Evidence map›Paper›PMID 39605341›Full record

ArticlebioRxiv : the preprint server for biology2024

Leveraging chromatin packing domains to target chemoevasion

Jane Frederick, Ranya K A Virk, I Chae Ye, Luay M Almassalha, Greta M Wodarcyk, David VanDerway, Paola Carrillo Gonzalez, Rikkert J Nap, Vasundhara Agrawal, Nicholas M Anthony and 10 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

5 · Who and what money

Authors and funding

20 authors.

Jane FrederickDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.ORCID 0000-0003-3007-9197
Ranya K A VirkDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
I Chae YeDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Luay M AlmassalhaCenter for Physical Genomics and Engineering, Northwestern University, Evanston, IL 60208, USA.
Greta M WodarcykDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
David VanDerwayDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Paola Carrillo GonzalezDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Rikkert J NapDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Vasundhara AgrawalDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Nicholas M AnthonyDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
John CarinatoDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Wing Shun LiDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Cody L DuntonDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Karla I MedinaDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Rivaan KakkaramadamDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Surbhi JainDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Shohreh ShahabiDepartment of Obstetrics and Gynecology, Prentice Women's Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
Guillermo AmeerDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Igal G SzleiferDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.
Vadim BackmanDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA.ORCID 0000-0003-1981-1818

Funding

Tumor Environment and Metastasis (TEAM) Research ProgramP30CA060553 · NCI · NORTHWESTERN UNIVERSITY AT CHICAGO · PI Devalingam Mahalingam · 1993 to 2026
$153.9M
MEDICAL SCIENTIST TRAINING PROGRAMT32GM008152 · NIGMS · NORTHWESTERN UNIVERSITY AT CHICAGO · PI ARDEHALI, HOSSEIN · 1987 to 2021
$24.0M
Spatio-Temporal Organization of Chromatin and Information Transfer in CancerU54CA193419 · NCI · NORTHWESTERN UNIVERSITY AT CHICAGO · PI BACKMAN, VADIM · 2015 to 2020
$10.4M
Technology Development UnitU54CA268084 · NCI · NORTHWESTERN UNIVERSITY · PI Vadim Backman, Daniela E Matei · 2022 to 2026
$10.0M
Training Program In Lung SciencesT32HL076139 · NHLBI · NORTHWESTERN UNIVERSITY AT CHICAGO · PI KAREN M RIDGE, Jacob I Sznajder · 2004 to 2026
$9.6M
Translating buccal nanocytology for lung cancer screening into clinical practiceR01CA225002 · NCI · NORTHWESTERN UNIVERSITY · PI Vadim Backman, HARIHARAN SUBRAMANIAN · 2018 to 2026
$5.0M
Reducing Cancer Transcriptional Heterogeneity through Regulation of Chromatin StructureR01CA228272 · NCI · NORTHWESTERN UNIVERSITY · PI BACKMAN, VADIM, ROY, HEMANT K. · 2018 to 2022
$3.2M
Nanoscale/Molecular analysis of Fecal Colonocytes for Colorectal Cancer ScreeningR01CA165309 · NCI · NORTHWESTERN UNIVERSITY · PI BACKMAN, VADIM, ROY, HEMANT K. · 2012 to 2016
$2.8M
Optical Nanoscale Analysis of Buccal Cells: Transforming Lung Cancer ScreeningR01CA155284 · NCI · NORTHWESTERN UNIVERSITY · PI BACKMAN, VADIM, ROY, HEMANT K. · 2011 to 2014
$2.3M
DNA repair pathway choice mediates somatic cell reprogrammingR01GM132604 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI EGLI, DIETER MEINRAD · 2020 to 2023
$1.9M
NCI NIH HHS P30 CA060553NCI NIH HHS R01 CA155284NCI NIH HHS R01 CA165309NCI NIH HHS R01 CA225002NCI NIH HHS R01 CA228272NCI NIH HHS U54 CA193419NCI NIH HHS U54 CA268084NHLBI NIH HHS T32 HL076139NIGMS NIH HHS R01 GM132604NIGMS NIH HHS T32 GM008152
6 · The paper itself

Abstract

Cancer cells exhibit a remarkable resilience to cytotoxic stress, often adapting through transcriptional changes linked to alterations in chromatin structure. In several types of cancer, these adaptations involve epigenetic modifications and restructuring of topologically associating domains (TADs). However, the underlying principles by which chromatin architecture facilitates such adaptability across different cancers remain poorly understood. To investigate the role of chromatin in this process, we developed a physics-based mechanistic model that connects chromatin organization to cell fate decisions, specifically survival following chemotherapy. Our model builds on the observation that chromatin forms packing domains, which influence transcriptional efficiency through macromolecular crowding. The model accurately predicts chemoevasion

Indexed as

BiophysicsCancerChemotherapyChromatinPlasticity

Identifiers

PMID39605341
PMCPMC11601449

What OpenQuestion holds

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LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.