Issues
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Cover Image
Cover Image
Genomic copy number alterations are common features of human cancers that distinguish them from normal cells. Baker and colleagues developed Gain Route Identification and Timing in Cancer (GRITIC), a computational method for timing genomic gains leading to complex copy number states from singlesample bulk whole-genome sequencing data. GRITIC exploits the relationship between single nucleotide variant read counts, copy number, and tumor purity and uses a Bayesian Markov Chain Monte Carlo approach to infer the probability of all possible routes and timings to reach a particular copy number state. Application of GRITIC to over 6,000 tumors led to the unexpected observation that in many cases, particularly in tumors that have undergone whole-genome duplication (WGD), copy number states are not formed in the minimum number of steps possible. Punctuated bursts of copy number gains were also common independent of WGD, but late WGD accelerated the rate of copy number gains. Pinpointing when copy number changes occur can provide insight into tumor evolution and mechanisms underlying chromosomal instability. For more information, see the article by Baker and colleagues on page 1810. Artwork by Bianca Dunn. - PDF Icon PDF LinkTable of Contents
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In This Issue
In the Spotlight
Science in Society
A New Era of Data-Driven Cancer Research and Care: Opportunities and Challenges
In Focus
Cancer Hallmarks Review
Research Briefs
The History of Chromosomal Instability in Genome-Doubled Tumors
A novel Bayesian method to time the occurrence of complex copy number gains was applied to thousands of tumor whole genome sequences, allowing the temporal dynamics between whole genome doubling and other copy number events to be evaluated.
Perivascular NOTCH3+ Stem Cells Drive Meningioma Tumorigenesis and Resistance to Radiotherapy
NOTCH3+ cells present in the perivascular stem cell niche promote tumor-initiation, proliferation, and angiogenesis in meningiomas and are a therapeutic vulnerability.
Research Articles
Biologic and Clinical Analysis of Childhood Gamma Delta T-ALL Identifies LMO2/STAG2 Rearrangements as Extremely High Risk
STAG2/LMO2 T-ALL is common in very young children with γδ T-ALL, is high risk, and is characterized by altered chromatin looping, impaired hematopoietic differentiation, and vulnerability to PARP inhibition.
CRISPR Dependency Screens in Primary Hematopoietic Stem Cells Identify KDM3B as a Genotype-specific Vulnerability in IDH2- and TET2-mutant Cells
Functional genomic screens in mutant hematopoietic stem cells using an ex vivo co-culture platform nominate KDM3B and an epigenetically regulated signaling pathway as dependencies in a subset of clonal hematopoiesis.
CD28 Costimulation Augments CAR Signaling in NK Cells via the LCK/CD3ζ/ZAP70 Signaling Axis
While NK cells naturally lack CD28, incorporating CD28 costimulation into CAR design enhances the antitumor efficacy of CAR-NK cells by recruiting key signaling kinases, underscoring its potential for improving CAR-NK based cancer immunotherapy.
Iron Chelation Therapy Elicits Innate Immune Control of Metastatic Ovarian Cancer
Treatment with an iron chelator sensitizes ovarian tumors to innate immune attack, hindering disease progression and enhancing standard therapy.
Targeting Acute Myeloid Leukemia Stem Cells through Perturbation of Mitochondrial Calcium
Analysis of therapy-resistant leukemia stem cells (LSC) revealed that inhibition of mitochondrial calcium uptake acts to inhibit oxidative phosphorylation, thereby leading to subsequent eradication of LSCs.
Iron-(Fe3+)-Dependent Reactivation of Telomerase Drives Colorectal Cancers
This study identifies and characterizes a molecular pathway that causes re-activation of telomerase by high Fe3+-iron, thereby providing novel therapeutic targets for inhibiting this enzyme which drives 90% of human cancers.
Oncogenic KRAS-Dependent Stromal Interleukin-33 Directs the Pancreatic Microenvironment to Promote Tumor Growth
Tumor cell-derived signals induce stromal IL33 expression in pancreatic cancer and stromal IL33 promotes pancreatic cancer growth by supporting immunosuppression.
Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer
Applying a recordable barcode in a prostate cancer model delineates the clonal architecture, seeding topologies, and routes taken by distinct cancer clones that traverse metastatic sites.
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