Genetic Alterations of NF-κB and Its Regulators: A Rich Platform to Advance Colorectal Cancer Diagnosis and Treatment

Abstract

Colorectal cancer (CRC) is the third leading cause of cancer mortality in the United States, with an estimated 52,000 deaths in 2023. Though significant progress has been made in both diagnosis and treatment of CRC in recent years, genetic heterogeneity of CRC-the culprit for possible CRC relapse and drug resistance, is still an insurmountable challenge. Thus, developing more effective therapeutics to overcome this challenge in new CRC treatment strategies is imperative. Genetic and epigenetic changes are well recognized to be responsible for the stepwise development of CRC malignancy. In this review, we focus on detailed genetic alteration information about the nuclear factor (NF)-κB signaling, including both NF-κB family members, and their regulators, such as protein arginine methyltransferase 5 (PRMT5), and outer dynein arm docking complex subunit 2 (ODAD2, also named armadillo repeat-containing 4, ARMC4), etc., in CRC patients. Moreover, we provide deep insight into different CRC research models, with a particular focus on patient-derived xenografts (PDX) and organoid models, and their potential applications in CRC research. Genetic alterations on NF-κB signaling components are estimated to be more than 50% of the overall genetic changes identified in CRC patients collected by cBioportal for Cancer Genomics; thus, emphasizing its paramount importance in CRC progression. Consequently, various genetic alterations on NF-κB signaling may hold great promise for novel therapeutic development in CRC. Future endeavors may focus on utilizing CRC models (e.g., PDX or organoids, or isogenic human embryonic stem cell (hESC)-derived colonic cells, or human pluripotent stem cells (hPSC)-derived colonic organoids, etc.) to further uncover the underpinning mechanism of these genetic alterations in NF-κB signaling in CRC progression. Moreover, establishing platforms for drug discovery in dishes, and developing Biobanks, etc., may further pave the way for the development of innovative personalized medicine to treat CRC in the future.

Keywords: CRC; NF-κB; ODAD2; PDX; PRMT5; genetic alteration; organoid.

Figure 1

Schematic demonstrating the stepwise accumulation of genetic aberrations that lead to the development of CRC. Sporadic development of CRC occurs when normal colorectal epithelia are transformed into an early adenoma through the silencing of adenomatous polyposis coli (APC), or DNA mismatch repair (MMR) protein failure, and DNA hypermethylation, resulting in the enhanced expression of genes involved in cellular differentiation, growth, and cell cycle. Following the development of a dysplastic colorectal epithelia, the mutation of KRAS and inactivation of TP53, alongside other genetic and epigenetic changes, lead to the development and subsequent progression of CRC.

Figure 2

Schematic illustration of simplified NF-κB pathways. (Left): Canonical pathway: Upon stimulation by various factors, like cytokines or pathogen-associated molecular pattern molecules (PAMPs), IKK complex will be activated, leading to the phosphorylation of IκBα and its subsequent degradation. This will free up the p65/p50 heterodimer, which will then translocate into the nucleus, bind to κB-binding site, and trigger the transcription of NF-κB dependent genes. (Right): Non-canonical pathway. Upon stimulation by various factors, like lymphotoxin (LT) β or B lymphocyte activating factor of the tumor necrosis factor family (BAFF), NF-κB-inducing kinase (NIK) will be activated, leading to the phosphorylation and activation of IKKα, and the subsequent processing of p100 (p52 precursor)/RelB into mature p52/RelB heterodimer. This p52/RelB heterodimer will then translocate into the nucleus, bind to the κB-binding site, and trigger the transcription of NF-κB dependent genes. Symbol P: phosphorylation.

Figure 3

Genetic alterations on NF-κB family members RelA and RelB. (A) Schematic diagram of protein mutations on RelA identified in CRC patients. Data resource: cBioPortal for Cancer Genomics [31,32]. Note: RelA is 551 amino acids (aa) in length. Abbreviation: RHD: Rel homology domain. (B) Putative copy number alterations from Genomic Identification of Significant Targets in Cancer (GISTIC) for RelB. Data resource: cBioPortal for Cancer Genomics [31,32]. Symbol *: Nonsense mutations.

Figure 4

Genetic alterations on NF-κB signaling regulators PRMT5 and ODAD2. (A) Schematic diagram of protein mutations on PRMT5 identified in CRC patients. Data resource: cBioPortal for Cancer Genomics [31,32]. Note: PRMT5 is 637 amino acids (aa) in length. (B) Schematic diagram of protein mutations on ODAD2 identified in CRC patients. Data resource: cBioPortal for Cancer Genomics [31,32]. Note: ODAD2 is 1044aa in length. Note: Arm, Heat2 are domains on ODAD2. (C) Putative copy number alterations from GISTIC for ODAD2. Data resource: cBioPortal for Cancer Genomics [31,32]. Symbol *: Nonsense mutations.

Figure 5

Generation and application of CRC PDX and organoid models. Both PDX and organoid models can be generated from primary tumors within the colon or rectum, metastatic tumors, or CTCs, which are surgically resected, biopsied, or collected via peripheral blood. For the PDX model (Top, blue arrows), surgically resected tumor tissues or biopsies will be transplanted into immunodeficient or humanized mice. The sliced tumor tissue or cell sample is transplanted either heterotopically through subcutaneous implantation into the dorsal area or orthotopically through direct implantation into the colon. When the tumor reaches sufficient size, it is dissected, confirmed, and re-passaged into other mice. For the organoid model (Bottom, red arrows), surgically resected tumor tissues or biopsies can be dissociated into single cells and then cultured in a 3D medium usually containing Matrigel and growth factors which allow and optimize growth. Both the PDX model and the organoids model can then be utilized by enabling molecular profiling of patient tumors, drug discovery, to facilitating personalized medicine. For the PDX model, it also can be further used to generate organoids. While for the organoid model, it also can be further used to generate the PDX model.