Eli Van Allen Profile picture
Sep 8, 2021 11 tweets 6 min read Read on X
Here's our latest, a deep molecular dive into exceptional responders to anti-androgen therapy before surgery - congrats @aloktewar @alexorscanner Dr. Taplin @DanaFarber_GU et al!

cell.com/cell-reports/f… @CellReports

[1/n]
(See also co-published/co-submitted wonderful story by @Chris_Barbieri1 lab with convergent science! cell.com/cell-reports/f…)
High risk localized prostate cancer can be curable with existing modalities (e.g. surgery), though whether giving upfront anti-androgen therapy before surgery can expand the number of men who are cured is not yet known.

Many trials ongoing by Dr. Taplin + many others to assess
This clinical context also allows for a unique opportunity to directly study the effect of these therapies in human tumors, where we can ask why some patients' tumors exhibit deep biological responses vs. persistent high risk disease at surgery
Since the definition of "exceptional responder" will (of course) vary by study given the wide range of clinical contexts, therapies, and outcome measures in such work, for clarity in this study we defined these responses as follows:
We accessed pre-treatment biopsy specimens (often more than one sample per-patient to evaluate genomic heterogeneity) from men enrolled on these clinical studies...

...and did a deep dive into molecular differences between response groups to identify potential explanations
We found SPOP mutations (and, curiously, deletions in SPOPL - a paralog) highly enriched in patients with exceptional responses...

...whereas TP53 and PTEN mutations were enriched in nonresponders
This ties nicely into the biological investigations into SPOP and androgen biology that @Chris_Barbieri1 and I discussed at @PCFnews Annual Meeting 2019 that led to cosubmission! It also relates to an amazing @sowalsky study where this trend was also seen europeanurology.com/article/S0302-…
We also looked at transcriptional programs btwn clinical groups & noted androgen response elevated in responders (no surprise)...

...and TGF-beta signaling in nonresponders (see also: similar findings in metastatic prostate cancer h/t @MXresearch nature.com/articles/s4159…)
Using multi-regional analysis, we also looked for tumor heterogeneity patterns in responders (h/t @getz_lab @gaddyg + co.)

We noted that interesting mutations in this treatment context were truncal, but couldn't find global patterns related to response in this cohort
Much more to do...

Hope this study promotes new biology & clinical studies to learn more about underlying molecular states in anti-androgen sensitive tumors

Most importantly, thanks to prostate cancer patients participating in trials & enabling this type of research! [fin]

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More from @VanAllenLab

Sep 30, 2021
Our latest - introducing the Molecular Oncology Almanac (MOAlmanac): paired clinical interpretation algorithm + knowledge base for precision cancer medicine @moalmanac
Congrats @brendan_reardon et al! @DanaFarber @broadinstitute nature.com/articles/s4301… @NatureCancer [1/12]
(Plus shout outs to @natemoore and @NickMoore [no relation] who contributed greatly to this effort during their research time in med school. The co-authors, reviewers, editors, and those mentioned in acknowledgements were instrumental to both this resource and study)
We've long been interested in how to take molecular data from individual cancer patients and search for clinically + biologically relevant events - see below for our first attempt at this for cancer exomes via PHIAL (ca. 2014)
nature.com/articles/nm.35…
Read 12 tweets
Jun 8, 2021
Here’s our latest, a deep dive into fusions and partner or "collateral" cancer dependencies

Interesting findings for pediatric and adult cancers...

Congrats Dr. Riaz Gillani @BostonChildrens @DanaFarber @broadinstitute et al! @CR_AACR @AACR cancerres.aacrjournals.org/content/early/… [1/n]
Gene fusions can be important for cancer development, and prior work nicely demonstrated how such events can directly affect the expression or functionality of partner genes in cell line data, e.g.: nature.com/articles/s4146…
Riaz then asked - with CRISPR screening + molecular data from 645 cell lines - whether fusions create:
(i) functional dependencies on partner genes
and/or
(ii) “collateral dependencies” on genes w/in the same topologically associating domains (TADs) as fusion partners
Read 8 tweets
Jun 22, 2020
Interested to see how the forthcoming data behind the ‘TMB > 10 in all cancer types’ approval addresses a few key issues, having spent a long time thinking about this general topic - some thoughts to follow:

[1/n]
(Heeding wise words of @tmprowell - this is *not intended as critique*, but rather some open thoughts on the matter that I'm excited to see in the final data once available - feedback welcome! )
1) Technical:
- Many non-biological factors affect TMB calculation, like sample quality, tumor purity, sequencing artifacts, and NGS fails.

Difference btwn NGS from TCGA samples vs. clinical trial samples vs. real world clinical samples is large. Also: nejm.org/doi/full/10.10…
Read 15 tweets
Dec 3, 2019
A brief thread on our latest study, as well as a more general chat on biology & biomarkers for cancer immunogenomics - w/ longtime friend Dirk Schadendorf + rockstar jr faculty @dliu_ccb + more friends! @NatureMedicine @DanaFarber @broadinstitute
nature.com/articles/s4159… [1/n]
Many current biology & biomarkers blurry lines in cancer immunogenomics - e.g. our TMB melanoma work:

2014-15: Correlation btwn TMB + clinical benefit to ICB in melanoma → neoantigen biology

Though our 2015 data (ncbi.nlm.nih.gov/pubmed/26359337) suggested weak predictive effect...
...and then:

2018: TMB confounded by mutational signatures (ncbi.nlm.nih.gov/pubmed/30150660)

Here: TMB also confounded by histologic subtype

Cool biology: Yes!
Clinical biomarker: Err...probably not
Read 14 tweets
Nov 19, 2018
Here, we partnered w/ cancer patients + friends @KDeutsch @adamhayden @CultPerfectMoms @CurrentIncurSci @stephanie_mul to liberate their cancer genomic data from clinical labs.

It was a struggle…

...but there’s hope & we have a plan! [1/n] @OSFramework osf.io/gupvq
(Updated my bio to have a disclosures link, including consulting for genomics labs which is relevant for this effort. Also pasting here: goo.gl/6kfq2E)
Patients have a right to their data, and HIPAA states that data (whether clinical, molecular, or anything in between) should come in a computable form.

hhs.gov/hipaa/for-prof… cc @EricTopol @TheLizArmy
Read 13 tweets
Aug 29, 2018
A thread on our latest look at cancer genomics + immune checkpoint blockade → congrats @diana_miao, Claire, @NIVokes et al!

Thx @SU2C @BroadIgnite @HHMINEWS @theNCI for supporting this & the ppl doing it @NatureGenet @DanaFarber @broadinstitute

rdcu.be/5iVz [1/n]
We analyzed every tumor-normal exome from patients getting immune checkpoint blockade (ICB) we could get & integrated w/ clinical outcomes for biological and clinical exploration → lots of technical pain here + open questions re: defining clinical benefit
For context, lots of ongoing biology re: mutations/neoantigens driving response to immune checkpoint blockade by many groups (including ours).

In parallel, lots of buzz about tumor mutational burden (TMB) as a *clinical* biomarker for cancer ICB...
Read 13 tweets

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