Knockout Cell Lines Research Articles

MEDB-24. Tumour secreted extracellular matrix predicts survival and influences migration and cell death in SHH medulloblastoma 3D models

Medulloblastoma is the most common malignant paediatric brain tumour. Four molecular sub-groups exist (WNT, Sonic hedgehog (SHH), Group 3 and Group 4), each associated with different patterns of metastasis and chemoresistance. We have shown that within these sub-groups further clinically relevant sub-types exist, characterised by differential expression of extracellular matrix (ECM) proteins. For example, good overall survival in two-thirds of SHH sub-group patients is associated with the expression of specific ECM proteins. Our aim here is to further characterise these ECM components in SHH medulloblastoma and to determine how they confer better overall survival in this sub-group. Using a combination of 3D OrbiSIMs and immunohistochemical staining we have identified, that when grown in 3D hyaluronic acid hydrogels or as spheroids, SHH medulloblastoma cell lines form an ECM shell-like structure composed of laminin, collagen and lumican. In addition, scRNAseq of SHH hydrogel nodules revealed sub-group specific clusters of cells with high levels of ECM interaction and adhesion. We therefore hypothesise that ECM interaction restricts SHH tumour invasion and metastasis through this shell-like structure. To understand how this ECM shell-like structure potentiates better survival in SHH medulloblastoma we have created a CRISPRcas9 laminin knockout SHH medulloblastoma cell line. 3D culture of the laminin knockout cell line demonstrated that laminin is essential for the formation of 3D cell structures as well as migration in SHH medulloblastoma. Furthermore, we have identified that apoptosis is increased in the laminin knockout SHH cell line, suggesting that apoptosis-targeted therapeutics may represent a beneficial treatment option for SHH patients whose tumours exhibit this ECM shell. In summary, tumour-secreted ECM plays a major role in SHH medulloblastoma progression. Expression of laminin, collagen or lumican can be used to classify SHH patients into low and high-risk groups with different therapeutic outcomes and treatment options.

Coro1B and Coro1C regulate lamellipodia dynamics and cell motility by tuning branched actin turnover.

Actin filament dynamics must be precisely controlled in cells to execute behaviors such as vesicular trafficking, cytokinesis, and migration. Coronins are conserved actin-binding proteins that regulate several actin-dependent subcellular processes. Here, we describe a new conditional knockout cell line for two ubiquitous coronins, Coro1B and Coro1C. These coronins, which strongly co-localize with Arp2/3-branched actin, require Arp2/3 activity for proper subcellular localization. Coronin null cells have altered lamellipodial protrusion dynamics due to increased branched actin density and reduced actin turnover within lamellipodia, leading to defective haptotaxis. Surprisingly, excessive cofilin accumulates in coronin null lamellipodia, a result that is inconsistent with the current models of coronin-cofilin functional interaction. However, consistent with coronins playing a pro-cofilin role, coronin null cells have increased F-actin levels. Lastly, we demonstrate that the loss of coronins increases accompanied by an increase in cellular contractility. Together, our observations reveal that coronins are critical for proper turnover of branched actin networks and that decreased actin turnover leads to increased cellular contractility.

Rapid Antibody Glycoengineering in Chinese Hamster Ovary Cells.

Recombinant monoclonal antibodies bind specific molecular targets and, subsequently, induce an immune response or inhibit the binding of other ligands. However, monoclonal antibody functionality and half-life may be reduced by the type and distribution of host-specific glycosylation. Attempts to produce superior antibodies have inspired the development of genetically modified producer cells that synthesize glyco-optimized antibodies. Glycoengineering typically requires the generation of a stable knockout or knockin cell line using methods such as clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9. Monoclonal antibodies produced by engineered cells are then characterized using mass spectrometric methods to determine if the desired glycoprofile has been obtained. This strategy is time-consuming, technically challenging, and requires specialists. Therefore, an alternative strategy that utilizes streamlined protocols for genetic glycoengineering and glycan detection may assist endeavors toward optimal antibodies. In this proof-of-concept study, an IgG-producing Chinese hamster ovary cell served as an ideal host to optimize glycoengineering. Short interfering RNA targeting the Fut8 gene was delivered to Chinese hamster ovary cells, and the resulting changes in FUT8 protein expression were quantified. The results indicate that knockdown by this method was efficient, leading to a ~60% reduction in FUT8. Complementary analysis of the antibody glycoprofile was performed using a rapid yet highly sensitive technique: capillary gel electrophoresis and laser-induced fluorescence detection. All knockdown experiments showed an increase in afucosylated glycans; however, the greatest shift achieved in this study was ~20%. This protocol simplifies glycoengineering efforts by harnessing in silico design tools, commercially synthesized gene targeting reagents, and rapid quantification assays that do not require extensive prior experience. As such, the time efficiencies offered by this protocol may assist investigations into new gene targets.

Rapid Antibody Glycoengineering in Chinese Hamster Ovary Cells

Recombinant monoclonal antibodies bind specific molecular targets and, subsequently, induce an immune response or inhibit the binding of other ligands. However, monoclonal antibody functionality and half-life may be reduced by the type and distribution of host-specific glycosylation. Attempts to produce superior antibodies have inspired the development of genetically modified producer cells that synthesize glyco-optimized antibodies. Glycoengineering typically requires the generation of a stable knockout or knockin cell line using methods such as clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9. Monoclonal antibodies produced by engineered cells are then characterized using mass spectrometric methods to determine if the desired glycoprofile has been obtained. This strategy is time-consuming, technically challenging, and requires specialists. Therefore, an alternative strategy that utilizes streamlined protocols for genetic glycoengineering and glycan detection may assist endeavors toward optimal antibodies. In this proof-of-concept study, an IgG-producing Chinese hamster ovary cell served as an ideal host to optimize glycoengineering. Short interfering RNA targeting the Fut8 gene was delivered to Chinese hamster ovary cells, and the resulting changes in FUT8 protein expression were quantified. The results indicate that knockdown by this method was efficient, leading to a ~60% reduction in FUT8. Complementary analysis of the antibody glycoprofile was performed using a rapid yet highly sensitive technique: capillary gel electrophoresis and laser-induced fluorescence detection. All knockdown experiments showed an increase in afucosylated glycans; however, the greatest shift achieved in this study was ~20%. This protocol simplifies glycoengineering efforts by harnessing in silico design tools, commercially synthesized gene targeting reagents, and rapid quantification assays that do not require extensive prior experience. As such, the time efficiencies offered by this protocol may assist investigations into new gene targets.

SPATA33 affects the formation of cell adhesion complex by interacting with CTNNA3 in TM4 cells

Communication between Sertoli cell is essential during spermatogenesis and testicular development in mice, and the dynamic balance of this communication is regulated by some adhesion proteins. In this study, we found that SPATA33 and CTNNA3 were involved in this process. Quantitative real-time PCR and western blotting showed similar trend of expression of two proteins in the testis of mice of different ages. Subsequently, CRISPR-Cas9 technique was used to prepare Spata33 knockout cell lines with TM4 cells, cell wound scratch assay showed that Spata33 gene knockout affected cell migration, and flow cytometry assay showed that Spata33 knockout resulted in a decreased percentage of G1 phase cells in TM4 cell line. In addition, phalloidin staining assay showed that Spata33 gene knockout disrupted the formation of F-actin. Moreover, the protein immunoprecipitation experiment showed the interaction between SPATA33 and CTNNA3, which affected the interaction between CTNNA3 and CTNNB1. SPATA33 inhibits the formation of CDH1-CTNNB1-CTNNA3 complex through its interaction with CTNNA3, thus weakening adhesion between Sertoli cell and promoting cell migration.

Development of a LAG-3 immunohistochemistry assay for melanoma

AimsA robust immunohistochemistry (IHC) assay was developed to detect lymphocyte-activation gene 3 (LAG-3) expression by immune cells (ICs) in tumour tissues. LAG-3 is an immuno-oncology target with demonstrable clinical benefit,...

Isocitrate dehydrogenase 1 mutation in cholangiocarcinoma impairs tumor progression by sensitizing cells to ferroptosis.

The present study intends to clarify the hypothesis that isocitrate dehydrogenase 1 (IDH1) mutation in cholangiocarcinoma impairs tumor progression by sensitizing cells to ferroptosis through the in vitro and in vivo experiments. Cholangiocarcinoma RBE cell line was transfected with IDH1 R132C mutation plasmids and treated with erastin to induce ferroptosis, which were then microscopically photographed. Cell viability rate was calculated by trypan blue staining. The lipid ROS level was determined by using flow cytometer. The BALB/c nude mice were injected subcutaneously with IDH1 knockout (KO), WT, or R132C mutation cell line, followed by injecting erastin intraperitoneally. The tumor tissue was surgically separated for the measurement of tumor volume and weight. The results showed that IDH1 mutant RBE cell line are sensitive to erastin-induced ferroptosis, evidenced by the increased number of propidium iodide-positive cells, the decreased cell viability, and increased lipid ROS level. However, current targeted inhibitors of IDH1 mutation (AG120 and IDH305) reversed these effects caused by IDH1 mutation. The in vivo experiment showed that IDH1 mutation in cholangiocarcinoma impairs tumor progression by sensitizing cells to erastin-induced ferroptosis. This study indicated that IDH1 mutation in cholangiocarcinoma impairs tumor progression by sensitizing cells to erastin-induced ferroptosis.

Discovery and Use of Long dsRNA Mediated RNA Interference to Stimulate Antiviral Protection in Interferon Competent Mammalian Cells.

In invertebrate cells, RNA interference (RNAi) acts as a powerful immune defense that stimulates viral gene knockdown thereby preventing infection. With this pathway, virally produced long dsRNA (dsRNA) is cleaved into short interfering RNA (siRNA) by Dicer and loaded into the RNA-induced silencing complex (RISC) which can then destroy/disrupt complementary viral mRNA sequences. Comparatively, in mammalian cells it is believed that the type I interferon (IFN) pathway is the cornerstone of the innate antiviral response. In these cells, dsRNA acts as a potent inducer of the IFN system, which is dependent on dsRNA length, but not sequence, to stimulate an antiviral state. Although the cellular machinery for RNAi is intact and functioning in mammalian cells, its role to trigger an antiviral response using long dsRNA (dsRNAi) remains controversial. Here we show that dsRNAi is not only functional but has a significant antiviral effect in IFN competent mammalian cells. We found that pre-soaking mammalian cells with concentrations of sequence specific dsRNA too low to induce IFN production could significantly inhibit vesicular stomatitis virus expressing green fluorescent protein (VSV-GFP), and the human coronaviruses (CoV) HCoV-229E and SARS-CoV-2 replication. This phenomenon was shown to be dependent on dsRNA length, was comparable in effect to transfected siRNAs, and could knockdown multiple sequences at once. Additionally, knockout cell lines revealed that functional Dicer was required for viral inhibition, revealing that the RNAi pathway was indeed responsible. These results provide the first evidence that soaking with gene-specific long dsRNA can generate viral knockdown in mammalian cells. We believe that this novel discovery provides an explanation as to why the mammalian lineage retained its RNAi machinery and why vertebrate viruses have evolved methods to suppress RNAi. Furthermore, demonstrating RNAi below the threshold of IFN induction has uses as a novel therapeutic platform, both antiviral and gene targeting in nature.

Generation of homozygous PRKN, PINK1 and double PINK1/PRKN knockout cell lines from healthy induced pluripotent stem cells using CRISPR/Cas9 editing

Autosomal recessive mutations in either PRKN or PINK1 are associated with early-onset Parkinson’s disease. The corresponding proteins, PRKN, an E3 ubiquitin ligase, and the mitochondrial serine/threonine-protein kinase PINK1 play a role in mitochondrial quality control. Using CRISPR/CAS9 technology we generated three human iPSC lines from the well characterized AIW002-02 control line. These isogenic iPSCs contain homozygous knockouts of PRKN (PRKN-KO, CBIGi001-A-1), PINK1 (PINK1-KO, CBIGi001-A-2) or both PINK1 and PRKN (PINK1-KO/PRKN-KO, CBIGi001-A-3). The knockout lines display normal karyotypes, express pluripotency markers and upon differentiation into relevant brain cells or midbrain organoids may be valuable tools to model Parkinson’s disease.

Generation of a MIR5004 knockout cell line from human induced pluripotent stem cells by CRISPR/Cas9 gene editing

MIR5004 is located in the intronic region of SYNGAP1, a genetic risk factor for Autism Spectrum Disorders (ASD), and co-expressed with SYNGAP1 in brain tissue, which indicates that MIR5004 may play an important role in ASD pathogenesis through the regulation of SYNGAP1. Here, we generated a MIR5004 knockout human induced pluripotent stem cell (iPSC) line SHCDCLi001-B. SHCDCLi001-B shows expression of pluripotent markers, three lineage differentiation capacity, normal morphology and karyotypes, the same DNA origin with wild type iPSC (iPSC-WT) and no off-target effects, making it as a valuable tool for studying the interplay between MIR5004 and SYNGAP1 in ASD pathogenesis.

FC023: Human Adult Renal Progenitor Cells Secrete in the Kidney Very High Levels of the Anti-Ageing Protein Klotho Sustained by the Long No-Coding RNA Hotair

Abstract BACKGROUND AND AIMS The complex system of human adult renal stem/progenitor cells (ARPCs) and their crucial role in the renewal of epithelial renal cells and regenerative processes in the adult kidneys have been recently discovered. In the human kidney, CD133+/CD24+ ARPCs are present within different segments of the nephron as a population with epithelial expansion, self-renewal and differentiation capabilities. Understanding the factors that regulate the ARPCs behaviour is fundamental to completely take advantage of their potential and to develop treatments for renal injury. Recent studies showed that long no-coding RNA (lncRNAs) are essential to establish developmental patterning and maintain the stem cell pluripotency network, further underscoring their important role in stem cell biology/technology and cellular reprogramming. lncRNAs can be dysregulated in different types of diseases and can also modulate the cellular senescence processes. For the first time, we studied their function in ARPCs showing that they express high levels of a particular lncRNA, HOTAIR, influencing cell senescence. METHOD Whole-genome lncRNA expression was performed by Agilent microarray. lncRNA expression was validated by real-time PCR. CRISPR/Cas9 system has been used to knock-down HOTAIR lncRNA. SA-β-Gal experiments were used to evaluate cellular senescence in normal ARPCs and ARPCs knock-out for HOTAIR. By ELISA, it was evaluated the expression of secreted anti-ageing protein Klotho. Fluorescence-activated cell sorting (FACS) was applied to measure CD133 and protein p15 expression in normal and transfected cells. Chromatin immunoprecipitation assay (ChIP) was used to evaluate H3K27me3 in the promoter of p15. RESULTS We studied the lncRNA profile of renal proximal tubular cells (RPTEC) and tubular ARPCs. We found 611 lncRNAs specifically expressed in ARPCs compared with RPTECs (Fold Change > 2; FDR < 0.05). Among the most significantly modulated lncRNAs, we demonstrated that the lncRNA HOX Transcript Antisense RNA (HOTAIR) is highly expressed in ARPCs (Fold change = 15; P < 0.001). To study the functions related to the ARPCs properties, knock-out cell lines for HOTAIR were created by the CRISPR/Cas9 technique. The silenced lines for HOTAIR immediately assumed a senescent phenotype confirmed by the beta-galactosidase assay and decreased proliferation (proliferation rate of ˂60%, P < 0.001). Moreover, we found that the constitutional, functional and inverse-senescence marker CD133+ was downregulated in knock-out cells (Fold change = 15; P < 0.01). We then studied the secreted levels of the anti-ageing protein α-Klotho which is essential to the maintenance of normal renal function and has potential clinical applications in the diagnosis of acute renal failure (AKI) and chronic kidney disease (CKD). We discovered that ARPCs produce α-Klotho at much higher levels compared to RPTEC, at a mean concentration of 200 pg/mL versus 33 pg/mL (Fold increase = 6.6; P < 0.001). Interestingly, following the HOTAIR knock-out, the levels of α-Klotho secreted by the ARPCs dropped sharply, with a 4-fold decrease (P < .001). In addition, we found that HOTAIR was responsible for the ARPC self-renewal through the epigenetic induction of the cell cycle inhibitor p15 through the trimethylation of histone H3K27 associated with the promoter region of p15. In ARPCs knock-out for HOTAIR p15 increased significantly (Fold increase = 3; P < 0.005) and the H3K27me3 in the promoter of p15 was less enriched (Fold decrease = 1.5; P < 0.05), leading to the increase of the cell cycle inhibitor and cell senescence. CONCLUSION These data demonstrated that HOTAIR regulates the self-renewal capacity of ARPCs and prevents them from becoming senescent in the short term. Moreover, HOTAIR influences ARPC ability to secrete high levels of α-Klotho, and those renal progenitors, through α-Klotho secretion, are able to influence its levels in surrounding tissues and to modulate, therefore, kidney ageing.

A SUMO‐dependent Pathway for Cytosolic Protein Quality Control

Protein quality control (PQC) maintains proteostasis in cells, whereas PQC dysregulation is found in diseases such as cancers, cardiovascular diseases, and neurodegenerative disorders. Over the past few decades, remarkable progress has been made in understanding compartmentalized PQC pathways that operate inside the nucleus and the endoplasmic reticulum (ER). The small ubiquitin‐related modifiers (SUMOs), for example, were recently found to participate in a nuclear PQC pathway that involves selective sumoylation of misfolded proteins by the SUMO E3 ligase PML, and subsequent recognition and ubiquitylation by the SUMO‐targeted ubiquitin E3 ligase RNF4 (Guo et al., Mol Cell, 2014). Roles of SUMOs in cytoplasmic PQC, however, have not previously been reported. Using yeast mutants and human knockout cell lines, our lab has recently identified a conserved SUMO‐dependent pathway for degradation of a cytosolic, misfolded protein model substrate. The substrate consists of GFP fused to an N‐terminal nuclear export signal (NES) and a C‐terminal hydrophobic degron known as CL1 (NES‐GFP‐CL1). Using protein stability assays, we observed a decrease in the turnover rate of NES‐GFP‐CL1 in a yeast SUMO mutant strain and a human U2OS SUMO1 knockout cell line. Further exploration using nuclear and ER‐localized substrates revealed that this pathway is specific for soluble, cytosolic proteins. In addition, analysis of a U2OS SUMO2 knockout cell line revealed that the observed PQC pathway is specific for the SUMO1 paralogue. This suggests a distinct mechanism from the previously characterized nuclear PML‐SUMO‐RNF4 pathway, which targets misfolded proteins modified by SUMO2/3 polymeric chains. Using cellular fractionation studies, we observed an increase in levels of insoluble NES‐GFP‐CL1 specifically in SUMO1 knockout cells compared to wild type cells. We therefore propose a model where SUMO1 modification of misfolded cytosolic proteins promotes their turnover by enhancing solubility and preventing aggregation. Results from our studies reveal a novel cytosolic PQC regulatory network and provide insights into roles for sumoylation in PQC‐associated diseases.

SUMO Regulates Histone mRNA Processing and Polyadenylation

Replication‐dependent histone genes encode the only non‐polyadenylated mRNAs in mammals. Histone pre‐mRNAs, which do not contain introns, therefore require only one processing step that involves 3’ end recognition and cleavage. Both histone gene expression and pre‐mRNA processing take place in specialized nuclear organelles known as histone locus bodies. Recent studies have revealed that polyadenylation of histone mRNAs does occur, however, under specific physiological conditions. These include during normal terminal cellular differentiation, tumorigenesis, and in disease patients with Aicardi–Goutières syndrome. Despite these links between polyadenylation of histone mRNAs, human physiology, and disease, the triggers, the mechanisms, and the consequences of histone mRNA polyadenylation remain poorly defined. In recent studies of small ubiquitin‐related modifier (SUMO) knockout cell lines, we have obtained evidence that SUMO1 and SUMO2 play roles in regulating histone pre‐mRNA 3’ end processing and polyadenylation. This evidence includes alterations in histone locus body size and structure in SUMO1 and SUMO2 knockout cells, as well as mislocalization of key pre‐mRNA processing factors required for normal processing. Collectively, our findings provide new insights into control of histone pre‐mRNA processing that involves posttranslational protein modifications by SUMO1 and SUMO2.

Inhibition of Core Binding Factor Transcriptional Complex Provides a Novel Pharmacological Target for Osteosarcoma

Osteosarcoma (OS) is the most common primary malignant bone tumor in canines and humans. However, there have been no new successful therapies that improve long‐term survival in several decades. This indicates the need for novel therapeutic targets for treating OS. Core binding factor is a heterodimeric transcriptional complex, comprised of proteins runt‐related transcription factor 2 (RUNX2) and core‐binding factor subunit Beta (CBFβ), that promotes transcription of genes related to bone formation, osteoblast differentiation, and bone mineralization. RUNX2 protein expression is deregulated in OS tumors which contributes to chemoresistance, increased proliferation, and defective differentiation, suggesting it could be a therapeutic target in OS. This study utilizes small molecule allosteric inhibitor of CBFβ, AI‐14‐91, to target the interaction of RUNX2 and CBFβ, thereby reducing RUNX2 binding to target genes, in order to evaluate the CBFβ and RUNX2 interaction as a pharmacological target in OS. We hypothesized that AI‐14‐91 will reduce the malignant phenotype of human OS cell lines by disrupting the RUNX2‐CBFβ interaction.In vitro assays with compound AI‐14‐91 were performed with a panel of unique human OS cell lines (LM7, MG‐63, Saos‐2, SJSA‐1, and U2OS). This panel contains unique genetic mutations in key tumor‐related genes such as p53, MDM2, Rb1, or CDKN2A. RUNX2 knockout (KO) and CBFβ KO cell lines were also generated from the parental U2OS by CRISPR/Cas9 editing, which was confirmed via sequencing and western blot. Concentration‐ and time‐dependent proliferation assays were performed with all cell lines, demonstrating AI‐14‐91 IC50 values ranging from 13‐25 µM across the panel. Clonogenic assays showed AI‐14‐91 treatment significantly reduced colony formation in the majority of cell lines. Flow cytometry revealed cell cycle progression was altered in the parental U2OS and the RUNX2 KO and CBFβ KO cell lines with a significant decrease of cell number in G0/G1 phase and an increase in S phase upon 48 exposure to 20 µM AI‐14‐91. Apoptotic and necrotic cell populations in parental U2OS and KO lines were quantified by flow cytometry bivariate analysis with Annexin V/PI co‐stain. Batch 3’ Tag‐Seq RNAseq analysis was performed on parental U2OS cells exposed to 5 or 20 µM AI‐14‐91 for 6 or 48 hours and on RUNX2 KO and CBFβ KO cell lines. Differential gene expression (DGE) and enrichment analysis was performed to evaluate pertinent transcriptional pathways altered by inhibitor treatment, and to compare the effects of inhibitor treatment with knockout of putative inhibitor targets.Treatment with AI‐14‐91 has shown desirable antitumor effects in human OS cell lines that may be independent of the absence of proteins RUNX2 or CBFβ. Further analysis into DGE pathways combined with ChIP assays will help delineate mechanisms of action and identify additional potential targets for combination treatments. Orthotopic mouse models utilizing the metastasizing LM7 cell line with provide further information on the potential clinical utility of targeting the RUNX2‐CBFβ interaction in OS.

SUMO 2 the rescue: how SUMO2 regulates the mitochondria via Drp1 modification

Mitochondria are dynamic powerhouses of cells and their fission and fusion must be tightly regulated for normal cell function. Mitochondrial fission is mediated by the GTPase, Drp1, and mis‐regulation of Drp1 leads to mitochondrial hyper‐fragmentation, a known marker of disease. It has been reported that Drp1 is modified by SUMO1 and SUMO2/3, however, the mechanisms of Drp1 regulation by individual SUMO paralogs remain to be fully understood. Here, we have used CRISPR/Cas9 derived SUMO1 and SUMO2 knockout (KO) cell lines, to perform a systematic investigation of paralog‐specific effects on mitochondrial maintenance and function. In contrast to expectations, we observed multiple mitochondrial defects specifically in SUMO2 KO, but not SUMO1 KO, cells. SUMO2 KO cells had reduced mitochondrial activity based on results of MTT assays. By immunofluorescence microscopy, we also observed an increase in mitochondrial fragmentation in SUMO2 KO cells. Paradoxically, increased fragmentation occurred despite reduced levels of Drp1 protein expression and sequestration of Drp1 in large cytosolic foci. Taken together, our findings indicate that SUMO2 plays a non‐redundant, paralog‐specific role in regulating mitochondrial function, in part through effects on Drp1. We anticipate that a more detailed understanding of the molecular effects of SUMO2 on Drp1 may lead to novel therapeutic approaches to treat or prevent ischemic injury, neurodegeneration, and other mitochondrial‐related maladies.

Acute Manipulation of Outer Membrane Phospholipid Composition Directly Alters Mitochondrial Dynamics and Ultrastructure

Mitochondria undergo coordinated rounds of fusion and fission that are critical for maintaining the functional integrity of this essential organelle. While a growing number of proteins have been identified as important regulators of mitochondrial dynamics, the direct role of membrane lipid composition during the fusion and fission processes is poorly understood. To address these shortcomings, we devised a protein‐engineering platform that allows for the acute remodeling of structural phospholipids within the outer mitochondrial membrane (OMM) of intact cells. Specifically, we modified a bacterial phospholipase C (Bacillus cereus (Bc)PI‐PLC) to initiate the rapid hydrolysis of phosphatidylinositol (PI) and locally generate diacylglycerol (DAG); an important intracellular signaling molecule and metabolic precursor that is used in diverse lipid biosynthetic pathways. Spatial restriction of enzyme activity was achieved using a chemically inducible system consisting of a rapamycin‐dependent dimerization module (FKBP‐BcPI‐PLC) along with an OMM targeting sequence tagged with the FKBP‐rapamycin binding domain (OMM‐FRB). Using these unique molecular tools, we show that recruitment of FKBP‐BcPI‐PLC to the OMM not only causes the expected local accumulation of DAG, but also initiates the rapid and uniform fragmentation of the mitochondrial network. Mitochondrial fission induced by FKBP‐BcPI‐PLC is accompanied by profound swelling of the mitochondrial matrix along with vesiculation of the inner mitochondrial membrane (IMM) and a general loss of cristae, which all occur within minutes of tethering FKBP‐BcPI‐PLC to the OMM. Expression of dominant‐negative constructs targeting essential GTPases known to regulate OMM fission suggest that both dynamin‐related protein 1 (Drp1) and dynamin 2 (Dnm2) work together to drive efficient BcPI‐PLC‐induced mitochondrial division. However, results using a validated Drp1 knockout cell line show that the loss of Drp1 alone is sufficient to prevent the mitochondrial fragmentation initiated by FKBP‐BcPI‐PLC recruitment, indicating that Drp1 likely functions upstream or independent of Dnm2 in this context. Interestingly, unlike the induced OMM fission, removal of Drp1 from cells does not prevent the matrix swelling or OMM constrictions observed in response to acute generation of DAG within the OMM. Ongoing experiments are now focused on characterizing new methods to sequentially metabolize the DAG generated within the OMM as well as investigate how local lipid composition influences the binding and oligomerization of membrane‐shaping proteins that may function in concert with Drp1 to regulate mitochondrial remodeling. Overall, these studies establish a direct relationship between lipid metabolism within the OMM and clinically relevant morphological changes that are known to manifest in mitochondrial‐associated diseases.

TFEB and TFE3 Depletion Increases Cancer Stem Cell Characteristics and EMT in Triple‐Negative Breast Cancer

Breast cancer is currently the second leading cause of death for women worldwide. One subtype of breast cancer with poor prognosis is triple‐negative breast cancer (TNBC), which is characterized by the lack of expression of estrogen, progesterone, and human epidermal growth factor 2 (HER2) receptors. TNBC is difficult to treat due to its drug resistance and aggressiveness. Tumor invasiveness is driven by epithelial‐mesenchymal transition (EMT), which allows cells to acquire mobility to metastasize. EMT is also relevant to maintaining cancer stem cell (CSC) characteristics. Drug resistance is driven by CSCs, which are slow to divide, thus surviving chemotherapies, the standard of treatment. Thus, new treatments that inhibit CSCs and/or EMT in TNBC are highly desirable. TFEB and TFE3, two transcription factors of the MiT‐TFE family that operate as a complex, are involved in regulating lysosome biogenesis and autophagy. Our preliminary data and other studies have shown that TFEB and TFE3 regulate pluripotency and EMT in various in vitro models such as gastric and pancreatic cancer, but this regulation is poorly understood in TNBC. To develop new targeted therapies for TNBC, this study aimed to investigate the effects of depleting TFEB and TFE3 on CSC abundance and EMT. CSC renewal capacity was assessed via mammosphere assays and flow cytometry using CD44 and ALDH1A. The MDA MB 231 TFEBKO cells grew the highest number and largest mammospheres compared to the control, TFE3 knock‐down, and double knock‐out cell lines. TFEBKO and TFEBKOTFE3sh showed increases in CD44 expression and ALDH1A activity. While ALDH1A positivity was 1.16% in controls, TFEBKO and TFEBKOTFE3sh significantly increased the population to 22.6% and 21.9%, respectively. Western blotting and a wound healing assay were used to evaluate EMT marker expression and migration, respectively. Quantification revealed that TFEBKO had a two‐fold increase in protein expression levels of EMT markers Vimentin, Snail, and Slug, while TFE3sh showed higher protein expression levels of Vimentin and Slug. TFEBKOTFE3sh showed higher protein expression levels of Slug. The TFEBKO cell line had the highest rate of migration when compared to the control. In conclusion, the data showed that knockout of TFEB and combined knockout of TFEB and TFE3 resulted in an increase in stem cell character and EMT, which could correlate to increased tumor metastasis and poorer prognosis. These results are promising to investigate how depletion or inhibition of TFEB and TFE3 can affect TNBC tumor cell stem cell character and EMT.

Loss of Cingulin‐like 1 in Dahl Salt‐Sensitive Rats Leads to Reduced Renal Injury and Blood Pressure

Hypertension is both a cause and effect of chronic kidney disease (CKD) and impacts a significant proportion of patients, with a worldwide prevalence of 10‐15%. Previous genetic studies involving the Dahl salt‐sensitive (SS) rat, a model of hypertensive CKD, identified multiple genetic loci linked to kidney injury, including a region on chromosome (Chr) 8. Subsequently, an S.SHR(8) congenic (i.e. transfer of kidney injury resistant SHR genome onto the SS background) demonstrated significantly reduced proteinuria and improved renal function compared to SS control. To identify the gene/s responsible, genome sequencing and bioinformatics analysis identified cingulin‐like 1 (Cgnl1) as a putative gene linked to kidney injury on Chr. 8. Cgnl1 is known to localize to adherens and tight cell‐cell junctions, mediating junction assembly via regulating the activity of the small GTPases such as RhoA and Rac1. A SS‐Cgnl1−/− knockout (KO) was developed to test the hypothesis that loss of Cgnl1 will result in a significant attenuation of kidney injury compared to SS (WT). Both on low and high‐salt (LS=0.3% or HS=2.0% NaCl), KO animals (n=6) demonstrated reduced proteinuria compared to WT animals (n=6) for the entirety of the experiment (HS; KO= 28.7 ± 2.9 versus WT= 161.4 ± 33.1 mg/24hr at week 15, p<0.0001). To further validate Cgnl1’s effect on blood pressure and kidney injury, a temporal analysis (6‐12 weeks) using telemetry and additional renal measurements were conducted on WT and KO animals. On HS, KO animals (n=6) demonstrated reduced proteinuria compared to WT (n=6) for the entirety of the experiment (52.1 ± 7.2 versus 395.9 ± 29.8 mg/24hr at week 12, p<0.0001). While HS fed WT animals exhibited a significant increase in BP compared to LS WT (MAP=197.0 ± 5.0 versus 142.8 ± 3.5 mmHg, p<0001), KO remained unchanged (MAP= 127.6 ± 2.7 and 133.9 ± 3.7 mmHg respectively, NS). Kidney pathology measures, including glomerular and tubular injury were all significantly improved (all p<0.05) in KO compared to WT. Nephron number was measured with no significant difference between WT and KO in young animals, but HS fed WT demonstrated a significant loss of nephrons compared to KO. Bulk RNAseq of kidneys from WT and KO identified Cgnl1 as top downregulated gene with altered expression of many known genes linked with Cgnl1 compared to WT, along downregulation of genes associated with renal injury, mainly reflective of physiological differences from week12‐15. To better identify genes involved in onset of injury, single nuclei RNAseq was performed at week 4 (before physiological differences) to evaluate impact of Cgnl1 in distinct cell populations initiating injury. Additional work is also currently being done on HEK293‐ Cgnl1 knockout cell lines for more mechanistic study of Cgnl1 and pathways. In total, the molecular work, along with the physiological characterization of the SS‐Cgnl1−/−, is expected to provide insight into the role of Cgnl1 in the onset and progression of hypertensive kidney disease and identify new therapeutic targets.

Characterization of the Impact of the MYBBP1A Gene and rs3809849 on Asparaginase Sensitivity and Cellular Functions

Aims: To investigate the role of MYBBP1A gene and rs3809849 in pancreatic cancer (PANC1) and lymphoblastic leukemia (NALM6) cell lines and their response to asparaginase treatment. Materials & methods: The authors applied CRISPR-Cas9 to produce MYBBP1A knock-out (KO) and rs3809849 knock-in (KI) cell lines. The authors also interrogated rs3809849's impact on PANC1 cells through allele-specific overexpression. Results: PANC1 MYBBP1A KO cells exhibited lower proliferation capacity (p≤0.05), higher asparaginase sensitivity (p=0.01), reduced colony-forming potential (p=0.001), cell cycle blockage in S phase, induction of apoptosis and remarkable morphology changes suggestive of an epithelial-mesenchymal transition. Overexpression of the wild-type(but not the mutant)allele ofMYBBP1A-rs3809849 in PANC1 cells increased asparaginase sensitivity. NALM6 MYBBP1A KO displayed resistance to asparaginase (p<0.0001), whereas no effect for rs3809849 KI was noted. Conclusions: MYBBP1A is important for regulating various cellular functions, and it plays, along with its rs3809849 polymorphism, a tissue-specific role in asparaginase treatment response.

CRISPR/Cas9-Mediated Knockout of the Dicer and Ago2 Genes in BHK-21 Cell Promoted Seneca Virus A Replication and Enhanced Autophagy.

RNA interference (RNAi) is a major form of antiviral defense in host cells, and Ago2 and Dicer are the major proteins of RNAi. The Senecavirus A (SVA) is a reemerging virus, resulting in vesicular lesions in sows and a sharp decline in neonatal piglet production. In this study, CRISPR/Cas9 technology was used to knock out Ago2 and Dicer genes in BHK-21 cell lines used for SVA vaccine production. Cell clones with homozygous frameshift mutations of Ago2 and Dicer genes were successfully identified. The two knockout cell lines were named BHK-DicerΔ- and BHK-Ago2Δ-. Results showed that the two genes’ knockout cell lines were capable of stable passage and the cell growth rate did not change significantly. The replication rate and virus titers of SVA were significantly increased in knockout cell lines, indicating that RNAi could inhibit SVA replication. In addition, compared with normal cells, autophagy was significantly enhanced after SVA-infected knockout cell lines, while there was no significant difference in autophagy between the knockout and normal cell lines without SVA. The results confirmed that SVA could enhance the autophagy in knockout cells and promote viral replication. The two knockout cell lines can obtain viruses with high viral titers and have good application prospects in the production of SVA vaccine. At the same time, the RNAi knockout cell lines provide convenience for further studies on RNAi and SVA resistance to RNAi, and it lays a foundation for further study of SVA infection characteristics and screening of new therapeutic drugs and drug targets.