Host CLIC4 expression in the tumor microenvironment is essential for breast cancer metastatic competence

scPRINT: pre-training on 50 million cells allows robust gene network predictions

A cell is governed by the interaction of myriads of macromolecules. Inferring such a network of interactions has remained an elusive milestone in cellular biology. Building on recent advances in large foundation models and their ability to learn without supervision, we present scPRINT, a large cell model for the inference of gene networks pre-trained on more than 50 million cells from the cellxgene database. Using innovative pretraining tasks and model architecture, scPRINT pushes large transformer models towards more interpretability and usability when uncovering the complex biology of the cell. Based on our atlas-level benchmarks, scPRINT demonstrates superior performance in gene network inference to the state of the art, as well as competitive zero-shot abilities in denoising, batch effect correction, and cell label prediction. On an atlas of benign prostatic hyperplasia, scPRINT highlights the profound connections between ion exchange, senescence, and chronic inflammation.

Chloride intracellular channel (CLIC) protein function in S1P-induced Rac1 activation requires membrane localization of the C-terminus, but not thiol-transferase nor ion channel activities

We have established a novel and evolutionarily-conserved function for chloride intracellular channel proteins (CLICs) in regulating Rho/Rac GTPases downstream of G protein-coupled receptors (GPCRs). Endothelial CLIC1 and CLIC4 are rapidly and transiently re-localized from the cytoplasm to the plasma membrane in response to the GPCR ligand sphingosine-1-phosphate (S1P), and both CLICs are required to activate Rac1 in response to S1P, but how they perform this function remains unknown. Biochemical studies suggest that CLICs act as non-specific ion channels and/or as glutathione-S-transferases, dependent on N-terminal features, in vitro. Here we investigate CLIC functional domains and membrane localization requirements for their function in S1P-mediated Rac1 signaling. Structure-function analyses of CLIC function in endothelial cells demonstrate that CLIC1 and CLIC4-specific functions reside at their C-termini, and that the CLIC4 N-terminus encodes determinants required for S1P-induced re-localization to the plasma membrane but is dispensable for S1P-induced Rac1 activation when the C-terminus is localized to the plasma membrane via a heterologous signal. Our results demonstrate that the postulated ion channel and thiol-transferase activities of CLICs are not required for Rac1 activation and suggests that sequences in the CLIC C-termini are critical for this function. Given the importance of S1P signaling in vascular biology and disease, our work establishes a platform to further our understanding of the membrane-localized proteins required to link GPCR activity to Rho/Rac regulation.

The role of chloride intracellular channel 4 in tumors

Tumors are among the most predominant health problems in the world, and the annual incidence of cancer is increasing globally; therefore, there is an urgent need to identify effective therapeutic targets. Chloride intracellular channel 4 (CLIC4) belongs to the family of chloride intracellular channels (CLICs), which are widely expressed in various tissues and organs, such as the brain, lung, pancreas, colorectum, and ovary, and play important roles in promoting apoptosis, promoting angiogenesis, maintaining normal proliferation of endothelial cells, and regulating the assembly and reconstruction of the cytoskeleton. The expression and function of CLIC4 in tumors varies. It has been reported that CLIC4 is low expressed in gastric cancer, skin cancer and prostate cancer, suggesting a tumor suppressor role. Interestingly, CLIC4 is overexpressed in pancreatic, ovarian and breast cancers, indicating a cancer-promoting role. CLIC4 expression is dysregulated in some solid tumors, which may be because CLIC4 is involved in the growth, migration or invasion of some cancer cells through various mechanisms. Regulation of CLIC4 expression may be a potential therapeutic strategy for some tumors. CLIC4 may be a promising therapeutic target and a biomarker for some cancers. In this study, we review the role of CLIC4 in several cancers and its value in the diagnosis and treatment of tumors.

The Unique Roles of Ion Channels in Pluripotent Stem Cells in Response to Biological Stimuli

Ion channels are essential for mineral ion homeostasis in mammalian cells, and these are activated or inhibited by environmental stimuli such as heat, cold, mechanical, acidic, or basic stresses. These expressions and functions are quite diverse between cell types. The function and importance of ion channels are well-studied in neurons and cardiac cells, while those functions in pluripotent stem cells (PSCs) were not fully understood. Some sodium, potassium, chloride, calcium, transient receptor potential channels and mechanosensitive Piezo channels are found to be expressed and implicated in pluripotency and self-renewal capacity in PSCs. This review summarizes present and previous reports about ion channels and their response to environmental stimuli in PSCs. Furthermore, we compare the expressions and roles between PSCs and their differentiated embryoid bodies. We then discuss those contributions to pluripotency and differentiation.

Chloride intracellular channel 4 participates in the regulation of lipopolysaccharide-induced inflammatory responses in human bronchial epithelial cells

The airway epithelium is located at the interactional boundary between the external and internal environments of the organism and is often exposed to harmful environmental stimuli. Inflammatory response that occurs after airway epithelial stress is the basis of many lung and systemic diseases. Chloride intracellular channel 4 (CLIC4) is abundantly expressed in epithelial cells. The purpose of this study was to investigate whether CLIC4 is involved in the regulation of lipopolysaccharide (LPS)-induced inflammatory response in airway epithelial cells and to clarify its potential mechanism. Our results showed that LPS induced inflammatory response and decreased CLIC4 levels in vivo and in vitro. CLIC4 silencing aggravated the inflammatory response in epithelial cells, while overexpression of CLIC4 combined with LPS exposure significantly decreased the inflammatory response compared with cells exposed to LPS without CLIC4 overexpression. By labeling intracellular chloride ions with chloride fluorescent probe MQAE, we showed that CLIC4 mediated intracellular chloride ion-regulated LPS-induced cellular inflammatory response.

Breast cancer patient-derived organoids for the investigation of patient-specific tumour evolution

BACKGROUND

A reliable preclinical model of patient-derived organoids (PDOs) was developed in a case study of a 69-year-old woman diagnosed with breast cancer (BC) to investigate the tumour evolution before and after neoadjuvant chemotherapy and surgery. The results were achieved due to the development of PDOs from tissues collected before (O-PRE) and after (O-POST) treatment.

METHODS

PDO cultures were characterized by histology, immunohistochemistry (IHC), transmission electron microscopy (TEM), scanning electron microscopy (SEM), confocal microscopy, flow cytometry, real-time PCR, bulk RNA-seq, single-cell RNA sequencing (scRNA-seq) and drug screening.

RESULTS

Both PDO cultures recapitulated the histological and molecular profiles of the original tissues, and they showed typical mammary gland organization, confirming their reliability as a personalized in vitro model. Compared with O-PRE, O-POST had a greater proliferation rate with a significant increase in the Ki67 proliferation index. Moreover O-POST exhibited a more stem-like and aggressive phenotype, with increases in the CD24low/CD44low and EPCAMlow/CD49fhigh cell populations characterized by increased tumour initiation potential and multipotency and metastatic potential in invasive lobular carcinoma. Analysis of ErbB receptor expression indicated a decrease in HER-2 expression coupled with an increase in EGFR expression in O-POST. In this context, deregulation of the PI3K/Akt signalling pathway was assessed by transcriptomic analysis, confirming the altered transcriptional profile. Finally, transcriptomic single-cell analysis identified 11 cell type clusters, highlighting the selection of the luminal component and the decrease in the number of Epithelial-mesenchymal transition cell types in O-POST.

CONCLUSION

Neoadjuvant treatment contributed to the enrichment of cell populations with luminal phenotypes that were more resistant to chemotherapy in O-POST. PDOs represent an excellent 3D cell model for assessing disease evolution.

Chloride intracellular channels in oncology as potential novel biomarkers and personalized therapy targets: a systematic review

Background

The chloride intracellular channels (CLICs) family includes six ion channels (CLIC1-CLIC6) expressed on the cellular level and secreted into interstitial fluid and blood. They are involved in the physiological functioning of multiple systems as well as the pathogenetic processes of cancer. CLICs play essential roles in the tumor microenvironment. The current systematic review aimed at identifying and summarizing the research of CLICs in oncology on clinical material to assess CLICs' potential as novel biomarkers and personalized therapy targets.

Materials and methods

The authors systematically searched the PubMed database for original articles concerning CLIC research on clinical material of all types of cancer - fluids and tissues.

Results

Fifty-three articles investigating in summary 3944 clinical samples were qualified for the current review. Studied material included 3438 tumor samples (87%), 437 blood samples (11%), and 69 interstitial fluid samples (2%). Studies investigated 21 cancer types, mostly hepatocellular carcinoma, colorectal, ovarian, and gastric cancer. Importantly, CLIC1, CLIC2, CLIC3, CLIC4, and CLIC5 were differently expressed in cancerous tissues and patients' blood compared to healthy controls. Moreover, CLICs were found to be involved in several cancer-associated signaling pathways, such as PI3K/AKT, MAPK/ERK, and MAPK/p38.

Conclusion

CLIC family members may be candidates for potential novel cancer biomarkers due to the contrast in their expression between cancerous and healthy tissues and secretion to the interstitial fluid and blood. CLICs are investigated as potential therapeutic targets because of their involvement in cancer pathogenesis and tumor microenvironment.

Crosstalk between tumor and stroma modifies CLIC4 cargo in extracellular vesicles

Mouse models of breast cancer have revealed that tumor-bearing hosts must express the oxidoreductase CLIC4 to develop lung metastases. In the absence of host CLIC4, primary tumors grow but the lung premetastatic niche is defective for metastatic seeding. Primary breast cancer cells release EVs that incorporate CLIC4 as cargo and circulate in plasma of wildtype tumor-bearing hosts. CLIC4-deficient breast cancer cells also form tumors in wildtype hosts and release EVs in plasma, but these EVs lack CLIC4, suggesting that the tumor is the source of the plasma-derived EVs that carry CLIC4 as cargo. Paradoxically, circulating EVs are also devoid of CLIC4 when CLIC4-expressing primary tumors are grown in CLIC4 knockout hosts. Thus, the incorporation of CLIC4 (and perhaps other factors) as EV cargo released from tumors involves specific signals from the surrounding stroma determined by its genetic composition. Since CLIC4 is also detected in circulating EVs from human breast cancer patients, future studies will address its association with disease.