Evidence map›Paper›PMID 42239335›Full record

ArticlebioRxiv : the preprint server for biology2026

Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets.

Audrey Kishishita, Sabine Cismoski, Tianna Grant, Rucha Deo, Sanjana Prudhvi, Catherine Sue, Abhilash Barpanda, Clinton Yu, Sanjyot Shenoy, Sarah Berman and 22 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

32 authors.

Audrey KishishitaGraduate Program in Chemistry and Chemical Biology, University of California-San Francisco, San Francisco, CA, USA.
Sabine CismoskiGraduate Program in Chemistry and Chemical Biology, University of California-San Francisco, San Francisco, CA, USA.
Tianna GrantDivision of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Rucha DeoDepartment of Laboratory Medicine, University of California-San Francisco, San Francisco, CA, USA.
Sanjana PrudhviDepartment of Laboratory Medicine, University of California-San Francisco, San Francisco, CA, USA.
Catherine SueDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA.
Abhilash BarpandaDepartment of Laboratory Medicine, University of California-San Francisco, San Francisco, CA, USA.
Clinton YuDepartment of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA.
Sanjyot ShenoyDepartment of Mathematics, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.
Sarah BermanDepartment of Laboratory Medicine, University of California-San Francisco, San Francisco, CA, USA.
Audrey G ReevesDepartment of Laboratory Medicine, University of California-San Francisco, San Francisco, CA, USA.
Haolong LiHuman Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Tianyi LiuHelen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
Akul NaikDepartment of Laboratory Medicine, University of California-San Francisco, San Francisco, CA, USA.
Deeptarup BiswasDepartment of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.
Fenglong JiaoDepartment of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA.
Yi HeThermo Fisher Scientific, San Jose, CA, USA.
Matthew HancockDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA.
Radhika DalalDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA.
Arther ZalevskyDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA.
Michael R HoopmannInstitute for Systems Biology-Seattle, Seattle, WA, USA.
Chun Jimmie YeDivision of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Rosa VinerThermo Fisher Scientific, San Jose, CA, USA.
Felix FengDepartment of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
Kamal MandalDepartment of Laboratory Medicine, University of California-San Francisco, San Francisco, CA, USA.
Robert L MoritzInstitute for Systems Biology-Seattle, Seattle, WA, USA.
Ignacia Echeverria RiescoDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA.
Andrej SaliDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA.
James A WellsDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
Sanjeeva SrivastavaDepartment of Mathematics, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.
Lan HuangDepartment of Physiology & Biophysics, University of California, Irvine, Irvine, CA, USA.
Arun P WiitaDepartment of Laboratory Medicine, University of California-San Francisco, San Francisco, CA, USA.

Funding

Structural surfaceomics to probe conformation-selective immunotherapy targetsR01CA290875 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Lan Huang, Arun P. Wiita · 2024 to 2026
$2.7M
NCI NIH HHS R01 CA290875
6 · The paper itself

Abstract

The complement of tumor cell surface proteins, or "surfaceome", is a rich source of potential immunotherapy targets. To move beyond expression-based target discovery, we previously described "structural surfaceomics," combining crosslinking mass spectrometry (XL-MS) with surface protein biotinylation to identify conformation-selective targets. In our prior work, we applied this method to a single model of acute myeloid leukemia (AML), identifying active integrin beta-2 as a promising target. Here, we expand structural surfaceomics to identify additional immunotherapy targets and surface protein biology across additional models of AML, multiple myeloma, and prostate cancer, as well as donor peripheral blood mononuclear cells. Utilizing these models and different chemical crosslinkers, we compile an extensive database of 5,209 crosslinks. We characterize both shared and unique crosslink-based features, identifying 1,612 disease model-specific crosslinks, including 212 potentially defining tumor-specific conformations based on distance constraint violations relative to AlphaFold predictions. We further implement a suite of emerging modeling tools to predict tumor-specific protein structures. We probe crosslinking patterns suggesting multiple myeloma-specific CD48 and AML-specific integrin α1/β4 heterodimer conformations. This work establishes a resource for cancer structural biology by implementation of structural surfaceomics. Our findings also point toward more realistic protein design models, potentially enabling systematic detection of targetable cancer-specific epitopes for next-generation immunotherapies.

Identifiers

PMID42239335
PMCPMC13228367

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