Disrupting cellular memory to overcome drug resistance

Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells

(2023) Yogesh Goyal et al.   NATURE

Subcellular Detection of SARS-CoV-2 RNA in Human Tissue Reveals Distinct Localization in Alveolar Type 2 Pneumocytes and Alveolar Macrophages

(2022) Kofi K. Acheampong et al.   mBio

Intermittent treatment of BRAF V600E melanoma cells delays resistance by adaptive resensitization to drug rechallenge

(2022) Andrew J. Kavran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeting SOX10-deficient cells to reduce the dormant-invasive phenotype state in melanoma

(2022) Claudia Capparelli et al.   Nature Communications

Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

(2022) Dalia Barkley et al.   NATURE GENETICS

A cellular hierarchy in melanoma uncouples growth and metastasis

(2022) Panagiotis Karras et al.   NATURE

Genetic screening for single-cell variability modulators driving therapy resistance

(2021) Eduardo A. Torre et al.   NATURE GENETICS

DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with Kubernetes

(2021) Dylan Bannon et al.   NATURE METHODS

Variability within rare cell states enables multiple paths toward drug resistance

(2021) Benjamin L. Emert et al.   NATURE BIOTECHNOLOGY

Epithelial‐to‐mesenchymal‐like transition events in melanoma

(2021) Dennis Pedri et al.   FEBS Journal

Toxicity of Combinations of Kinase Pathway Inhibitors to Normal Human Cells in a Three-Dimensional Culture

(2021) Pouria Rafsanjani Nejad et al.   SLAS Technology

Cycling cancer persister cells arise from lineages with distinct programs

(2021) Yaara Oren et al.   NATURE

Human melanocyte development and melanoma dedifferentiation at single-cell resolution

(2021) Rachel L. Belote et al.   NATURE CELL BIOLOGY

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

(2021) Srivatsan Raghavan et al.   CELL

Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning

(2021) Noah F. Greenwald et al.   NATURE BIOTECHNOLOGY

Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

(2021) Ronan Chaligne et al.   NATURE GENETICS

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

Efficacy and safety of anticancer drug combinations: a meta-analysis of randomized trials with a focus on immunotherapeutics and gene-targeted compounds

(2020) Denis L. Jardim et al.   OncoImmunology

Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition

(2020) Jenny H. Lee et al.   Nature Communications

Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors

(2020) Sydney M. Shaffer et al.   CELL

EMT-Inducing Transcription Factors, Drivers of Melanoma Phenotype Switching, and Resistance to Treatment

(2020) Yaqi Tang et al.   Cancers

Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq

(2020) Qi Qiu et al.   NATURE METHODS

Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals

(2020) Eric M Sanford et al.   eLife

Phase Ib study of the MEK inhibitor cobimetinib (GDC-0973) in combination with the PI3K inhibitor pictilisib (GDC-0941) in patients with advanced solid tumors

(2019) Geoffrey I. Shapiro et al.   INVESTIGATIONAL NEW DRUGS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

(2019) Cyril Neftel et al.   CELL

CD271 is a molecular switch with divergent roles in melanoma and melanocyte development

(2019) Fabian V. Filipp et al.   Scientific Reports

Effective Treatment of Metastatic Melanoma by Combining MAPK and PI3K Signaling Pathway Inhibitors

(2019) Aasen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Phase Ib Study of Combination Therapy with MEK Inhibitor Binimetinib and Phosphatidylinositol 3‐Kinase Inhibitor Buparlisib in Patients with Advanced Solid Tumors with RAS/RAF Alterations

(2019) Aditya Bardia et al.   ONCOLOGIST

Combination of Selected MET and EGFR Inhibitors Decreases Melanoma Cells’ Invasive Abilities

(2019) Aleksandra Simiczyjew et al.   Frontiers in Pharmacology

Leveraging transcriptional dynamics to improve BRAF inhibitor responses in melanoma

(2019) Inna Smalley et al.   EBioMedicine

Toward Minimal Residual Disease-Directed Therapy in Melanoma

(2018) Florian Rambow et al.   CELL

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

AXL/AKT axis mediated-resistance to BRAF inhibitor depends on PTEN status in melanoma

(2018) Qiang Zuo et al.   ONCOGENE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Oncogenic PI3K/AKT promotes the step-wise evolution of combination BRAF/MEK inhibitor resistance in melanoma

(2018) Mal Irvine et al.   Oncogenesis

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

Organoid Modeling of the Tumor Immune Microenvironment

(2018) James T. Neal et al.   CELL

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Combination therapy with potent PI3K and MAPK inhibitors overcomes adaptive kinome resistance to single agents in preclinical models of glioblastoma

(2017) Robert S McNeill et al.   NEURO-ONCOLOGY

Integrating evolutionary dynamics into treatment of metastatic castrate-resistant prostate cancer

(2017) Jingsong Zhang et al.   Nature Communications

CD271 determines migratory properties of melanoma cells

(2017) Josefine Radke et al.   Scientific Reports

Inhibiting Drivers of Non-mutational Drug Tolerance Is a Salvage Strategy for Targeted Melanoma Therapy

(2016) Michael P. Smith et al.   CANCER CELL

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Exploiting evolutionary principles to prolong tumor control in preclinical models of breast cancer

(2016) Pedro M. Enriquez-Navas et al.   Science Translational Medicine

Starcode: sequence clustering based on all-pairs search

(2015) Eduard Zorita et al.   BIOINFORMATICS

MITF Modulates Therapeutic Resistance through EGFR Signaling

(2015) Zhenyu Ji et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

(2015) Hyo-eun C Bhang et al.   NATURE MEDICINE

NFATc2 is an intrinsic regulator of melanoma dedifferentiation

(2015) V Perotti et al.   ONCOGENE

The transcription cofactor c-JUN mediates phenotype switching and BRAF inhibitor resistance in melanoma

(2015) Rachel Ramsdale et al.   Science Signaling

Using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling

(2015) Rawane Samb et al.   Statistical Applications in Genetics and Molecular Biology

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

(2015) Annelien Verfaillie et al.   Nature Communications

Using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling

(2015) Rawane Samb et al.   Statistical Applications in Genetics and Molecular Biology

The transcription cofactor c-JUN mediates phenotype switching and BRAF inhibitor resistance in melanoma

(2015) Rachel Ramsdale et al.   Science Signaling

PI3K signalling is required for a TGFβ-induced epithelial-mesenchymal-like transition (EMT-like) in human melanoma cells

(2014) Natalie C. Schlegel et al.   EXPERIMENTAL DERMATOLOGY

Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma

(2014) Chong Sun et al.   NATURE

Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma

(2014) Judith Müller et al.   Nature Communications

A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors

(2014) D. J. Konieczkowski et al.   Cancer Discovery

Modelling vemurafenib resistance in melanoma reveals a strategy to forestall drug resistance

(2013) Meghna Das Thakur et al.   NATURE

Safety and feasibility of targeted agent combinations in solid tumours

(2013) Sook Ryun Park et al.   Nature Reviews Clinical Oncology

Signaling interplay between transforming growth factor-β receptor and PI3K/AKT pathways in cancer

(2013) Long Zhang et al.   TRENDS IN BIOCHEMICAL SCIENCES

Inhibiting EGF Receptor or SRC Family Kinase Signaling Overcomes BRAF Inhibitor Resistance in Melanoma

(2012) Maria R. Girotti et al.   Cancer Discovery

Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells

(2011) Piyush B. Gupta et al.   CELL

A Polycomb-based switch underlying quantitative epigenetic memory

(2011) Andrew Angel et al.   NATURE

The Ras-ERK and PI3K-mTOR pathways: cross-talk and compensation

(2011) Michelle C. Mendoza et al.   TRENDS IN BIOCHEMICAL SCIENCES

Acquired Resistance to BRAF Inhibitors Mediated by a RAF Kinase Switch in Melanoma Can Be Overcome by Cotargeting MEK and IGF-1R/PI3K

(2010) Jessie Villanueva et al.   CANCER CELL

A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations

(2010) Sreenath V. Sharma et al.   CELL

flowCore: a Bioconductor package for high throughput flow cytometry

(2009) Florian Hahne et al.   BMC BIOINFORMATICS

TGF-β-induced epithelial to mesenchymal transition

(2009) Jian Xu et al.   CELL RESEARCH

In vivo Switching of Human Melanoma Cells between Proliferative and Invasive States

(2008) K. S. Hoek et al.   CANCER RESEARCH

Non-Smad pathways in TGF-β signaling

(2008) Ying E Zhang   CELL RESEARCH