs to control the Intracellular Pathogen Response (IPR). The IPR is a protective transcriptional response, which is activated upon infection by two molecularly distinct natural intracellular pathogens of C. elegans – the Orsay virus and the fungus Nematocida parisii from the microsporidia phylum. In this study, we identify a previously uncharacterized member of the pals family, pals-17, as a newly described negative regulator of the IPR. pals-17 mutants show constitutive upregulation of IPR gene expression, increased immunity against intracellular pathogens, as well as impaired development and reproduction. We also find that two other previously uncharacterized pals genes, pals-20 and pals-16, are positive regulators of the IPR, acting downstream of pals-17. These positive regulators reverse the effects caused by the loss of pals-17 on IPR gene expression, immunity and development. We show that the negative IPR regulator protein PALS-17 and the positive IPR regulator protein PALS-20 colocalize inside intestinal epithelial cells, which are the sites of infection for IPR-inducing pathogens. In summary, our study demonstrates that several pals genes from the expanded pals gene family act as ON/OFF switch modules to regulate a balance between organismal development and immunity against natural intracellular pathogens in C. elegans.

overall_design: Synchronized populations of wild-type, pals-16 pals-17, pals-16 pals-17 pals-20 and pals-17 pals-20 mutant animals were grown at 20°C for 48 h. Total RNA was isolated. 4 experimental replicates were performed.

first: Vladimir

last: Lažetić

last: Blanchard

first: Theresa

last: Bui


title: Multiple pals gene modules control a balance between immunity and development in Caenorhabditis elegans

overall_design: Refer to individual Series


title: Hematopoiesis and cell growth are differentially regulated by TAL1 isoforms [ChIP-seq]

first: Inbar

last: Plaschkes

overall_design: we silenced endogenous TAL1 by stably transfecting Jurkat cells with inducible TAL1 shRNA targeting its 3’ UTR, and by that targeting only the endogenous mRNA. We continued by transfecting either empty vector, TAL1-short or TAL1-long and monitored total mRNA amount of the targets.

first: Aveksha

last: Sharma

first: Shani

last: Mistriel-Zerbib

first: Rauf

last: Najar

first: Maayan

last: Salton


title: GTN enhances antitumor effects of doxorubicin in TNBC by targeting the immunosuppressive activity of PMN-MDSC

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

institute: UMR INSERM 1231

summary: An immunosuppressive tumor microenvironment is one of the major obstacles to the efficacy of standard chemotherapies, such as doxorubicin, used to treat triple negative breast cancer (TNBC). Combination therapy may be a potential way to overcome this barrier. A nitric oxide (NO) donor such as glyceryl trinitrate (GTN) has shown beneficial effects in combination with standard chemotherapy/radiotherapy in patients with cancer. In this study, we investigated the combination of doxorubicin/GTN in a mouse model of TNBC. The results indicated that GTN significantly improved the anti-tumor efficacy of doxorubicin in mouse models of BC. Flow cytometry and immunohistochemistry analysis revealed that the GTN/doxorubicin combination increases the intra-tumor recruitment and activation of CD8+ lymphocytes that is associated with the ability of doxorubicin and doxorubicin/GTN to recruit and dampen the immunosuppressive function of PMN-MDSCs PD-L1low. Mechanistically, in PMN-MDSC, doxorubicin/GTN combination reduced STAT5 phosphorylation, while GTN +/- doxorubicin induced a ROS-dependent cleavage of STAT5 associated with a decrease of FATP2. Our results identify a new combination enhancing the immune-mediated anticancer therapy in a TNBC mouse model through a ROS-dependent reprograming of PMN-MDSCs towards a less immunosuppressive phenotype. These findings open up a new therapeutic perspective by combining GTN to doxorubicin for patients with TNBC.

overall_design: RNA pofiles of 4T1-tumor bearing Balb/c mice treated ot not by doxorubicin +/- GTN

first: Nesrine

last: Mabrouk

first: Cindy

last: Racoeur

first: Jingxuan

last: Shanuk

first: Aurélie

last: Massot

first: Silvia

last: Ghione

first: Malorie

last: Privat

first: Lucile

last: Dondaine

first: Elise

last: Ballot

first: Caroline

last: Truntzer

first: Romain

last: Boidot

last: Hermetet

first: Valentin

last: Derangère

first: Mélanie

last: Bruchard

first: Frédérique

last: Végran

first: Lotfi

last: Chouchane

first: Ali

last: Bettaieb

first: Catherine

last: Paul


title: Chromatin opening by p53 is confined by Trim24 in a histone methylation-dependent manner [ATAC-seq]

first: Luke

last: Isbel

overall_design: Examination of p53 and Trim24 function in cell lines including mouse embryonic stem cells. Includes ATACseq in WT mouse ESCs in untreated/p53activated conditions (duplicates), ATACseq in p53-degron tagged mouse ESC lines under p53degraded/untreated/p53activated conditions (duplicates), ATACseq in Trim24-degron tagged mouse ESC lines under Trim24degraded/untreated/p53activated/p53activated;Trim24degraded conditions (duplicates),  ATACseq in Trim24-degron tagged mouse ESC line under p53activated/p53activated;Trim24degraded conditions at multiple timepoints after treatment including 0 hours/1 hours (duplicates)/2 hours (duplicates)/4 hours (duplicates)/8 hours (duplicates)/12 hours,  ATACseq in Trim24-degron tagged mouse ESC line under p53activated/p53activated;Trim24degraded conditions with alternative p53 activation conditions by nutlin3a (20uM) or irradiation (60Gy)(duplicates). All conditions to activate p53 or degrade degron tagged alleles performed for 4 hours unless specified in a timecourse series.

first: Murat

last: Iskar

first: Dirk

last: Schübeler


title: Multiple pals gene modules control a balance between immunity and development in Caenorhabditis elegans [RNA-Seq 1]

first: Emily

last: Troemel

overall_design: Synchronized populations of wild-type (N2) and pals-17(-) mutant animals were grown at 20°C for 48 h and 72 h, respectively. Total RNA was isolated. 4 experimental replicates were performed.

first: Vladimir

last: Lažetić

first: Michael

last: Blanchard

first: Theresa

last: Bui


title: The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]

city: St. Louis

first: Yasuhiro

last: Yoshimura

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

summary: We performed cleavage under targets and release using nuclease (CUT&RUN) sequencing to characterize ATAC peaks identified by snATAC-seq.

overall_design: Cleavage under targets and release using nuclease (CUT&RUN) sequencing for histone modifications (H3K4me3 and H3K27Ac) in human kidney organoids and kidney organoid-drived proximal tubule cells.

first: Yoshiharu

last: Muto

first: Benjamin

last: Humphreys


title: YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

country: China

institute: CAS Center for Excellence in Molecular Cell Science, CAS

type: Methylation profiling by high throughput sequencing

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


title: YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [RIP-Seq]

summary: RNA N6-methyladenosine (m6A) modification is implicated in cancer progression. However, the impact of m6A on the antitumor effects of radiotherapy and the related mechanisms are unknown. Here we show that ionizing radiation (IR) induces immunosuppressive myeloid-derived suppressor cell (MDSC) expansion and YTHDF2 expression in both murine models and humans. Following IR, loss of Ythdf2 in myeloid cells augments antitumor immunity and overcomes tumor radioresistance by altering MDSC differentiation and inhibiting MDSC infiltration and suppressive function. The remodeling of the landscape of MDSC populations by local IR is reversed by Ythdf2 deficiency. IR-induced YTHDF2 expression relies on NF-κB signaling; YTHDF2 in turn leads to NF-κB activation by directly binding and degrading transcripts encoding negative regulators of NF-κB signaling, resulting in an IR-YTHDF2-NF-κB circuit. Pharmacological inhibition of YTHDF2 overcomes MDSC-induced immunosuppression and improves combined IR and/or anti-PD-L1 treatment. Thus, YTHDF2 is a promising target to improve radiotherapy (RT) and RT/immunotherapy combinations.

overall_design: We performed YTHDF2 RIP-seq to examine YTHDF2 targets

first: Liangliang

last: Wang

first: Hua

middle: L

last: Liang

first: Chuan

last: He

first: Ralph

last: Weichselbaum


title: The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [multi-omics]

summary: We performed single nucleus RNA sequencing (snRNA-seq) and assay for transposase-accessible chromatin with sequencing (snATAC-seq) to map the epigenetic and gene expression signatures of human kidney organoids during the organoid differentiation time course.

overall_design: Expression profiling by high throughput sequencing


title: Age-dependent immune and lymphatic responses after spinal cord injury [FACS-LECs]

city: Saint Louis

first: Jonathan

last: Kipnis

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: We used single-cell RNA sequencing to profile immune cells in the injured spinal cord parenchyma and lymphatic endothelial cells in the spinal cord meninges from young and aged mice. This help us understand the heterogeneity of the immune response after injury and how it is altered in aging. Moreover, the data obtained from the spinal cord meninges provides novel molecular insights into how the meninges may contribute to the repair process.

first: Andrea

last: Salvador

first: Taitea

last: Dykstra


title: Transcriptomic clustering of critically-ill COVID-19 patients [Day 4 RNAseq]

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

summary: Infections caused by SARS-CoV-2 may cause a severe disease, termed COVID-19, with significant mortality. Host responses to this infection, mainly in terms of systemic inflammation, have emerged as key pathogenetic mechanisms, and their modulation is the only therapeutic strategy that has shown a mortality benefit. Herein, we used peripheral blood transcriptomes of critically-ill COVID-19 patients obtained at admission in an Intensive Care Unit, to identify two clusters that, in spite of no major clinical differences, have different gene expression profiles that reveal different underlying pathogenetic mechanisms and ultimately have different ICU outcome. A transcriptomic signature was used to identify these clusters in an external validation cohort, yielding a similar result. These results illustrate the potential of transcriptomic profiles to identify patient endotypes and point to relevant pathogenetic mechanisms in COVID-19.

overall_design: In 27 patients, clustered using their peripheral blood gene expression at day 1 after ICU admission, day 4 transcriptomes were compared between those receiving or not steroids

first: Laura

last: Amado-Rodríguez

first: Cecilia

last: López-Martínez

first: Inés

last: López-Alonso


title: YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [scRNA-Seq]

overall_design: CD45+cells were sorted from MC38 tumors of MC38 tumor-bearing mice were analyzed using scRNAseq.


title: YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [CITE-Seq]

overall_design: CD45+CD11b+Ly6Chi were sorted from MC38 tumors or blood of MC38 tumor-bearing mice and analyzed using scRNA-seq.


title: IDENTIFICATION AND FUNCTIONAL DEMONSTRATION OF A FETAL-SPECIFIC AXIS THAT POTENTLY SUPPRESSES MLL-FUSION DRIVEN MURINE AML miRNA-seq [L28BME vs ME]

city: Lund

first: Mohamed

last: Eldeeb

address: DMH, BMC B12

country: Sweden

institute: Lund University

type: Non-coding RNA profiling by high throughput sequencing

summary: LIN28B suppresses MLL-ENL driven AML. The tumor suppressor effects of LIN28B are largely driven by positive regulation of MYBBP1A.

overall_design: miRNA-seq was performed on GMLPs from ME or L28BME mice (3 replicates per group).

first: Ouyang

last: Yuan

first: Nicola

last: Guzzi

first: Phuong

middle: C

last: Ngoc

first: Trine

last: Kristiansen

first: Sowndarya

last: Muthukumar

first: Cristian

last: Bellodi

first: Joan

first: David

last: Bryder


title: The Drosophila gene encoding JIG protein (CG14850) is required to modulate nuclear-mitochondrial communication during development

city: Grand Forks

first: Alexei

last: Tulin

state: NORTH DAKOTA

address: 501 N Columbia Rd, Columbia Hall Rm 1733B

department: Biomedical Science

institute: University of North Dakota

summary: Coordination of mitochondrial and nuclear processes is key to cellular health; however, very little is known about the molecular mechanisms regulating these processes.  Here, we report a novel molecular mechanism controlling the shuttling of CREB (cAMP response element-binding protein) protein complex between mitochondria and nucleoplasm.  We show that a previously unknown protein, herein termed as Jig, functions as a tissue-specific and developmental timing-specific coregulator in the CREB pathway.  Jig is a small protein that shuttles between mitochondria and nucleoplasm.  Our results demonstrate that Jig interacts with CrebA protein and controls its delivery to the nucleus, thus triggering CREB-dependent transcription in nuclear chromatin and mitochondria.  Ablating the expression of Jig prevents CrebA from localizing to the nucleoplasm, affecting mitochondrial functioning and morphology and leads to Drosophila developmental arrest at the early third instar larval stage.  Together, these results implicate Jig as an essential mediator of nuclear and mitochondrial processes.  We also found that Jig belongs to a family of nine similar proteins, each of which has its own tissue- and time-specific expression profile.  Thus, our results are the first to describe the molecular mechanism regulating nuclear and mitochondrial processes in a tissue- and time-specific manner.

overall_design: In total 6 samples: 3 biological replicates of early (1st 12 hrs) 3rd instar larvae  from flies expressing JIG-GFP and 3 biological replicates of early 3rd instar larvae from wild type flies.

first: Bhuiyan

last: Sayem H

first: Bordet

last: Guillaume

first: Bamgbose

last: Gbolahan

first: Tulin

last: Alexei


title: IDENTIFICATION AND FUNCTIONAL DEMONSTRATION OF A FETAL-SPECIFIC AXIS THAT POTENTLY SUPPRESSES MLL-FUSION DRIVEN MURINE AML RNA-seq [L28BME vs ME]

overall_design: RNA-seq was performed on GMLPs (Lin- Kit+ SCa1+ CD48+ CD150-) from ME or L28BME mice (3 replicates per group).


title: Age-dependent immune and lymphatic responses after spinal cord injury [RNA-seq, aged]

first: Jonathan

last: Kipnis

overall_design: For the contusion injury, mice were anesthetized with ketamine (100 mg/kg)-xylazine (10 mg/kg) mixture. A 15-mm midline skin incision was made, and the connective tissue and muscles were bluntly dissected to expose T6-T13. Laminectomy was performed at T9 to expose the dorsal spinal cord, and the vertebral column was stabilized with angled clamps attached to the T7 and T12 transverse processes. The contusion injury was delivered using an Infinite Horizon Impactor (IH-0400 Impactor) with a force of 90 dynes. After injury, the muscles and skin were sutured separately. Mice were humanely euthanized with an intraperitoneal injection of a lethal dose of Euthasol® (10% v/v), followed by transcardiac perfusion of PBS with 5 U/mL of Heparin. Vertebral columns were obtained, and spinal cords were flushed from the vertebral column using a PBS-filled syringe. Spinal cords were enzymatically digested with prewarmed RPMI containing 1 mg/mL collagenase VIII, 0.5 mg/mL DNase, and 2% FBS for 30 minutes at 37°C with trituration every 15 minutes. The enzymes were neutralized using RPMI with 10% FBS.  Samples were passed through a 70 µm filter to obtain single-cell suspensions and pelleted 380 xg for 5 minutes. CD45+ cells were enriched from the spinal cord single-cell suspensions following the protocol for CD45+ microbeads (Miltenyi Biotec) and LS columns (Miltenyi Biotec). Two spinal cords per sample were pooled and applied to each column. Isolated cells per sample were pooled and were passed through the column again to increase purity. Cells were resuspended to a concentration of 1000 cells/uL in PBS supplemented with 0.04% non-acetylated BSA (Thermo Fisher Scientific). The CD45+ cells enriched from the spinal cord were loaded onto a 10X Genomics Chromium platform for GEM and cDNA generation with cell- and transcript-specific barcodes and sequencing libraries made using the Chromium Single Cell 3’ Library and Gel Bead Kit v3. Libraries were then sequenced using the Illumina NovaSeq6000 targeting 100,000 reads per cell.

first: Andrea

last: Salvador

first: Taitea

last: Dykstra


title: IDENTIFICATION AND FUNCTIONAL DEMONSTRATION OF A FETAL-SPECIFIC AXIS THAT POTENTLY SUPPRESSES MLL-FUSION DRIVEN MURINE AML miRNA-seq [WT vs ME]

first: Mohamed

overall_design: miRNA-seq was performed on GMLPs from WT or iME mice (4 replicates per group).


title: Age-dependent immune and lymphatic responses after spinal cord injury [RNA-seq, young]


title: Transcriptome of FERRY component knock-out cell lines

status: Public on Apr 27 2023

city: Dresden

first: Scientific Computing

last: Facility

address: Pfotenhauerstrasse 108

institute: MPI-CBG

summary:
Goal: elucidate transcriptomic changes upon knock-out of components of the FERRY complex
Methods: RNA extraction from HeLa wildtype and fy-1, fy-2, fy-4 and fy-5 knock-out celllines and subsequent RNASeq
Results: We observed differences in the transcriptome of all four knock-out cell lines
Conclusions: In the Analysis we focused on genes that were differentially expressed in all four KO cell lines or upon KO of fy-1 and fy-2.

overall_design: RNA extraction from HeLa wildtype and fy-1, fy-2, fy-4 and fy-5 knock-out celllines, in triplicates.

first: Jan

last: Schuhmacher

first: Lena

last: Hersemann

first: Marino

last: Zerial


title: Cell-Type Profiling of the Sympathetic Nervous System Using Spatial Transcriptomics and Spatial Mapping of mRNA [Spatial Transcriptomics]

city: Kansas City

first: Madelaine

last: Gogol

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: Background: The molecular identification of neural progenitor cell populations that connect to establish the sympathetic nervous system (SNS) remains unclear. This is  due to technical limitations in the acquisition and spatial mapping of molecular information to tissue architecture.  Results: To address this, we applied Slide-seq spatial transcriptomics to intact fresh frozen chick trunk tissue transversely cryo-sectioned at the developmental stage prior to  SNS formation. In parallel, we performed age- and location-matched single cell (sc) RNA-seq and 10x Genomics Visium to inform our analysis. Downstream bioinformatic  analyses led to the unique molecular identification of neural progenitor cells within the peripheral sympathetic ganglia (SG) and spinal cord preganglionic neurons (PGNs). We  then successfully applied the HiPlex RNAscope fluorescence in situ hybridization and multispectral confocal microscopy to visualize 12 gene targets in stage-, age- and  location-matched chick trunk tissue sections.  Conclusions: Together, these data demonstrate a robust strategy to acquire and integrate single cell and spatial transcriptomic information, resulting in improved  resolution of molecular heterogeneities in complex neural tissue architectures. Successful application of this strategy to the developing SNS provides a roadmap for  functional studies of neural connectivity and platform to address complex questions in neural development and regeneration.

overall_design: Visium spatial transcriptomics to intact fresh frozen chick trunk tissue transversely cryo-sectioned at the developmental stage prior to SNS formation

first: Jennifer

last: Kasemeier-Kulesa

first: Jason

last: Morrison

first: Sean

last: McKinney

first: Hua

last: Li

first: Kate

last: Hall

first: Shiyuan

last: Chen

first: Yongfu

last: Wang

first: Anoja

last: Perera

first: Rebecca

last: McLennan

first: Paul

last: Kulesa


title: Cell-Type Profiling of the Sympathetic Nervous System Using Spatial Transcriptomics and Spatial Mapping of mRNA [Slide-seq]

overall_design: Slide-seq spatial transcriptomics to intact fresh frozen chick trunk tissue transversely cryo-sectioned at the developmental stage prior to SNS formation


title: Haploinsufficiency of NFKBIA reshapes the epigenome and imparts disease fate in diffuse gliomas

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

institute: Hospital del Mar

summary: This dataset used H3K27me3 ChIP-seq profiling of normal immortalized human astrocytes that are wild-type or have been genetically modified to by CRISPR to knockout NFKBIA or by siRNA to mimic a hemizygous NFKBIA loss

overall_design: 3 samples analyzed, plus 3 different inputs

first: Markus

last: Bredel

first: Lluís

first: Teresa

last: Lobo-Jarne


title: Alteration of gene expression in E11.5 XY Cdyl deficient gonadal somatic cells

city: Suita

first: Naoki

last: Okashita

address: 1-3 Yamadaoka

institute: Osaka university

summary: Cdyl deficient mice exhibited partial sex reversal. To determine this cause, RNA-seq was used to identify genes with altered expression in Cdyl deficient gonads.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cdyl hetero deficient gonads and Cdyl homo deficient gonads

first: Ryo

last: Maeda

first: Makoto

last: Tachibana


title: Age-dependent immune and lymphatic responses after spinal cord injury

first: Jonathan

last: Kipnis

overall_design: Refer to individual Series


title: Stem cell decoupling underlies impaired lymphoid development during aging

city: Bordeaux

first: Stephania

last: Contreras Castillo

address: 2, Docteur Hoffman Martinot

institute: Université de Bordeaux

summary: Mammalian aging is associated with multiple defects of hematopoiesis, most prominently with the impaired development of T and B lymphocytes. This defect is thought to originate in hematopoietic stem cells (HSCs) of the bone marrow, specifically due to the age-dependent accumulation of HSCs with preferential megakaryocytic and/or myeloid potential (“myeloid bias”). Here, we tested this notion using inducible genetic labeling and tracing of HSCs in unmanipulated animals. We found that the endogenous HSC population in old mice shows reduced differentiation into all lineages including lymphoid, myeloid, and megakaryocytic. Single-cell RNA sequencing and immunophenotyping (CITE-Seq) showed that HSC progeny in old animals comprised balanced lineage spectrum including lymphoid progenitors. Lineage tracing using the aging-induced HSC marker Aldh1a1 confirmed the low contribution of old HSCs across all lineages. Competitive transplantations of total bone marrow cells with genetically marked HSCs revealed that the contribution of old HSCs was reduced, but compensated by other donor cells in myeloid cells but not in lymphocytes. Thus, the HSC population in old animals becomes globally decoupled from hematopoiesis, which cannot be compensated in lymphoid lineages. We propose that this partially compensated decoupling, rather than myeloid bias, is the primary cause of the selective impairment of lymphopoiesis in older mice.

overall_design:
CITE-seq-4wks was performed using Lin-cKit+Tom+ cells from 3 old and 3 young mice.
CITE-seq-8wks was performed using Lin-Flt3+Tom+ cells from 3 old and 3 young mice
Old_ATAC-seq was performed using HSCs.


title: YTHDF2 inhibition potentiates radiotherapy by reprogramming suppressive myeloid cells [MeRIP-Seq]

first: Xiaoyang

last: Dou

overall_design: We performed m6A MeRIP-seq to examine mRNA m6A modification level

first: Liangliang

last: Liang

first: Chuan

last: He

first: Ralph

last: Weichselbaum


title: Spatial transcriptomics of murine bone marrow megakaryocytes at single-cell resolution

city: Boston

first: James

middle: M.

last: Billingsley

state: MA

address: Landmark Center, 3rd Floor East, 401 Park Drive

institute: harvard T.H. Chan school of public health

summary: Megakaryocytes are bone marrow (BM) resident cells that derive from hematopoietic stem cells. A pivotal function of megakaryocytes is the generation of platelets through the release of long protrusions called proplatelets into sinusoidal vessels. single-cell RNA-sequencing on murine BM megakaryocytes has previously revealed transcriptional heterogeneity with segmentation into four distinct categories. These studies postulated functions beyond platelet production with evidence for immunoregulatory and stem cell niche supporting subtypes, as well as a cycling population. The spatial context and transcriptional heterogeneity of megakaryocytes is of great interest as localization of for instance the vasculature is a necessity for platelet production. For single-cell RNA sequencing this spatial orientation is however lost due to the dissociation of tissues. Recent technological advances have enabled the interrogation of gene expression profiles of tissues in situ. This enables the integration of morphological, situational and transcriptional information to classify cells in the context of their microenvironment. In the following we present, for the first time, the application of this technology to BM megakaryocytes at a single cell level.

overall_design: The femur of a healthy 3 and 18 month old mice was collected and parafin sections were prepared. Using the Nanostring GeoMx spatial transcritomics platform individual megakaryocytes (guided by CD41 IF staining) were selected as regions of interest and their transcriptome was determined using the murine whole transcriptome atlas.

first: Andrew

middle: P

last: Stone

first: Julia

last: Tilburg

first: David

last: Scoville

first: Joseph

middle: E

last: Italiano

first: Kellie

last: Machlus


title: Cell-Type Profiling of the Sympathetic Nervous System Using Spatial Transcriptomics and Spatial Mapping of mRNA [RNA-seq]

first: Madelaine

last: Gogol

overall_design: RNA-seq transcriptomics to intact fresh frozen chick trunk tissue transversely cryo-sectioned at the developmental stage prior to SNS formation

first: Jennifer

last: Kasemeier-Kulesa

first: Jason

last: Morrison

first: Sean

last: McKinney

first: Hua

last: Li

first: Kate

last: Hall

first: Shiyuan

last: Chen

first: Yongfu

last: Wang

first: Anoja

last: Perera

first: Rebecca

last: McLennan

first: Paul

last: Kulesa


title: WashU Primary and Metastatic Tumors with Survival in High-Grade Serous Ovarian Cancer RNA-seq

first: Emilee

last: Kotnik

address: 660 S. Euclid Ave

department: Center for Reproductive Health Sciences

summary: High-grade serous ovarian cancer (HGSC) is the most lethal histotype of ovarian cancer and the majority of cases present with metastasis and late stage disease.  We aimed to better characterize the distinctions between primary and metastatic tumors based on short- or long-term survival.

overall_design: We characterized matched primary and metastatic tumors by whole exome and RNA sequencing. Of these, 23 were short-term (ST) survivors (overall survival (OS) <3.5 years) and 16 were long-term (LT) survivors (OS >5 years).

first: Katherine

last: Fuh

first: Christopher

last: Miller


title: Diversity of phytoviral RNA U-tailing among ss(+) RNA phytoviruses

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

institute: CNRS

summary: Using 3' RACE-seq method, we analyzed global 3’ terminal RNA uridylation profiles for representatives of the main families of positive single-stranded RNA phytoviruses.

sample_organism:
Spinacia oleracea
Arabidopsis thaliana
Nicotiana benthamiana
Vitis vinifera
Chenopodium quinoa
Nicotiana obtusifolia

overall_design: 3’ RACE-seq method was used to measure poly(A) tail sizes and analyze uridylation levels. This protocol is based on the ligation of a primer at the 3’ end of RNA, and the subsequent targeted amplification by PCR of amplicons suitable for Illumina sequencing.

first: Anne-Caroline

last: Joly

first: Shahinez

last: Garcia

first: Hélène

last: Zuber


title: Long non-coding RNAs induced by TGF-beta in three breast (cancer) cell lines

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

institute: Leiden University Medical Center

summary: Long non-coding RNAs (lncRNAs) are emerging as pivotal modulators of signaling trnasduction, and thereby regulate multiple pathological processes including cancer. TGF-beta signaling contributes to cancer metastasis by inducing epithelial-to-mesenchymal transition (EMT). To screen lncRNAs that are induced by TGF-beta, MCF10A-M1, MCF10A-M2 and MDA-MB-231 cells were stimulated with TGF-beta (5 ng/mL) fo 0 h, 2 h, 8 h and 24 h. RNA was extracted from those cells and analyzed by RNA-seq.

overall_design: MCF10A-M1, MCF10A-M2 and MDA-MB-231 cells in biological triplicates were stimulated with TGF-beta signaling inhibitor SB431542 (SB) or TGF-beta ligand fo 0 h, 2 h, 8 h and 24 h. In total, 36 samples were analyzed.

first: Chuannan

last: Fan

first: Davy

last: Cats

first: Peter

last: ten Dijke


title: A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest

city: Basel

first: Filippo

last: RIJLI

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research


title: A fetal tumor suppressor axis abrogates MLL-fusion-driven acute myeloid leukemia

first: Mohamed

last: Eldeeb


title: Transcriptome analysis of A549 cells upon lncRNA ectopic LETS1 expression

summary: We identified a tumor-promoting long non-coding RNA (lncRNA) named lncRNA enabling TGF-beta signaling 1 (LETS1). It was found to potentiate epithelial-to-mesenchymal transition (EMT), cell migration and extravasation in a zebrafish xenograft model. To better dissect the downstream target genes and elucidate the signaling pathways altered by LETS1, we ectopically expressed LETS1 in A549 cells. Total RNA was collected and sent for RNA sequencing analysis. Afterwards, differentially expressed genes were used for the pathway enrichment analysis and gene set enrichment analysis (GSEA).

overall_design: LETS1 was overexpressed by a lentiviral vector in A549 cells. RNA from cells transduced with an empty vector (Co.vec) was set as a control. Three biological replicates were included in each group.

first: Tom

last: Kuipers


title: Screen for Ferry-associated RNAs

first: Scientific Computing

last: Facility

summary:
Goal: Identification of RNAs that are associated with the novel Ferry complex
Methods: We performed a GST pulldown experiment, where GST-Ferry and GST were incubated with a HEK 293 cell lysate and extensively washed prior to elution. Subsequently, RNA was extracted from the elution and sequenced.
Results: We identifed around 17 588 different transcripts and found a set of 252 mRNAs that are specifically enriched in the GST-Ferry sample.
Conclusions: The Ferry complex seems to interact with a specific subset of mRNAs

overall_design: mRNA extraction from a GST pulldown experiment using GST and GST-Ferry, incubated with HEK 293 lysate, in triplicates.

first: Jan

middle: S

last: Schuhmacher

first: Lena

last: Hersemann

first: Marino

last: Zerial


title: Enhancer analysis by H3K27ac ChIP-seq in HNSCC T-HEP3 and D-HEp3 cell lines

city: Bronx

first: Julio

last: Aguirre-Ghiso

address: 1301 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: Identification of active and differentially enriched enhancers in T-HEp3 and D-HEp3 cell lines.

overall_design:
ChIP-seq was performed in T-HEp3 (P0, primary cells extracted from tumor grown on chicken CAM and plated on dish) and D-HEp3 grown in vitro (passage later than 130).

ChIP-seq was performed in T-HEp3 (P0, primary cells extracted from tumor grown on chicken CAM and plated on dish) treated with PBS+DMSO (control) or AZA (5 nM)+atRA (1uM).

first: Deepak

last: Singh

first: Dan

last: Hasson

first: Saul

last: Carcamo

first: Emily

last: Bernstein


title: CTLA4 limits expansion of human cytotoxic CD4+ T cells to prevent B cell apoptosis

city: Acton

first: Zhi-Ping

last: Feng

state: ACT

address:
131 Garran Road, John Curtin School Of Medical Research Building (Level 3, Stage 1)
, The Australian National University

institute: JCSMR

summary: High throughput sequencing of RNA expression profiling

overall_design: RNA sequencing of CD57+ CD4+ TEM, CD57+ CD4+ TEMRA, CD57- CD4+ TEM and CD57+ CD8+ T cells from PBMCs of three healthy donos.

first: Yuwei

last: Hao

first: Rochna

last: Chand

first: Bahar

last: Miraghazadeh

first: Ainsley

last: Davies

first: Chelisa

last: Cardinez

first: Kristy

last: Kwong

first: Morgan

middle: B

last: Downes

first: Rebecca

last: Sweet

first: Pablo

middle: F

last: Cañete

first: Lloyd

last: D’Orsogna

first: David

last: Fulcher

first: Sharon

last: Choo

first: Desmond

last: Yip

first: Geoffrey

last: Peters

first: Sonia

first: Matthew

last: Witney

last: Tscharke

first: Carola

middle: G

last: Vinuesa

last: Cook


title: AZA+atRA reprogramming of head and neck squamous cell carcinoma cell line T-HEp3

first: Julio

last: Aguirre-Ghiso

summary: We report the RNA expression profile in the AZA+atRA reprogrammed tumorigenic (T-HEp3) HNSCC cell line. T-HEp3 is a human epidermoid carcinoma, which grows on chorioallantoic membrane and metastasizes with high efficiency into the organs of chick embryo. Upon serial passage for more than 40 times in vitro, T-HEp3 loses tumorigenic and metastatic potential and termed as dormant D-HEp3. This is an ideal cell line model system to study cancer dormancy.

overall_design: RNA sequencing was performed in T-HEp3 cell line treated (in vitro) with 1. DMSO control, 2. AZA +atRA reprogrammed, 3. NR2F1 knock down DMSO, and 4. NR2F1 knock down AZA + atRA reprogrammed.

first: Deepak

middle: K

last: Singh


title: Single-cell transcriptomics of NRAS-mutated melanoma transitioning to drug resistance: elevated P2RX7 levels indicate response to targeted therapy

status: Public on Apr 26 2023

city: Esch-sur-Alzette

first: Kamil

last: Grzyb

email: kamilgen@gmail.com, kamil.grzyb@uni.lu

address: 2, avenue de l'Université

country: Luxembourg

institute: University of Luxembourg - LCSB

summary: While effective therapy is available for melanoma patients harbouring BRAF mutations, to date, the efficient therapeutic approaches for NRAS-mutant melanoma patients are limited. Therapeutic regimen involving combinatorial inhibition of MEK1/2 and CDK4/6 prove to be beneficial as targeted therapy for NRAS-mutant melanoma. Yet, only a subset of melanoma patients responded to this treatment, whereas acquired resistance eventually emerge in responders. Upon prolonged therapy with MEK1/2 and CDK4/6 inhibitors cells switch to fully drug-resistant or senescent phenotype in vitro. Consequently, there is a necessity to portray cell populations sensitive to targeted therapy, but also cell transitions associated with NRAS-mutant melanoma resistance. To define transcriptional states arising under indicated therapy and cell fate decisions governing resistance, we performed single-cell RNA sequencing at four distinguished time points during treatment. In this study, we identified a cell population highly enriched in calcium signalling, among others, associated with positive drug response. In particular, prolonged expression of ATP-gated ion channel P2RX7 was related to a senescent-like phenotype. Next, we described an immune-like melanoma state that acquired drug resistance and re-enter the cell cycle under treatment, as well as cell populations with intrinsic potential to evade drug pressure.

overall_design: NRAS-mutant melanoma cell lines were treated with a drug combination involving MEK and CDK4/6 inhibitors over a prolonged period (~1 month), whereas sampling and sequencing were performed on drug-naïve and treated cells collected at distinct time points of treatment (1, 4 and 33 days) of treatment. Single-cell RNA sequencing was conducted via Drop-Seq and the NextSeq 500 (Illumina) was used for library preparation.

first: Tijana

last: Randic

first: Stephanie

last: Kreis

first: Alexander

last: Skupin


title: Exercise training markedly augments dietary weight loss-induced improvements in multi-organ system metabolic function in people with obesity and prediabetes

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

institute: Faculty of Medicine, Shimane University

summary: The additional therapeutic effects of regular exercise during a dietary weight loss program in people with obesity and prediabetes are unclear. We evaluated the effect of 10% weight loss, induced within ~5 months by calorie-restriction alone (Diet-ONLY, n=8) or calorie-restriction plus multi-modal exercise training (Diet+EX, n=8), on metabolic function in people with obesity and prediabetes. Whole-body (primarily muscle) and hepatic insulin sensitivity were 2-3 fold greater in the Diet+EX than the Diet-ONLY group, and were accompanied by increased muscle expression of genes involved in mitochondrial biogenesis, energy metabolism and angiogenesis in the Diet+EX group without any change in the Diet-ONLY group. There were no differences between groups in plasma branched-chain amino acids or markers of inflammation, and both interventions caused similar changes in the gut microbiome. These results demonstrate that adding regular exercise to a diet-induced weight loss program has profound metabolic benefits in people with obesity and prediabetes.

overall_design: We obtained skeletal muscle samples from people with obesity and prediabetes before and after 10% weight loss, induced within ~5 months by calorie-restriction alone (Diet-ONLY, n=6) or calorie-restriction plus multi-modal exercise training (Diet+EX, n=7) and evaluated the effects of weight loss on skeletal muscle transcriptome by conducting RNA-seq.

first: Joseph

middle: W

last: Beals

first: Brandon

last: Kayser

first: Gordon

middle: I

last: Smith

first: George

last: Schweitzer

first: Kyleigh

last: Kirbach

first: M

last: Kearney

first: Gibraan

last: Rahman

first: Rob

last: Knight

first: Bruce

last: Patterson

first: Samuel

last: Klein


title: Single cell ATAC sequencing data of neuroblastoma infiltrated bone marrow

city: Salzburg

first: Wolfgang

last: Esser-Skala

address: Hellbrunner Strasse 34

country: Austria

institute: University of Salzburg

summary: We report genome-wide ATAC-seq analyses at single cell resolution of 16 bone marrow samples with and without neuroblastoma infiltration. Our samples span across several neuroblastoma models, including MYCN amplified, ATRX mutated, and sporadic (lacking either alteration).

overall_design:
16 scATAC-seq samples on bone marrows derived from 16 patients. The sequencing dataset consists of 5 samples without bone marrow infiltration, defined as controls (C1, C2, C3, C4, and C5) and 11 neuroblastoma infiltrated bone marrow samples from patients with MYCN amplification (M1, M2, M3, M4), ATRX mutations (A1, A2), and cases lacking either alteration (S1, S2, S3, S4, S5).
*** Submitter declares:  Due to data protection regulations, raw data have been uploaded, but rather deposited in the EGA (accession EGAS00001006106).***

first: Irfete

last: Fetahu

first: Rohit

last: Dnyansagar

last: Sindelar

first: Fikret

last: Rifatbegovic

first: Andrea

last: Bileck

first: Lukas

last: Skos

first: Eva

last: Bozsaky

first: Daria

last: Lazic

first: Lisa

last: Shaw

first: Marcus

last: Tötzl

first: Dora

last: Tarlungeanu

first: Marie

last: Bernkopf

last: Weninger

first: Eleni

last: Tomazou

first: Christoph

last: Bock

first: Christopher

last: Gerner

first: Ruth

last: Ladenstein

first: Matthias

last: Farlik

first: Nikolaus

last: Fortelny

first: Sabine

last: Taschner-Mandl


title: Single cell analyses of transcriptome and epigenome in neuroblastoma infiltrated bone marrow

first: Wolfgang

last: Esser-Skala

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


title: The Fgf/Erf/NCoR1/2 repressive axis controls trophoblast cell fate

city: Vienna

first: Andreas

last: Lackner

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

institute: Medical University of Vienna

summary: Placental development relies on coordinated cell fate decisions governed by signalling inputs. However, little is known about how signalling cues are transformed into repressive lineage-specific transcriptional signatures. Here, we demonstrate that upon inhibition of the Fgf/Erk pathway in mouse trophoblast stem cells (TSCs), the Ets2 repressor factor (Erf) interacts with the Nuclear Receptor Corepressor Complex 1 and 2 (NCoR1/2) and recruits it to key trophoblast genes.  Genetic ablation of Erf or Tbl1x (a component of the NCoR1/2 complex) abrogates the Erf/NCoR1/2 interaction. This leads to mis-expression of Erf/NCor1/2 target genes resulting in a TSC differentiation defect. Mechanistically, Erf regulates expression of these genes by recruiting the NCoR1/2 complex to their enhancers and modulation of H3K27ac. Our findings uncover how the Fgf/Erf/NCoR1/2 repressive axis governs cell fate and placental development, providing a new paradigm for Fgf-mediated transcriptional control.

overall_design: 3'RNAseq of Erf and Tbl1x depleted (shRNA, CRISPR/Cas9 KO) and respective rescue TSCs in self-renewal conditions and differentiated for 24h by MEKi treatment (PD) or for 6 days by Fgf withdrawal (WD). ChIPseq of histone modifications and Erf/Ncor1/2 subunits in WT and KO cell lines including rescues in self-renewal conditions and differentiated for 24h by MEKi treatment (PD).

first: Paulina

last: Latos


title: A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2 [bulk RNA-seq]

first: Iros

last: Barozzi

address: Borschkegasse 8a

institute: Medical University Vienna

summary: During development cell fates are specified by tightly controlled gene expression programs. PBX TALE transcription factors control gene regulatory networks (GRN) that direct vertebrate tissue patterning and organ morphogenesis. How PBX1/2 proteins achieve context-specific functions, despite widespread embryonic Pbx expression, remains elusive. In mouse limbs, mesenchymal-specific loss of PBX1/2 or of the limb regulator HAND2 results in strikingly similar phenotypes, suggesting that PBX1/2- and HAND2-dependent programs converge to control limb development. To investigate this scenario using the murine hindlimb model, we combined tissue-specific and temporally controlled mutagenesis to multi-omics approaches on dissected hindlimb buds. This resulted in the reconstruction of a GRN that is collaboratively directed by PBX1/2-HAND2, demonstrating that Pbx1-Hand2 genetically interact in vivo during pentadactylous hindlimb patterning, with PBX1 concomitantly acting as an upstream regulator of Hand2. At organismal-level resolution the GRN is active within restricted subsets of posterior-proximal hindlimb mesenchymal cells, wherein Pbx1/2 and Hand2 are co-expressed with their target genes. Profiling the binding of Pbx1 and Hand2 genome-wide across multiple tissues revealed that HAND2 can act selectively on a subset of PBX-bound regions to impart limb patterning functionality. Our research elucidates mechanisms on the limb-specific activities of PBX1/2, while informing general principles by which promiscuous transcription factors cooperate with select cofactors to instruct distinct developmental programs.

overall_design: Total RNA-seq profiling of hindlimb buds from e10.5 mouse embryos with indicated genotypes and respective controls.

first: M

last: Losa

first: I

last: Osterwalder

first: P

last: Zarrineh

first: J

last: Benazet

first: B

last: Chacon

first: A

last: Girdzuisaite

last: Morabito

first: F

last: Blasi

last: Zhu

first: S

last: Mackem

first: T

last: Capellini

first: N

last: Bobola

first: D

last: Dickel

last: Zuniga

last: Visel

first: R

last: Zeller

first: L

last: Selleri


title: A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2 [ChIP-seq]

last: Barozzi

overall_design: Chromatin-immunoprecipitation of Pbx1, Hand2, H3K27ac and H3K27me3 from hindlimb buds of e10.5 mouse embryos.

last: Losa


title: An allosteric pan-TEAD inhibitor blocks oncogenic YAP/TAZ signaling and overcomes KRAS G12C inhibitor resistance

city: South San Francisco

first: Marc

last: Hafner

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

summary: The Hippo pathway is a key growth-control pathway conserved across species. The downstream effectors of the Hippo pathway YAP/TAZ are frequently activated in cancer cells by a diverse array of mechanisms to drive proliferation and survival. Based on the premise that sustained interactions between YAP/TAZ and TEADs are central to their transcriptional activities, we discovered a potent small molecule inhibitor (SMI) GNE-7883 that allosterically blocks the interactions between YAP/TAZ and all four TEAD paralogs in human cells through binding to the TEAD lipid pocket. GNE-7883 effectively reduces chromatin accessibility specifically at TEAD motifs, suppresses cell proliferation in a variety of cell line models, and achieved strong anti-tumor efficacy in vivo. Furthermore, we uncovered that GNE-7883 effectively overcomes resistance to the recently approved KRAS G12C inhibitor sotorasib in both treatment-refractory and acquired resistance cell line models, providing strong proof-of-concept of TEAD SMIs in targeting YAP/TAZ-mediated KRAS inhibitor resistance. Taken together, this work demonstrates activities of TEAD SMIs in YAP/TAZ-dependent cancers and highlights their potential broad applications in precision oncology and therapy resistance.

overall_design: Refer to individual Series


title: A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2 [single-cell RNA-seq]

overall_design: Single-cell RNA-seq of hindlimb buds from e10.5 mouse embryos, generated using 10x Chromium and subjected to high-throughput sequencing.

last: Osterwalder

last: Zarrineh

last: Benazet


title: Salivary gland cancer organoids are valid for preclinical genotype-oriented medical precision trials

city: Sendai

first: Tomohiko

last: Ishikawa

state: Miyagi

address: 1-1 Seiryo-machi, Aoba-ku

department: Otolaryngology - Head and Neck Surgery

institute: Tohoku University Graduate School of Medicine

summary: We established patient-derived organoids and monolayer culture cells from the salivary gland cancer cases. To compare the RNA profiles of primary culture cells (Organoids and monolayer culture cells) and their parental tumors, we isolated total RNA from 2 cases of the salivary gland cancer and performed transcriptome sequencing for the organoids, monolayer culture cells, and their parental tumors of both cases. Case 6 is a case of adenoid cystic carcinoma and Case 11 is a case of salivary duct carcinoma.

overall_design: Comparative gene expression profiling analysis of the primary tumor, the organoids, and the monolayer culture cells from cases 6 and 11.

first: Toru

last: Furukawa


title: Proteogenomic and V(D)J Analysis of Human Decidual T cells Highlights Unique Transcriptional Programming and Clonal Distribution [VDJ-seq]

city: Madison

first: Aleksandar

middle: K.

last: Stanic

state: WI

address: 202 S. Park St., Meriter Atrium B

department: Obstetrics and Gynecology

institute: University of Wisconsin - Madison

summary: Immunological tolerance towards the semi-allogeneic fetus is one of many maternal adaptations required for a successful pregnancy. T cells are major players of the adaptive immune system and balance tolerance and protection at the maternal-fetal interface, however, their repertoire and subset programming is still poorly understood. Utilizing emerging scRNA-seq technologies we simultaneously obtained transcript, limited protein, and receptor repertoire at the single-cell level, from decidual and matched maternal peripheral T cells. In agreement with previous work, we find that the decidua maintains a tissue-specific distribution of T cells compared to the periphery. We find that decidual T cells maintain a unique transcriptome programming, characterized by restraint of inflammatory pathways by overexpression of negative regulators. Furthermore, we show little clonal overlap between the decidua and periphery, suggesting minimal ongoing traffic between these scites. Overall, our data demonstrate the power of multi-omic analysis in revealing regulation of fetal-maternal immune co-existence.

overall_design: CD3+ T cells were obtained from matched decidua basalis and peripheral blood samples from three individuals and submitted for single cell RNA, antibody capture, and V(D)J sequencing.

first: Deborah

last: Chasman

first: Rene

last: Welch Schwartz

first: Jessica

last: Vazquez

first: Melina

last: Chavarria

first: Eryne

middle: T

last: Jenkins

first: Gladys

last: Lopez

first: Chanel

last: Tyler

first: Irene

last: Ong


title: In vivo single-cell profiling of lncRNAs during Ebola virus infection (Zyagen)

first: luisa

last: santus

address: Plaça d'Eusebi Güell, 1-3

institute: Barcelona Supercomputing Center

summary: Long non-coding RNAs (lncRNAs) are pivotal mediators of systemic immune response to viral infection yet most studies concerning their expression and functions upon immune stimulation are limited to in vitro bulk cell populations. This strongly constrains our understanding of how lncRNA expression varies at single-cell resolution, and whether differences with protein coding genes exist in their cell-type specific immune regulatory roles. Here, we perform the first in-depth characterization of lncRNA expression variation at single-cell resolution during Ebola virus (EBOV) infection in vivo. Using bulk RNA-sequencing from 119 samples and 12 tissue types, we significantly expand the current macaque lncRNA annotation. We then profile lncRNA expression variation in immune circulating single-cells during EBOV infection and find that lncRNAs’ expression in fewer cells is a major differentiating factor to their protein coding gene counterparts. Upon EBOV infection, lncRNAs present dynamic and mostly cell-type specific changes in their expression profiles especially in monocytes, the main cell type targeted by EBOV. Such changes are associated with gene regulatory modules related to important innate immune responses such as interferon response and purine metabolism. Within infected cells, several lncRNAs have correlated and anti-correlated expression with viral load, suggesting that expression of some of these lncRNAs might be directly hijacked by EBOV to attack host cells. This study provides novel insights on the roles that lncRNAs play in the host response to acute viral infection and paves the way for future lncRNA studies at single-cell resolution.

overall_design: Bulk RNA-Seq of healthy macaque tissues.

first: Luisa

last: Santus


title: In vivo single-cell profiling of lncRNAs during Ebola virus infection (SABio)

overall_design: Bulk RNA sequencing of tissues from infected macaques infected with EBOV. Some of the macaques were subministered an anti-Ebola virus IgG immunoglobulins cocktail.


title: A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2

first: Iros

last: Barozzi


title: DNA Binding Specificities of Fkh1, Fkh2, Hcm1, and Fhl1 Revealed by SELEX-seq

city: Los Angeles

first: Remo

last: Rohs

address: 1050 Childs Way

department: Quantitative and Computational Biology

institute: University of Southern California

summary: Quantifying the preferences of DNA binding proteins is an essential step in determining how transcription factors (TFs) interact with their targets in the genome. High-throughput in vitro binding assays have been used to identify the inherent DNA preferences of TFs in a controlled environment isolated from confounding factors such as genome accessibility, DNA methylation, and TF binding cooperativity. Unfortunately, the limited variable region or sequencing depth typically utilized by many of the available experimental approaches makes it difficult to measure the preferences of moderate- to low-affinity binding sites, and impossible to measure small-scale differences between closely related homologs. The Forkhead box (FOX) family of TFs is known to play a crucial role in regulating a variety of key processes from proliferation and development, to tumor suppression and aging. By using the high-sequencing depth SELEX-seq approach to study all four FOX homologs in Saccharomyces cerevisiae, we have been able to precisely quantify the contribution and importance of nucleotide positions flanking the core of the binding sites. Essential to this process was the alignment of our SELEX-seq reads to a set of candidate core sequences determined by two newly developed strategies of alignment and reprioritization applied to enriched k-mers.

overall_design: SELEX-seq was performed on Fkh1, Fkh2, Hcm1, and Fhl1 constructs as described in Cooper et al. (to be submitted). We provide sequencing results for both the intial library (R0) as well as the selected libraries after one (R1) or two (R2) rounds of selection. A test experiment was performed using just the Fkh1 construct with a shallower depth of sequencing. The final, large-scale experiments were performed on both all constructs. The initial libraries included a 16 bp randomized region flanked by two fixed adapters absent of any known binding site for the used transcription factors.

first: Brendon

middle: H

last: Cooper

first: Ana

last: Machado

first: Yan

last: Gan

first: Oscar

last: Aparicio