Proteomic and Interactome Approaches Reveal PAK4, PHB-2, and 14-3-3η as Targets of Overactivated Cdc42 in Cellular Responses to Genomic Instability

Overexpression of CDC42 causes accumulation of DNA damage leading to failure of oogenesis in triploid Pacific oyster Crassostrea gigas

Triploid Pacific oyster Crassostrea gigas exhibits notable differences in fecundity, with the majority being sterile individuals, referred to as female β, which produce few oocytes, while a minority are fertile individuals, referred to as female α, which produce abundant oocytes. However, the molecular mechanisms underlying these differences in triploid fecundity remain poorly understood. CDC42 has been implicated in processes related to increased DNA damage and genomic instability. Here, we investigate the crucial role of CDC42 in DNA damage repair during oogenesis in triploid C. gigas. Immunofluorescence analysis of γH2AX, a marker for DNA double-stranded breaks, showed significantly higher levels of DNA damage in gonadal cells of triploids compared to diploids, particularly in female β. Histological and ultrastructural analyses revealed abnormal germ cells, termed β gonia, characterized by giant nuclei condensed into irregular chromosome-like chromatin, present in triploid gonadal follicles. RNAseq and proteomic analyses revealed significantly elevated CDC42 expression in triploid gonads compared to the diploids. Inhibition of CDC42 activity in triploids using ZCL278, a CDC42-specific inhibitor, resulted in a significant reduction in DNA damage, increased oocyte numbers, and a decrease in β gonia count. Transcriptome profiling revealed that CDC42 inhibition upregulated the PI3K-AKT signaling pathway along with DNA repair activation. Overall, our findings suggest that overexpression of CDC42 during oogenesis in triploid C. gigas impedes DNA repair, leading to the accumulation of DNA damage, and consequently, oogenesis blockade and abnormal germ cell differentiation. Conversely, inhibition of CDC42 activity activates the PI3K-AKT signaling pathway and promotes DNA repair, thereby mitigating DNA damage and facilitating oogenesis in triploids. This study provides new insights into the molecular mechanisms of sterility in female triploid C. gigas.

Prohibitin 2: A key regulator of cell function

The PHB2 gene is located on chromosome 12p13 and encodes prohibitin 2, a highly conserved protein of 37 kDa. PHB2 is a dimer with antiparallel coils, possessing a unique negatively charged region crucial for its mitochondrial molecular chaperone functions. Thus, PHB2 plays a significant role in cell life activities such as mitosis, mitochondrial autophagy, signal transduction, and cell death. This review discusses how PHB2 inhibits transcription factors or nuclear receptors to maintain normal cell functions; how PHB2 in the cytoplasm or membrane ensures normal cell mitosis and regulates cell differentiation; how PHB2 affects mitochondrial structure, function, and cell apoptosis through mitochondrial intimal integrity and mitochondrial autophagy; how PHB2 affects mitochondrial stress and inhibits cell apoptosis by regulating cytochrome c migration and other pathways; how PHB2 affects cell growth, proliferation, and metastasis through a mitochondrial independent mechanism; and how PHB2 could be applied in disease treatment. We provide a theoretical basis and an innovative perspective for a comprehensive understanding of the role and mechanism of PHB2 in cell function regulation.

Nucleo-cytoplasmic shuttling of 14-3-3 epsilon carrying hnRNP C promotes autophagy

Translocation of 14-3-3 protein epsilon (14-3-3ε) was found to be involved in Triptolide (Tp)-induced inhibition of colorectal cancer (CRC) cell proliferation. However, the form of cell death induced by 14-3-3ε translocation and mechanisms underlying this effect remain unclear. This study employed label-free LC-MS/MS to identify 14-3-3ε-associated proteins in CRC cells treated with or without Tp. Our results confirmed that heterogeneous nuclear ribonucleoproteins C1/C2 (hnRNP C) were exported out of the nucleus by 14-3-3ε and degraded by ubiquitination. The nucleo-cytoplasmic shuttling of 14-3-3ε carrying hnRNP C mediated Tp-induced proliferation inhibition, cell cycle arrest and autophagic processes. These findings have broad implications for our understanding of 14-3-3ε function, provide an explanation for the mechanism of nucleo-cytoplasmic shuttling of hnRNP C and provide new insights into the complex regulation of autophagy.

GPR19 Coordinates Multiple Molecular Aspects of Stress Responses Associated with the Aging Process

G protein-coupled receptors (GPCRs) play a significant role in controlling biological paradigms such as aging and aging-related disease. We have previously identified receptor signaling systems that are specifically associated with controlling molecular pathologies associated with the aging process. Here, we have identified a pseudo-orphan GPCR, G protein-coupled receptor 19 (GPR19), that is sensitive to many molecular aspects of the aging process. Through an in-depth molecular investigation process that involved proteomic, molecular biological, and advanced informatic experimentation, this study found that the functionality of GPR19 is specifically linked to sensory, protective, and remedial signaling systems associated with aging-related pathology. This study suggests that the activity of this receptor may play a role in mitigating the effects of aging-related pathology by promoting protective and remedial signaling systems. GPR19 expression variation demonstrates variability in the molecular activity in this larger process. At low expression levels in HEK293 cells, GPR19 expression regulates signaling paradigms linked with stress responses and metabolic responses to these. At higher expression levels, GPR19 expression co-regulates systems involved in sensing and repairing DNA damage, while at the highest levels of GPR19 expression, a functional link to processes of cellular senescence is seen. In this manner, GPR19 may function as a coordinator of aging-associated metabolic dysfunction, stress response, DNA integrity management, and eventual senescence.

Role of a small GTPase Cdc42 in aging and age-related diseases

A small GTPase, Cdc42 is evolutionarily one of the most ancient members of the Rho family, which is ubiquitously expressed and involved in a wide range of fundamental cellular functions. The crucial role of Cdc42 includes regulation of the actin cytoskeleton, cell polarity, morphology and migration, endocytosis and exocytosis, cell cycle, and proliferation in many different cell types. Many studies have provided compelling yet contradicting evidence that Cdc42 dysregulation plays an important role in cellular and tissue aging. Furthermore, Cdc42 is a critical factor in the development and progression of aging-related pathologies, such as neurodegenerative and cardiovascular disorders, diabetes type 2, and aging-related disorders of the joints and bones, and the inhibition of the Cdc42 demonstrates potentially significant therapeutic and anti-aging effects in animal models of aging and disease. However, regulation of Cdc42 expression and activity is very complex and depends on many factors, such as the origin and complexity of the tissues, hormonal status, etc. Therefore, this review is focused on current advances in understanding the underlying cellular and molecular mechanisms associated with Cdc42 activity and regulation of senescence in different cell types since they may provide a foundation for novel therapeutic strategies and targeted drugs to reverse the aging process and treat aging-associated disorders.

Rho family GTPase signaling through type II p21-activated kinases

Signaling from the Rho family small GTPases controls a wide range of signaling outcomes. Key among the downstream effectors for many of the Rho GTPases are the p21-activated kinases, or PAK group. The PAK family comprises two types, the type I PAKs (PAK1, 2 and 3) and the type II PAKs (PAK4, 5 and 6), which have distinct structures and mechanisms of regulation. In this review, we discuss signal transduction from Rho GTPases with a focus on the type II PAKs. We discuss the role of PAKs in signal transduction pathways and selectivity of Rho GTPases for PAK family members. We consider the less well studied of the Rho GTPases and their PAK-related signaling. We then discuss the molecular basis for kinase domain recognition of substrates and for regulation of signaling. We conclude with a discussion of the role of PAKs in cross talk between Rho family small GTPases and the roles of PAKs in disease.

Interactions between 14-3-3 Proteins and Actin Cytoskeleton and Its Regulation by microRNAs and Long Non-Coding RNAs in Cancer

14-3-3s are a family of structurally similar proteins that bind to phosphoserine or phosphothreonine residues, forming the central signaling hub that coordinates or integrates various cellular functions, thereby controlling many pathways important in cancer, cell motility, cell death, cytoskeletal remodeling, neuro-degenerative disorders and many more. Their targets are present in all cellular compartments, and when they bind to proteins they alter their subcellular localization, stability, and molecular interactions with other proteins. Changes in environmental conditions that result in altered homeostasis trigger the interaction between 14-3-3 and other proteins to retrieve or rescue homeostasis. In circumstances where these regulatory proteins are dysregulated, it leads to pathological conditions. Therefore, deeper understanding is needed on how 14-3-3 proteins bind, and how these proteins are regulated or modified. This will help to detect disease in early stages or design inhibitors to block certain pathways. Recently, more research has been devoted to identifying the role of MicroRNAs, and long non-coding RNAs, which play an important role in regulating gene expression. Although there are many reviews on the role of 14-3-3 proteins in cancer, they do not provide a holistic view of the changes in the cell, which is the focus of this review. The unique feature of the review is that it not only focuses on how the 14-3-3 subunits associate and dissociate with their binding and regulatory proteins, but also includes the role of micro-RNAs and long non-coding RNAs and how they regulate 14-3-3 isoforms. The highlight of the review is that it focuses on the role of 14-3-3, actin, actin binding proteins and Rho GTPases in cancer, and how this complex is important for cell migration and invasion. Finally, the reader is provided with super-resolution high-clarity images of each subunit of the 14-3-3 protein family, further depicting their distribution in HeLa cells to illustrate their interactions in a cancer cell.

A rigorous in silico genomic interrogation at 1p13.3 reveals 16 autosomal dominant candidate genes in syndromic neurodevelopmental disorders

Genome-wide chromosomal microarray is extensively used to detect copy number variations (CNVs), which can diagnose microdeletion and microduplication syndromes. These small unbalanced chromosomal structural rearrangements ranging from 1 kb to 10 Mb comprise up to 15% of human mutations leading to monogenic or contiguous genomic disorders. Albeit rare, CNVs at 1p13.3 cause a variety of neurodevelopmental disorders (NDDs) including development delay (DD), intellectual disability (ID), autism, epilepsy, and craniofacial anomalies (CFA). Most of the 1p13.3 CNV cases reported in the pre-microarray era encompassed a large number of genes and lacked the demarcating genomic coordinates, hampering the discovery of positional candidate genes within the boundaries. In this study, we present four subjects with 1p13.3 microdeletions displaying DD, ID, autism, epilepsy, and CFA. In silico comparative genomic mapping with three previously reported subjects with CNVs and 22 unreported DECIPHER CNV cases has resulted in the identification of four different sub-genomic loci harboring five positional candidate genes for DD, ID, and CFA at 1p13.3. Most of these genes have pathogenic variants reported, and their interacting genes are involved in NDDs. RT-qPCR in various human tissues revealed a high expression pattern in the brain and fetal brain, supporting their functional roles in NDDs. Interrogation of variant databases and interacting protein partners led to the identification of another set of 11 potential candidate genes, which might have been dysregulated by the position effect of these CNVs at 1p13.3. Our studies define 1p13.3 as a genomic region harboring 16 NDD candidate genes and underscore the critical roles of small CNVs in in silico comparative genomic mapping for disease gene discovery. Our candidate genes will help accelerate the isolation of pathogenic heterozygous variants from exome/genome sequencing (ES/GS) databases.

Clinical Chemistry for Developing Countries: Mass Spectrometry

Early disease diagnosis is necessary to enable timely interventions. Implementation of this vital task in the developing world is challenging owing to limited resources. Diagnostic approaches developed for resource-limited settings have often involved colorimetric tests (based on immunoassays) due to their low cost. Unfortunately, the performance/sensitivity of such simplistic tests are often limited and significantly hinder opportunities for early disease detection. A new criterion for selecting diagnostic tests in low- and middle-income countries is proposed here that is based on performance-to-cost ratio. For example, modern mass spectrometry (MS) now involves analysis of the native sample in the open laboratory environment, enabling applications in many fields, including clinical research, forensic science, environmental analysis, and agriculture. In this critical review, we summarize recent developments in chemistry that enable MS to be applied effectively in developing countries. In particular, we argue that closed automated analytical systems may not offer the analytical flexibility needed in resource-limited settings. Alternative strategies proposed here have potential to be widely accepted in low- and middle-income countries through the utilization of the open-source ambient MS platform that enables microsampling techniques such as dried blood spot to be coupled with miniature mass spectrometers in a centralized analytical platform. Consequently, costs associated with sample handling and maintenance can be reduced by >50% of the total ownership cost, permitting analytical measurements to be operated at high performance-to-cost ratios in the developing world.

GTPases, genome, actin: A hidden story in DNA damage response and repair mechanisms

The classical small Rho GTPase (Rho, Rac, and Cdc42) protein family is mainly responsible for regulating cell motility and polarity, membrane trafficking, cell cycle control, and gene transcription. Cumulative recent evidence supports important roles for these proteins in the maintenance of genomic stability. Indeed, DNA damage response (DDR) and repair mechanisms are some of the prime biological processes that underlie several disease phenotypes, including genetic disorders, cancer, senescence, and premature aging. Many reports guided by different experimental approaches and molecular hypotheses have demonstrated that, to some extent, direct modulation of Rho GTPase activity, their downstream effectors, or actin cytoskeleton regulation contribute to these cellular events. Although much attention has been paid to this family in the context of canonical actin cytoskeleton remodeling, here we provide a contextualized review of the interplay between Rho GTPase signaling pathways and the DDR and DNA repair signaling components. Interesting questions yet to be addressed relate to the spatiotemporal dynamics of this collective response and whether it correlates with different subcellular pools of Rho GTPases. We highlight the direct and indirect targets, some of which still lack experimental validation data, likely associated with Rho GTPase activation that provides compelling evidence for further investigation in DNA damage-associated events and with potential therapeutic applications in translational medicine.

Overactivated Cdc42 acts through Cdc42EP3/Borg2 and NCK to trigger DNA damage response signaling and sensitize cells to DNA-damaging agents

The small GTPase Cdc42, a member of the Rho family, regulates essential biological processes such as cytoskeleton remodeling, migration, vesicular trafficking and cell cycle. It was demonstrated that Cdc42 overactivation through different molecular strategies increases cell sensitivity to genotoxic stress and affects the phosphorylation status of DNA damage response proteins by unknown mechanisms. By using a combination of approaches including affinity purification/mass spectrometry (AP/MS) and colocalization microscopy analysis we were able to identify Cdc42EP3/Borg2 as a putative molecular effector of these molecular and cellular events that seem to be independent of cell line or DNA damage stimuli. We then investigated the influence of Cdc42EP3/Borg2 and other potential protein partners, such as the NCK and Septin2 proteins, which could mediate cellular responses to genotoxic stress under different backgrounds of Cdc42 activity. Clonogenic assays showed a reduced cell survival when ectopically expressing the Cdc42EP3/Borg2, NCK2 or Septin2 in an overactivated Cdc42-dependent background. Moreover, endogenous NCK appears to relocate into the nucleus upon Cdc42 overactivation, especially under genotoxic stress, and promotes the suppression of Chk1 phosphorylation. In sum, our findings reinforce Cdc42 as an important player involved in the DNA damage response acting through Cdc42EP3/Borg2 and NCK proteins following genomic instability conditions.