The Cellular Geography of Therapeutic Resistance in Cancer

Written and checked by a reviewer, not generated from metadata.

1. 1. Where within a tumor do cells that survive therapy actually reside?

   Needs approved accessHUMAN

   Multiplexed tissue imaging with single-cell RNA sequencing on the same specimens, in an atlas designed around this question, with therapy records available as a clinical component to define the treatment context.

   Statistical note: Spatial analyses are specimen-level; patient numbers are small and the appropriate unit of inference is the region or cell neighborhood, with patient as a random effect.

   NeedsMultiplexed tissue imagingSingle-cell RNA sequencingTreatment records

2. 2. Do spatial niches associated with resistance recur across cancer types, or are they tissue-specific?

   Needs another datasetHUMAN

   Neighborhood definitions derived here can be tested against other HTAN atlases that share the multiplexed imaging component, giving cross-atlas comparison within a single access framework and a common data model.

   NeedsMultiplexed tissue imaging

3. 3. Can the extended clinical tier be used to relate spatial organization to real treatment sequences rather than to treatment as a single binary?

   Needs approved accessHUMAN

   This atlas carries the extended clinical data tier that most atlases lack, alongside therapy and follow-up. That is what allows spatial features to be related to what was actually given and what happened next.

   Statistical note: Confirm the completeness of the extended clinical fields in Synapse before designing; the portal metadata records their presence but not their coverage.

   NeedsMultiplexed tissue imagingTreatment recordsClinical data

Written by a reviewer against the source, not inferred from what is missing.

Articles that analyzed these data, counted separately from articles that only cited the paper. Only the first counts as reuse.

Analyses someone ran on these data end to end, each with a receipt recording when it ran, against which packages and for how long.

Starter code generated from this record’s own identifiers, then the access steps.

import synapseclient

syn = synapseclient.login()          # uses ~/.synapseConfig or SYNAPSE_AUTH_TOKEN
for sid in ["syn39259236","syn39259256","syn39259280","syn39259513"]:
    entity = syn.get(sid, downloadLocation="./htan")
    print(sid, entity.name)
# Browse the atlas at https://humantumoratlas.org/explore

curl -s https://cd2s.vercel.app/data/datasets/htan-the-cellular-geography-of-therapeutic-resistance-in-cancer.json | python3 -c '
import json, sys
r = json.load(sys.stdin)
for l in r["limitations"]:
    print(l["severity"].upper(), "-", l["statement"][:120])
print("survival endpoint:", r["longitudinal"]["has_survival_endpoint"], "| treatment response:", r["longitudinal"]["has_treatment_response"])'

Access steps

1. 1

   Contact the atlas team through the HTAN portalFor peopledays

   With no marker publication recorded, this is the fastest route to the design details you would normally get from a paper.

   https://humantumoratlas.org/
2. 2

   Register with Synapse and accept the HTAN data use termsFor people1 day

   Requires: Synapse account

   https://humantumoratlas.org/data-access
3. 3

   Verify participant counts and clinical field coverage before designingFor people2-3 hours
4. 4

   Give an agent a Synapse token, not a passwordFor agents

   Unauthenticated calls return metadata and no files, so an agent should report the credential requirement explicitly.

   Requires: SYNAPSE_AUTH_TOKEN

   export SYNAPSE_AUTH_TOKEN=...
   synapse get syn39259236

   https://help.synapse.org/docs/Getting-Started.2055471150.html

   Generated from repository policy. Check the linked policy before downloading.

All of it, and more, is in this record’s JSON.