Molecular principles underlying aggressive cancers

Abstract

Aggressive tumors pose ultra-challenges to drug resistance. Anti-cancer treatments are often unsuccessful, and single-cell technologies to rein drug resistance mechanisms are still fruitless. The National Cancer Institute defines aggressive cancers at the tissue level, describing them as those that spread rapidly, despite severe treatment. At the molecular, foundational level, the quantitative biophysics discipline defines aggressive cancers as harboring a large number of (overexpressed, or mutated) crucial signaling proteins in major proliferation pathways populating their active conformations, primed for their signal transduction roles. This comprehensive review explores highly aggressive cancers on the foundational and cell signaling levels, focusing on the differences between highly aggressive cancers and the more treatable ones. It showcases aggressive tumors as harboring massive, cancer-promoting, catalysis-primed oncogenic proteins, especially through certain overexpression scenarios, as predisposed aggressive tumor candidates. Our examples narrate strong activation of ERK1/2, and other oncogenic proteins, through malfunctioning chromatin and crosslinked signaling, and how they activate multiple proliferation pathways. They show the increased cancer heterogeneity, plasticity, and drug resistance. Our review formulates the principles underlying cancer aggressiveness on the molecular level, discusses scenarios, and describes drug regimen (single drugs and drug combinations) for PDAC, NSCLC, CRC, HCC, breast and prostate cancers, glioblastoma, neuroblastoma, and leukemia as examples. All show overexpression scenarios of master transcription factors, transcription factors with gene fusions, copy number alterations, dysregulation of the epigenetic codes and epithelial-to-mesenchymal transitions in aggressive tumors, as well as high mutation loads of vital upstream signaling regulators, such as EGFR, c-MET, and K-Ras, befitting these principles.

Fig. 1

The foundational principle underlying aggressive cancers: cancer aggressiveness by-the-numbers. We propose that the absolute number of active (oncogenic) conformations that the cancer harbors are a foundational hallmark of its aggressiveness. The higher the number—the more overspilled the signaling—the higher the heterogeneity. In aggressive cancers the number is extremely high. We dub this hallmark “cancer aggressiveness by-the-numbers”. In this molecular level definition, aggressive tumor candidates are those harboring massive, catalysis-primed oncogenic proteins, produced through overexpression scenarios and strong activating driver mutations. Both generate transcriptional landscapes signaling by-the-numbers scenario.^, Overexpression of oncogenic proteins is caused by an increase in gene expression due to epigenetic and genetic mechanisms, involving super-enhancers, hybrid gene fusions resulting from the combination of two independent genes, copy number alterations with lost or gained DNA segments, and an increase in signaling to target genes. A high propensity of active conformations shifts the population from an inactive state (gray spheres) to a constitutively active conformation (red RTKs and spheres). This leads to an increase in the number of active molecules (blue RTKs and spheres) of the corresponding protein node, resulting in an elevation in active transcription factors (small blue spheres with arrows), which in turn leads to the overexpression of oncogenes. Our molecular level definition updates the traditional definition of the National Cancer Institute, which defines an aggressive cancer as one that “forms, grows, or spreads rapidly and requires more intensive or severe treatment than usual”. For clarity, see the section on questions and clinical implications. It defines an active protein conformation, how their number can be assessed, explains why thresholds are still unavailable and challenging to establish. It also addresses how to measure expression of super-enhancers and overexpression, and more. Tumor suppressors are not included

Fig. 2

PAX3-FOXO1 fusion gene in rhabdomyosarcoma (RMS). RMS rare type of cancer that can be highly aggressive. It starts as a growth of cells in the soft tissue. There are several types of RMS, including embryonal (eRMS) and alveolar (aRMS), with aRMS being the far more aggressive. The PAX3-FOXO1 fusion gene is a signature genetic alteration for aRMS. It consists of a stable reciprocal translocation of chromosomes 2 and 13, t(2;13), which generates two derivative chromosomes, der(2) and der(13) (top left panel). The der(2) chromosome contains the FOXO1-PAK3 fusion gene, which encodes a protein lacking major functional domains, and the der(13) chromosome contains the PAX3-FOXO1 fusion gene, which encodes the PAX3-FOXO1 fusion transcription factor with enhanced transcriptional activity (top right panel). The PAX3 gene encodes a member of the PAX family of transcription factors. FOXO1 is also a transcription factor. In the PAX3-FOXO1 fusion, the in-frame DNA binding domain of PAX3 is fused with the transactivation domain of FOXO1, generating a transcription factor with powerful transcriptional power, altered post-translational regulation, and possibly new targets. As a pioneer factor, PAX3-FOXO1 alters the local chromatin structure and binding to repressed, inaccessible chromatin, and transcriptional activation (bottom panel). PAX3 paired box 3, FOXO1 forkhead box O1

Fig. 3

Schematic diagram of N-Myc mediated gene overexpression in aggressive neuroblastoma. Neuroblastoma is a rare pediatric cancer that develops in the nervous system of infants and children. It affects immature nerve tissue (neuroblasts) in the adrenal glands. The MYCN gene is amplified in multiple neuronal and nonneuronal tumors. Among these, its amplification, which encodes the N-Myc transcription factor, is a key prognostic factor in neuroblastoma. N-Myc binds to available promoters containing the TATA box with the help of WDR5, a conserved regulator of gene expression. Binding upregulates canonical Myc target genes (e.g., ALK), activating and promoting RNA polymerase II (Pol II), driving oncogenic gene expression and cell proliferation. Transcription factors PHOX2B, HAND2 and GATA3 support N-Myc’s binding to the super-enhancers and promoter, and subsequent gene expression. Super-enhancers are formed by multiple enhancers. The gray area represents the mediator complex, which regulates transcription by connecting enhancers to promoters

Fig. 4

Signaling pathways in glioblastoma. PI3K/AKT, MAPK, and JAK/STAT signaling pathways orchestrate cell growth, proliferation, survival, and apoptosis. Their dysregulation is a critical driver of glioblastoma aggressiveness. In the PI3K/AKT pathway, downstream targets like ribosomal proteins rpS6 and eIF4E foster cell growth through mTOR signaling. Loss-of-function mutations in the tumor suppressor NF1 abrogate its inhibitory role on Ras, leading to overactivation of the MAPK pathway. The MAPK and JAK/STAT pathways regulate cell proliferation and survival via the transcription factors such as c-Myc, Elk-1, c-Jun, and STAT3/5. VEGFR vascular endothelial growth factor receptor, EML4 echinoderm microtubule-associated protein-like 4, eIF4E eukaryotic translation initiation factor 4E

Fig. 5

Schematic representation of four major molecular lesions in pancreatic ductal adenocarcinoma (PDAC). PDAC is primarily caused by genetic mutations in four genes: an oncogene, KRAS (encoding K-Ras); and three tumor suppressor genes, TP53 (encoding p53, a transcription factor), CDKN2A (encoding p16^INK4A, a CDK inhibitor), and SMAD4 (encoding SMAD4, a transcription factor). Constitutively active K-Ras with the G12X mutation leads to increased activation of Raf, MEK, and ERK through a phosphorylation cascade. ERK activates transcription factors such as c-Myc, Elk-1, and c-Jun, leading to cell proliferation. Insulin binding to IR together with active K-Ras initiates PI3K activation. PI3K converts PIP₂ to PIP₃, leading to mTORC1 activation. This includes AKT activation by PDK1 and mTORC2. mTORC1 phosphorylates S6K1 and 4E-BP1. S6K1 activates rpS6. Phosphorylation of 4E-BP1 removes its inhibitory role on eIF4E, which is involved in translational activation and regulation of cell growth. Inactivation of p16^INK4A by mutation or genomic deletion impairs its function as a CDK4 inhibitor, leading to an unregulated cell cycle transition. Inactivation of p53 by mutation hinders its functions, such as blocking of angiogenesis, DNA repair, and induction of apoptosis. p53 mutant also impairs the expression of p21 (a CDK inhibitor), which is involved in G₁/S arrest due to damaged DNA. The TGFβ ligand binds to the TGFβ receptor type II (RII) dimer, which recruit the type I (RI) dimer to form a hetero-tetrameric complex. RII phosphorylates the serine/threonine kinase of RI. Under physiological conditions, RI phosphorylates the receptor-regulated SMAD (RSMAD), such as SMAD2 and SMAD3, causing them to dissociate from the receptor complex. The RSMAD complex associates with a common mediator SMAD (coSMAD), i.e., SMAD4, to form a complex that enters the nucleus to bind its target genes, leading to cell cycle arrest and apoptosis. Inactivation of SMAD4 by mutation or genomic deletion impairs its tumor suppressor function in PADC. As discussed in the text, as a highly aggressive cancer, it also involves overexpression of multiple genes, e.g., YAP1, MYC, HMGA2, IGF2BP1 and IGF2BP3, and dysregulation of epigenetics modulators, e.g., HDAC1/2/5, KDM6A, MLL histone methylases, and histone methyltransferases. IR insulin receptor, PDK1 phosphoinositide-dependent kinase 1, 4E-BP1 eukaryotic translation initiation factor 4E (eIF4E)-binding protein 1, IRS insulin receptor substrate

Fig. 6

Hallmarks of lung adenocarcinoma. Overexpression of active conformations such as catalytically primed kinases is associated with non-small cell lung cancer (NSCLC). These increased kinase activities are attributed to fusion genes, including NTRK fusion, AGK-BRAF fusion, EGFR-RAD51 fusion, EML4-ALK fusion, and RET fusion genes (see text for details). NSCLC also harbors HER2 alterations, MET overexpression, and K-Ras G12C mutation. Generic names of small drugs that inhibit these active molecules are shown in the figure with the brand name in parentheses