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Cancer-related molecular mechanisms research
Research Guide
What is Cancer-related molecular mechanisms research?
Cancer-related molecular mechanisms research is the study of long noncoding RNAs (lncRNAs) and their roles in cancer through transcriptional landscapes, epigenetic regulation, chromatin modification, competing endogenous RNA networks, and impacts on cell differentiation and genome regulation.
This field encompasses 131,595 works focused on lncRNAs in cancer, development, and genome regulation. Key areas include functional classification of lncRNAs and their molecular mechanisms in human diseases. Research highlights RNA-seq methods for transcript quantification and analysis during cell differentiation.
Topic Hierarchy
Research Sub-Topics
Long Noncoding RNAs in Cancer
This sub-topic explores lncRNAs dysregulated in cancer, their roles in oncogenesis, metastasis, and therapy resistance. Researchers profile lncRNA expression, validate functions via knockdown, and identify therapeutic targets.
LncRNA Epigenetic Regulation
LncRNA epigenetic regulation studies how lncRNAs recruit chromatin modifiers, control DNA methylation, and influence gene silencing. Researchers map lncRNA-chromatin interactions using ChIP-seq and CRISPR editing.
LncRNA Competing Endogenous RNAs
LncRNAs as competing endogenous RNAs (ceRNAs) sequester miRNAs to derepress target genes in regulatory networks. Researchers model ceRNA networks and test hypotheses in cancer and differentiation contexts.
LncRNA Chromatin Modification
LncRNA chromatin modification investigates lncRNA guidance of histone modifications and phase separation at gene loci. Researchers use proximity labeling and structural biology to elucidate mechanisms.
Transcriptional Landscape of LncRNAs
The transcriptional landscape of lncRNAs catalogs their expression patterns, enhancers, and bidirectional promoters across cell types. Researchers integrate RNA-seq with eQTL mapping for comprehensive profiling.
Why It Matters
Cancer-related molecular mechanisms research enables precise identification of transcript expression changes in tumors, supporting targeted therapies. For instance, "Integrated genomic analyses of ovarian carcinoma" (2011) analyzed mRNA expression, microRNA expression, promoter methylation, and DNA copy number in 489 high-grade tumors, creating a catalogue of molecular aberrations for therapy development. Tools like DESeq2 in "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2" by Love et al. (2014) with 93,376 citations standardize differential expression analysis across cancer studies. Recent NIH efforts released proteogenomic datasets from over 1,000 tumors across 10 cancer types, aiding researchers in unraveling molecular drivers. These advances inform immunotherapy and molecular targeted therapy based on genomic abnormalities and tumor microenvironments.
Reading Guide
Where to Start
"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2" by Love et al. (2014), as it provides the foundational statistical method for RNA-seq analysis central to studying lncRNA expression in cancer, with 93,376 citations.
Key Papers Explained
"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2" by Love et al. (2014) enables differential analysis building on "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation" by Trapnell et al. (2010), which uncovers lncRNAs in differentiation. "Salmon provides fast and bias-aware quantification of transcript expression" by Patro et al. (2017) refines quantification speed. MicroRNA foundations in "The functions of animal microRNAs" by Ambros (2004) connect to cancer classification in "MicroRNA expression profiles classify human cancers" by Lü et al. (2005), while circular RNA papers by Hansen et al. (2013) and Memczak et al. (2013) extend regulatory networks.
Paper Timeline
Most-cited paper highlighted in red. Papers ordered chronologically.
Advanced Directions
Recent preprints like "Drug resistance in cancer: molecular mechanisms and emerging treatment strategies" (2025) examine resistance across therapies. "Data-driven universal insights into tumorigenesis via hallmark networks" (2025) analyzes dysregulation in heterogeneous populations. NIH proteogenomic datasets from 1,000+ tumors and NOFOs on lipid metabolism-tumor links and immune evasion drive multi-omics integration.
Papers at a Glance
| # | Paper | Year | Venue | Citations | Open Access |
|---|---|---|---|---|---|
| 1 | Moderated estimation of fold change and dispersion for RNA-seq... | 2014 | Genome biology | 93.4K | ✓ |
| 2 | Transcript assembly and quantification by RNA-Seq reveals unan... | 2010 | Nature Biotechnology | 16.1K | ✕ |
| 3 | Salmon provides fast and bias-aware quantification of transcri... | 2017 | Nature Methods | 12.5K | ✓ |
| 4 | The functions of animal microRNAs | 2004 | Nature | 10.7K | ✕ |
| 5 | MicroRNA expression profiles classify human cancers | 2005 | Nature | 9.5K | ✕ |
| 6 | Natural RNA circles function as efficient microRNA sponges | 2013 | Nature | 8.3K | ✕ |
| 7 | Circular RNAs are a large class of animal RNAs with regulatory... | 2013 | Nature | 8.3K | ✕ |
| 8 | A scaling normalization method for differential expression ana... | 2010 | Genome biology | 8.1K | ✓ |
| 9 | 16S/23S rRNA sequencing | 1991 | Medical Entomology and... | 8.0K | ✕ |
| 10 | Integrated genomic analyses of ovarian carcinoma | 2011 | Nature | 7.9K | ✓ |
In the News
NIH unveils comprehensive proteogenomic dataset to help cancer researchers unravel molecular mysteries
The National Institutes of Health is releasing a comprehensive dataset that standardizes genomic, proteomic, imaging, and clinical data from individual studies of more than 1,000 tumors across 10 c...
Request for Proposals: Aging and Cancer
* Exploring the molecular mechanisms responsible for the age-related declines in stem cell numbers and function, such as hematopoietic, epithelial or mesenchymal stem cells, and their relationship ...
Advanced Development and Validation of Emerging Molecular and Cellular Analysis Technologies for Basic and Clinical Cancer Research (R33 Clinical Trial Not Allowed)
Through this Notice of Funding Opportunity (NOFO), the National Cancer Institute (NCI) invites grant applications proposing exploratory research projects focused on further development and validati...
Mechanistic links between diet, lipid metabolism, and tumor growth and progression (UH2 Clinical Trial Not Allowed)
Through this Notice of Funding Opportunity (NOFO), the National Cancer Institute (NCI) requests applications that propose mechanistic investigations of the links between diet, lipid metabolism and ...
Immune evasion in cancer: mechanisms and cutting-edge therapeutic approaches
This review article provides a complete summary of how cancer cells escape the immune system and the most recent breakthroughs in therapy to address these obstacles. We will look at the essential s...
Code & Tools
HoneyBee is a comprehensive multimodal AI framework designed specifically for oncology research and clinical applications. It seamlessly integrates...
## About SPARCED SPARCED is a**simple**and**efficient pipeline**for constructing, merging, expanding and simulating**large-scale**, single-cell m...
a framework for automatic and comprehensive knowledge extraction based on mutational data from sequenced tumor samples from patients. www.intogen....
This repository contains an example analysis of multiple scRNA-Seq datasets to identify cancer biomarkers, infer mechanistic relationships, and dev...
In this repository we provide implementations in both R and Matlab of _CIMLR_ ( https://www.nature.com/articles/s41467-018-06921-8 ). This method w...
Recent Preprints
Cancer Science
We are committed to fostering research that elucidates molecular mechanisms of cancer development, which pave the way for innovative cancer treatment, especially molecular targeted therapy and immu...
Nature Cancer
SubjectAll SubjectsAll SubjectsBiochemistryBiological techniquesBiophysicsBiotechnologyCancerCell biologyChemical biologyComputational biology and bioinformaticsDevelopmental biologyDrug discoveryE...
Drug resistance in cancer: molecular mechanisms and emerging treatment strategies
Therapeutic resistance remains a defining challenge in oncology, limiting the durability of current therapies and contributing to disease relapse and poor patient outcomes. This review systematical...
Data-driven universal insights into tumorigenesis via hallmark networks
Cancers are complex and dynamic diseases characterized by uncontrollable cell proliferation, genomic instability, and disruption of normal regulatory mechanisms, among others 1 , 2 , 3 . They evolv...
Cancer 3D Models: Essential Tools for Understanding and ...
Anticancer drug resistance remains a major challenge in cancer treatment hindering the efficacy of chemotherapy and targeted therapies. Conventional two-dimensional (2D) cell cultures cannot replic...
Latest Developments
Recent developments in cancer-related molecular mechanisms research as of February 2026 include advances in targeting the metabolic-epigenetic-immune axis for therapeutic implications (Nature), insights into the connection between MCL1 and mTORC1 pathways promoting cancer cell survival (ScienceDaily), and the ongoing exploration of molecular mechanisms underlying cancer metabolism and resistance, such as altered energy pathways and metabolic dysregulation (Molecular Cancer, Biomed Central).
Sources
Frequently Asked Questions
What role do lncRNAs play in cancer?
LncRNAs contribute to cancer via epigenetic regulation, chromatin modification, and competing endogenous RNA networks. They influence transcriptional landscapes and cell differentiation. This research cluster examines their functional classification in human diseases.
How is RNA-seq data analyzed for cancer transcriptomics?
"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2" by Love et al. (2014) provides moderated estimation for differential expression. "Salmon provides fast and bias-aware quantification of transcript expression" by Patro et al. (2017) enables rapid transcript quantification. These methods reveal unannotated transcripts and isoform switching in cancer.
What are circular RNAs in cancer regulation?
"Natural RNA circles function as efficient microRNA sponges" by Hansen et al. (2013) shows circular RNAs acting as microRNA sponges. "Circular RNAs are a large class of animal RNAs with regulatory potency" by Memczak et al. (2013) identifies them as a large regulatory class. They impact RNA networks in cancer.
How do microRNAs classify human cancers?
"MicroRNA expression profiles classify human cancers" by Lü et al. (2005) demonstrates microRNA profiles distinguishing cancer types. This builds on foundational work like "The functions of animal microRNAs" by Ambros (2004). Such profiles aid molecular diagnostics.
What genomic analyses are used in ovarian cancer?
"Integrated genomic analyses of ovarian carcinoma" (2011) integrates mRNA, microRNA expression, methylation, and copy number data from 489 tumors. It catalogues aberrations driving ovarian cancer. Findings support therapy deployment for patients.
What is the current state of lncRNA research in cancer?
The field includes 131,595 papers on lncRNAs in cancer and genome regulation. Recent preprints address drug resistance mechanisms and 3D tumor models for microenvironment studies. NIH datasets standardize multi-omics data across 10 cancer types.
Open Research Questions
- ? How do lncRNA competing endogenous RNA networks dynamically evolve in tumor microenvironments?
- ? What specific chromatin modifications by lncRNAs drive isoform switching in cancer cell differentiation?
- ? Which unannotated transcripts identified by RNA-seq function as key regulators in ovarian carcinoma progression?
- ? How do circular RNAs interact with microRNAs to confer drug resistance in heterogeneous tumors?
- ? What mechanistic links exist between lncRNA dysregulation and multi-omics aberrations in high-grade cancers?
Recent Trends
The field spans 131,595 works with sustained focus on lncRNA roles in cancer.
Preprints from late 2025, such as "Drug resistance in cancer: molecular mechanisms and emerging treatment strategies" and "Data-driven universal insights into tumorigenesis via hallmark networks" (2025-11-19), integrate multi-omics for resistance and hallmark pathways.
2025-11-17NIH released proteogenomic data from over 1,000 tumors across 10 types , standardizing genomic and proteomic analyses.
2025-05-14Research Cancer-related molecular mechanisms research with AI
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