April 2015

A $4.2B project, only a 57.5ft wide boring machine, what could go wrong? | BusinessWeek http://t.co/6mVhruPu52

10:10pm April 20th 2015 via Hootsuite

The Kids Are All Right: The Scientific Case Against Overprotective Parenting | RealClearScience http://t.co/uovDc9blX1

9:35pm April 20th 2015 via Hootsuite

OW: Aggressive prostate ca enriched for basal stem-like sig: CD49f hi score calc from 91 genes. 'More stem-like as they progress' #AACR15

5:56pm April 20th 2015 via Hootsuite

RT @AACR: New @SU2C @AmericanCancer #LungCancer Dream Team announced at #AACR15: http://t.co/klGV3COPqD

5:55pm April 20th 2015 via Hootsuite

OW: Found histological subtypes within CRPC metastatic biopsies. Then LCM + RNA-Seq; clear K-M curve differences by hist. type #AACR15

5:54pm April 20th 2015 via Hootsuite

OW: 3rd project SU2C, 'West Coast Dream Team': goal to study late-stage transition to androgen deprivation resistance mechanism #AACR15

5:52pm April 20th 2015 via Hootsuite

OW: For bone mets - not imaged well, used PET, clear evidence. Histology confirmed. Found 5 kinases: forming bone & visceral mets #AACR1

5:51pm April 20th 2015 via Hootsuite

OW: 19 kinases ID'd of the 125 promoting metastatic colonization to lung. 'Every member of the Ras family' & others #AACR15

5:50pm April 20th 2015 via Hootsuite

OW: Cloned 125 into lentiviral vectors for overexp. All w/epitope tags. Mouse line Cap8, each w/kinase + reporter, animal imaged #AACR15

5:49pm April 20th 2015 via Hootsuite

OW: Fn evaluation in-vitro and in-vivo assessment of kinases that promote metastases: 125 kinases ID'd #AACR15

5:47pm April 20th 2015 via Hootsuite

OW: Metastatic CRPC tissues show intra-pt similarities; inter-pt heterogeneity #AACR15

5:45pm April 20th 2015 via Hootsuite

OW: Kinases: Clinical targeting '14 MCB ref http://t.co/vFuVNxTRTh Robust tyr phosph apparent in CRPC; cell line sigs different #AACR15

5:45pm April 20th 2015 via Hootsuite

OW: Prostate-cancer: Trop2 and Notch1 are two likely targets #AACR15

5:42pm April 20th 2015 via Hootsuite

Owen Witte (UCLA CA) "Finding therapeutic targets for aggressive prostate cancer" OW #AACR15

5:40pm April 20th 2015 via Hootsuite

WH: Advice: "Do good science. And answer big questions." #AACR15

5:24pm April 20th 2015 via Hootsuite

WH: Special acknowledgements to Todd Golub, Levi Garraway and Matthew Meyerson 'helping me think about cancer problems' #AACR15

5:22pm April 20th 2015 via Hootsuite

WH: Integrated, systematic identification of cancer dependencies. List of >100 acknowledgements (longest list I've ever seen IMO) #AACR15

5:21pm April 20th 2015 via Hootsuite

WH: In pilot phase; from molecular alterations, to fn assessment; to computational analysis: then validate biology, then clin hypoth #AACR15

5:19pm April 20th 2015 via Hootsuite

WH: Can find epistatic and synergistic interactions; combine with PPI and find how pathways interact. #AACR15

5:19pm April 20th 2015 via Hootsuite

WH: Can multiple CRISPR - 2 sgRNAs/gene (52 genes). 13.4K combinations of sgRNAs 'not anytime soon'; 1325 unique gene combinations #AACR15

5:18pm April 20th 2015 via Hootsuite

WH: Use Silac-MS for 'moderate throughput PPI. Find validated b-catenin genetic co-dependencies. Can do network stability analysis #AACR15

5:17pm April 20th 2015 via Hootsuite

WH: Genome-scale studies lead to long gene lists; look at Prot-prot interactoin, also gene-gene interaction. #AACR15

5:15pm April 20th 2015 via Hootsuite

WH: May be able to look at pt-derived cell lines and their private dependencies using CRISPR #AACR15

5:13pm April 20th 2015 via Hootsuite

WH: Moving from shRNAs to CRISPR library of 80K. Shows data how specific it is. Strong KRAS, EGFR dependence. #AACR15

5:12pm April 20th 2015 via Hootsuite

WH: (last 3 classes of dependencies): ...CYCLOPS, redundant essentials, and synthetic lethals. #AACR15

5:05pm April 20th 2015 via Hootsuite

WH: Across all cell lines - <100 dependencies in total. 5 types of dependencies ID'd: oncogene addiction, master regulator... #AACR15

5:05pm April 20th 2015 via Hootsuite

WH: Achilles has been able to ID oncogenes with known dependencies & discover new ones. Can go through every gene in this way #AACR15

5:00pm April 20th 2015 via Hootsuite

WH: Able to computationally segregate on-target from off-target seed effects in both RNAi & shRNA screens. Tool called 'Demeter' #AACR15

4:58pm April 20th 2015 via Hootsuite

WH: Project Achilles - on for several years; ID4 as ovarian ca oncogene. #AACR15

4:57pm April 20th 2015 via Hootsuite

WH: The other type of expt: fn char of tumor phenotypes. Manipulate gene exp using shRNA, ORF or CRISPR. http://t.co/rpKYknu0g4 #AACR15

4:54pm April 20th 2015 via Hootsuite

WH: KRAS D33E: 1 instance in Pan Cancer 6K dataset. Now seen 3 in 15K, 2 colon, 1 lung. #AACR15

4:53pm April 20th 2015 via Hootsuite

WH: Some familiar genes (KRAS) others not so. Can get fn predictions about VUS in established oncogenes, also VUS in novel ones #AACR15

4:52pm April 20th 2015 via Hootsuite

WH: Fn of particular alleles - pairwise transformation screening. 8/512 combinations tested highly transformative #AACR15

4:50pm April 20th 2015 via Hootsuite

WH: Pancan project & connectivity map: gene expression to infer activity of spec alleles. GOF alleles scored very tumorigenic #AACR15

4:48pm April 20th 2015 via Hootsuite

William Hahn (DFCI Boston MA) "Systematic identification of cancer targets" WH #AACR15

4:46pm April 20th 2015 via Hootsuite

New #AACR15 video: A sneak peek at the newest real-time PCR system http://t.co/748KerXOHQ

3:10pm April 20th 2015 via Hootsuite

CJ: Manipulate diet, prebiotics, bacterio- or phage therapy, Rx targeting microbial cancer genes #AACR15

2:28pm April 20th 2015 via Hootsuite

CJ: ClbM transports pre-colibactin to periplasm, could be target. '14 review ref http://t.co/ImAQxzYFH1 Many options #AACR15

2:28pm April 20th 2015 via Hootsuite

CJ: ClbM gene needed for Ecoli NC101-induced genotoxicity in IEC-6 cells, shown via pks and Clbm knockouts (in Ecoli) #AACR15

2:22pm April 20th 2015 via Hootsuite

CJ: At 12w: ribosomal genes but also pks island (18 genes) 3% of Ecoli transcriptomic response spec to inflammation. #AACR15

2:21pm April 20th 2015 via Hootsuite

CJ: Abundance of cancer-assoc'd microbes isn't indicative of CRC; what about transcription of microbes? Did RNA-seq on E. coli #AACR15

2:18pm April 20th 2015 via Hootsuite

CJ:Germ-free Il-10 -/- vs. Il-10 -/- and Rag2 -/- mice: no inflammation, no tumor either. Fecal E. coli load similar #AACR15

2:17pm April 20th 2015 via Hootsuite

CJ: Rel between inflammation & microbial cancer - '14 Nature Comm. ref http://t.co/sTxs1DMKbh WT vs Il-10-/- mice PCA analysis #AACR15

2:14pm April 20th 2015 via Hootsuite

CJ: Can find E. coli carrying endotoxic pks island from IBD and CRC pts; what shfits to 'genotoxic microbiota'? #AACR15

2:13pm April 20th 2015 via Hootsuite

CJ: '12 ref http://t.co/Prl4PLLni0 'The enemy within' #AACR15

2:11pm April 20th 2015 via Hootsuite

CJ: '14 PNAS http://t.co/B2oQhX8Fqi 5x increase of CRC if biofilm present. But much work ahead. #AACR15

2:10pm April 20th 2015 via Hootsuite

CJ: Microbial dysbiosis in CRC - luminal bacteria between adenoma & adenocarcinoma. #AACR15

2:08pm April 20th 2015 via Hootsuite

CJ: CRC: host genetics, diet, inflammation, and newest, microbiota. Connection to all the others? ~100T cells, >1K spp., ~3M genes #AACR1

2:06pm April 20th 2015 via Hootsuite