DB: In #CancerFilm Emperor of All Maladies Howard wasn't mentioned; he grew up in Philadelphia and died at 59 in '94 of lung ca #AA5R16
5:38pm April 18th 2015 via Hootsuite
David Baltimore (CalTech) "MicroRNAs, leukemia and hematopoietic stem cell homeostasis" Starts w/ homage to Howard Temin #AACR15
5:37pm April 18th 2015 via Hootsuite
Nobel winner Dr. David Baltimore honored with the Irving Weinstein Foundation Distinguished Lectureship http://t.co/Soqvtk8ffV #AACR15
5:33pm April 18th 2015 via Hootsuite
ZS:Q:What are the best met's to assay? CTCs? cfDNA? A: Sometimes 80% both have same muts, sometimes 20%. No one reliable Dx source #AACR15
4:52pm April 18th 2015 via Hootsuite
ZS: Cites 2011 Cell ref http://t.co/onI5F3R9FG Could be a 'strong attractor'. #AACR15
4:48pm April 18th 2015 via Hootsuite
ZS: 2014 Nature paper: http://t.co/ZBNjjHkjFk Fast-growing cells may suppress other slower growing ones, leading to collapse. #AACR15
4:43pm April 18th 2015 via Hootsuite
ZS: Showing figure of Darwinian selection & branched evolution, from Normal to shared Primary, shared Met. SETD2 in sep places #AACR15
4:40pm April 18th 2015 via Hootsuite
ZS: In this 2011 Cancer Res http://t.co/0BgKaKOegm indivs with highest instability survived just as long, in 3 cancer types #AACR15
4:36pm April 18th 2015 via Hootsuite
ZS: Given the heterogeneity - what do you measure? You are bound to miss something. Can ITH be exploited? #AACR15
4:34pm April 18th 2015 via Hootsuite
ZS: Science 2014 ref http://t.co/3dfum78E3S sometimes resistance mut's are already present, selected for; other times arise. #AACR15
4:32pm April 18th 2015 via Hootsuite
ZS: Fourth time Wagle JCO paper referenced! http://t.co/QXWTavAQ8e Illustrating dramatic case of treatment #AACR15
4:30pm April 18th 2015 via Hootsuite
ZS: Heterogeneity paper http://t.co/90zXIaxLGt Now single-cell RNA-Seq highlights heterogeneity 2014 Science http://t.co/YX4hmNobPd #AACR15
4:29pm April 18th 2015 via Hootsuite
CM: Also endogenous mechanism - APOBEC the enzyme driving the mut process, for fighting virus, also age-rel C>T at CpG #AACR15
4:26pm April 18th 2015 via Hootsuite
ZS: Credits NGS as impetus for interest in heterogeneity. Now can be measured. Sci Trans Med 2015 fig http://t.co/a4LJyho5a6 #AACR15
4:25pm April 18th 2015 via Hootsuite
ZS: DNA index paper 2004 Cancer Res http://t.co/waSY5wcaCP And also true for normal cells too - mosaicism etc. #AACR15
4:22pm April 18th 2015 via Hootsuite
ZS: Intertumor heterogeneity 'has been known for ages'; a measure of malignancy, a DNA index as measure of instability #AACR15
4:20pm April 18th 2015 via Hootsuite
Zoltan Szallasi (Boston Children’s Hospital MA) “Biological and clinical implications of intratumor hetergeneity” ZS #AACR15
4:19pm April 18th 2015 via Hootsuite
CM: Credits R/Bioconductor community for 'enabling a huge amount of computational biology' #AACR15
4:13pm April 18th 2015 via Hootsuite
CM: Hodgkinson 2014 Nature Med paper http://t.co/dqmaFrytZ3 shows how much genomic heterogeneity there is in CTCs #AACR15
CM: And the proteome is not correlated well to gene expression. Evidence of stochasticity in yeast proteome http://t.co/VqbhDzrI67 #AACR15
4:10pm April 18th 2015 via Hootsuite
CM: Answering questions of gene expression (bursts? programmed? noise?) requires many single-cell experiments. #AACR15
4:08pm April 18th 2015 via Hootsuite
CM: Will need to do 1,000's of cells; need HPC analysis; comparisons approach Avogadro's number #AACR15
CM: Mentions this 2015 Nature Rev Genet on the analytical challenges of single-cell RNA-Seq http://t.co/GcTB8Hm2YC #AACR15
4:05pm April 18th 2015 via Hootsuite
CM: Are rare events even in the db's? Isoforms, genes? Can we 'annotate from scratch'? #AACR15
4:03pm April 18th 2015 via Hootsuite
CM: Every step of bulk RNA-Seq has differences w/single-cell. Example: low amount of RNA you can lose transcripts. #AACR15
4:01pm April 18th 2015 via Hootsuite
CM: But for cell cycle? 2014 ref http://t.co/6VSqRdwaz2 and expression levels are stochastic bursts. Some states are of interest. #AACR15
3:59pm April 18th 2015 via Hootsuite
CM: Will start w/RNA: starts with a figure from 2007 Cancer Res http://t.co/SRH12gDmkK and bulk tissue. #AACR15
3:56pm April 18th 2015 via Hootsuite
Crispin Miller CRUK “Approaches for global single cell profiling of DNA & RNA, and their application to circulating tumor cells” CM #AAC
3:53pm April 18th 2015 via Hootsuite
JH: Plans to use CyTOF from Fluidigm to do move onto single-cell proteomics #AACR15
3:50pm April 18th 2015 via Hootsuite
JH: Mentions this Dey et al 2015 Nature Biotech ref http://t.co/CTtcCTWagY sequencing DNA and RNA from single-cell. #AACR15
.@Fpicardo86 @priyaaav David Ting's talk was the highlight of my day - a veritable tour-de-force on pancreatic cancer single-cell work.
3:43pm April 18th 2015 via Hootsuite in reply to priyaaav
JH: Recommendations in CTC sorting from blood - 'go slow'. Sample handling critical; bone marrow, blood, tumor: they scan first #AACR15
3:39pm April 18th 2015 via Hootsuite
JH: Gingko software for CNV analysis of single-cell analysis http://t.co/LmuhIzweIy bioArxiv preprint http://t.co/nK7stFmsdZ #AACR15
3:37pm April 18th 2015 via Hootsuite
JH: Refers to Navin's 2011 Nature paper sorting nuclei; his group uses DOP-PCR (Signma WGA4, Rubicon PicoPlex). #AACR15
3:29pm April 18th 2015 via Hootsuite
JH: Isolation and DNA amplification (MDA, MALBAC, DOP PCR). His readout is CNV, integer-based. Normalize based on GC% (LOWESS) #AACR15
3:23pm April 18th 2015 via Hootsuite
JH: Now part of Michelson Center for Convergent Bioscience at Univ So Calif. (Solicits interested researchers to join.) #AACR15
3:20pm April 18th 2015 via Hootsuite
Jim Hicks (CSHL, NY) “Methods for rapid profiling of single cells to assess heterogeneity in solid tumors and circulating cells” JH #AACR15
3:18pm April 18th 2015 via Hootsuite
DT:Q:Diff between +/- selection? A:EPCAM RNA variable, and protein also not correlated well to RNA level. #AACR15
3:01pm April 18th 2015 via Hootsuite
DT: A: For human, flash freeze, of 500-600 whole transcriptomes, very similar results. Time is on the order of a few hours. #AACR15
2:55pm April 18th 2015 via Hootsuite
DT:Q:Cells in handling affecting RNA level? A:55/200 cells do not have RNA. Not only CTC problem though; timing is brief (3 min) #AACR15
DT: 2014 Cell ref http://t.co/TiIrx9SjSl with add'l ECM data. #AACR14
2:51pm April 18th 2015 via Hootsuite
DT: RNA in-situ - very important validation of their RNA-Seq data. Showed knockdown of SPARC. Other ECM proteins tissue-spec #AACR15
2:50pm April 18th 2015 via Hootsuite
DT: Comparing bulk primary vs single primary tumor - major loss of signal for ECM protein genes. SPARC RNA-ISH in mouse & human #AACR15
2:48pm April 18th 2015 via Hootsuite
DT: Showed majority of CTCs express Igfbp5 by RNA-ISH of primary tumor #AACR15
2:47pm April 18th 2015 via Hootsuite
DT: 7 pathways - MAPK, TGF-beta significant. 'CTC's have even more MAPK' than the primary tumor. #AACR15
2:44pm April 18th 2015 via Hootsuite
DT: Found 3 types of pancreatic CTC classes of genes, described in 2014 Cell Reports ref http://t.co/aKaDXZ8vV7 #AACR15
2:43pm April 18th 2015 via Hootsuite
DT: Due to high variability in transcriptome representation from single cells - high % of 'zero reads'; used rank product method #AACR15
2:41pm April 18th 2015 via Hootsuite
DT: Unsupervised clustering, primary tumors cluster together, showing 3 groups. Cell lines most homogeneous #AACR15
2:38pm April 18th 2015 via Hootsuite
DT: 3rd gen CTC-iChip has a single-file readout 2013 Sci Trans Med ref http://t.co/yw5nlTxA6P Used @Appliedbio 5500xl #AACR15
2:37pm April 18th 2015 via Hootsuite
DT: Many technologies; one review. http://t.co/3Lq4whktnQ ID'd Wnt2 in 2012 Nature but was EPCAM #AACR15
2:35pm April 18th 2015 via Hootsuite
