Single-cell RNA-seq reveals the transcriptional program underlying tumor progression and metastasis in neuroblastoma.

Neuroblastoma (NB) is one of the most common childhood malignancies. Sixty percent of patients present with widely disseminated clinical signs at diagnosis and exhibit poor outcomes. However, the molecular mechanisms triggering NB metastasis remain largely uncharacterized. In this study, we generated a transcriptomic atlas of 15 447 NB cells from eight NB samples, including paired samples of primary tumors and bone marrow metastases. We used time-resolved analysis to chart the evolutionary trajectory of NB cells from the primary tumor to the metastases in the same patient and identified a common 'starter' subpopulation that initiates tumor development and metastasis. The 'starter' population exhibited high expression levels of multiple cell cycle-related genes, indicating the important role of cell cycle upregulation in NB tumor progression. In addition, our evolutionary trajectory analysis demonstrated the involvement of partial epithelial-to-mesenchymal transition (p-EMT) along the metastatic route from the primary site to the bone marrow. Our study provides insights into the program driving NB metastasis and presents a signature of metastasis-initiating cells as an independent prognostic indicator and potential therapeutic target to inhibit the initiation of NB metastasis.

Rare manifestation of familial vitreous amyloidosis caused by Gly103Arg transthyretin.

AIM: To identify and analyze the genotype of the patients with special ocular manifestations of familial vitreous amyloidosis (FVA) in a Chinese Han family. METHODS: Pars plana vitrectomy (PPV) surgery was performed on a 52-year-old Chinese woman presented with vitreous amyloidosis and progressive visual impairment, without evidence of cardiac, renal, gastrointestinal, central nervous system or peripheral nervous system dysfunction. During the surgery, the patient presented with a gray-white dense and thick cotton wool-like change in the vitreous body, accompanied by complete retinal detachment. Additionally, hard, free and movable yellow-white deposits were observed in the posterior pole and surrounding retina, the vitreous and subretinal deposits were examined by Congo red staining and immunohistochemical pathological examination, and whole exome sequencing was performed on blood samples from the patient and her cousin. RESULTS: During the operation, it was discovered that there was a complete detachment of the retina and a significant amount of hard, free-floating yellow-white deposits were observed beneath the posterior pole and surrounding retina. This is an exceedingly rare ocular manifestation. Pathological examination of the vitreous and subretinal deposit specimens revealed positive Congo red staining, as well as elevated vascular endothelial growth factor (VEGF) expression in vascular endothelial cells within the sediment specimens upon immunohistochemical examination. The patient and her cousin both exhibited a heterozygous mutation in Glyl03Arg within the transthyretin (TTR) gene, resulting in a substitution of glycine (Gly) at position 103 with arginine (Arg). CONCLUSION: FVA may present with various ocular manifestations, but panretinal detachment is a rare occurrence. In cases where retinal detachment persists for an extended period of time, amyloid deposits may form under the retina through retinal tears, leading to subretinal deposits that can impede retinal reattachment and negatively impact visual prognosis. Elevated levels of VEGF in the eyes of FVA patients may indicate an overexpression state, necessitating careful postoperative follow-up. The heterozygous mutation Gly103Arg may represent a unique pathogenic site in Chinese individuals.

Noncoding SNP at rs1663689 represses ADGRG6 via interchromosomal interaction and reduces lung cancer progression.

A previous genome-wide association study (GWAS) revealed an association of the noncoding SNP rs1663689 with susceptibility to lung cancer in the Chinese population. However, the underlying mechanism is unknown. In this study, using allele-specific 4C-seq in heterozygous lung cancer cells combined with epigenetic information from CRISPR/Cas9-edited cell lines, we show that the rs1663689 C/C variant represses the expression of ADGRG6, a gene located on a separate chromosome, through an interchromosomal interaction of the rs1663689 bearing region with the ADGRG6 promoter. This reduces downstream cAMP-PKA signaling and subsequently tumor growth both in vitro and in xenograft models. Using patient-derived organoids, we show that rs1663689 T/T-but not C/C-bearing lung tumors are sensitive to the PKA inhibitor H89, potentially informing therapeutic strategies. Our study identifies a genetic variant-mediated interchromosomal interaction underlying ADGRG6 regulation and suggests that targeting the cAMP-PKA signaling pathway may be beneficial in lung cancer patients bearing the homozygous risk genotype at rs1663689.

Engineering single-domain antibodies targeting Gasdermin E activation by the chemotherapeutic agent cis-diaminodichloroplatinum.

As mediators of pyroptosis, gasdermins (GSDMs) are closely associated with systemic cytotoxicity or so-called side effects and are also involved in the inflammatory response during chemotherapy. Using in situ proximity ligation assay followed by sequencing (isPLA-seq), which we recently developed, we screened a single-domain antibody (sdAb) library and identified several sdAbs against Gasdermin E (GSDME) that specifically recognize the N-terminal domain (1-270 aa) of GSDME (GSDME-NT). One of them mitigated the release of inflammatory damage-associated molecular patterns (DAMPs) and cytokines, including high mobility group protein b1 (Hmgb1) and interleukin-1ß (Il-1ß), in isolated mouse alveolar epithelial cells (AECs) upon chemotherapeutic agent cis-diaminodichloroplatinum (CDDP) treatment. Further investigation showed that this anti-GSDME sdAb also alleviated CDDP-induced pyroptotic cell death and lung tissue injury and decreased systemic Hmgb1 release in C57/BL6 mice, due to GSDME inactivation. Collectively, our data define an inhibitory role of the specific sdAb against GSDME, providing a potential strategy for systemically alleviating chemotherapeutic toxicities in vivo.

Molecular features and evolutionary trajectory of ASCL1+ and NEUROD1+ SCLC cells.

BACKGROUND: Small cell lung cancer (SCLC) is the most aggressive subtype of lung cancer without recognised morphologic or genetic heterogeneity. Based on the expression of four transcription factors, ASCL1, NEUROD1, POU2F3, and YAP1, SCLCs are classified into four subtypes. However, biological functions of these different subtypes are largely uncharacterised. METHODS: We studied intratumoural heterogeneity of resected human primary SCLC tissues using single-cell RNA-Seq. In addition, we undertook a series of in vitro and in vivo functional studies to reveal the distinct features of SCLC subtypes. RESULTS: We identify the coexistence of ASCL1+ and NEUROD1+ SCLC cells within the same human primary SCLC tissue. Compared with ASCL1+ SCLC cells, NEUROD1+ SCLC cells show reduced epithelial features and lack EPCAM expression. Thus, EPCAM can be considered as a cell surface marker to distinguish ASCL1+ SCLC cells from NEUROD1+ SCLC cells. We further demonstrate that NEUROD1+ SCLC cells exhibit higher metastatic capability than ASCL1+ SCLC cells and can be derived from ASCL1+ SCLC cells. CONCLUSIONS: Our studies unveil the biology and evolutionary trajectory of ASCL1+ and NEUROD1+ SCLC cells, shedding light on SCLC tumourigenesis and progression.

Yeast-based evolutionary modeling of androgen receptor mutations and natural selection.

Cancer progression is associated with the evolutionary accumulation of genetic mutations that are biologically significant. Mutations of the androgen receptor (AR) are associated with the development of prostate cancer (PCa) by responding to non-androgenic hormones, and the lack of annotations in their responsiveness to hormone ligands remains a daunting challenge. Here, we have used a yeast reporter system to quickly evaluate the responsiveness of all fifty clinical AR mutations to a variety of steroidal ligands including dihydrotestosterone (DHT), 17ß-estradiol (E2), progesterone (PROG), and cyproterone acetate (CPA). Based on an AR-driven reporter that synthesizes histidine, a basic amino acid required for yeast survival and propagation, the yeast reporter system enabling clonal selection was further empowered by combining with a random DNA mutagenesis library to simulate the natural evolution of AR gene under the selective pressures of steroidal ligands. In a time-frame of 1-2 weeks, 19 AR mutants were identified, in which 11 AR mutants were validated for activation by tested steroidal compounds. The high efficiency of our artificial evolution strategy was further evidenced by a sequential selection that enabled the discovery of multipoint AR mutations and evolution directions under the pressure of steroidal ligands. In summary, our designer yeast is a portable reporter module that can be readily adapted to streamline high-throughput AR-compound screening, used as a PCa clinical reference, and combined with additional bioassay systems to further extend its potential.

Simulating androgen receptor selection in designer yeast.

Androgen receptor (AR) mutation is closely associated with prostate cancer (PCa) and is one of the mechanisms of resistance to PCa therapies such as AR antagonists. Although sequencing technologies like next-generation sequencing (NGS) contributes to the high-throughput and precise detection of AR mutations carried by PCa patients, the lack of interpretations of these clinical genetic variants has still been a roadblock for PCa-targeted precision medicine. Here, we established a designer yeast reporter assay to simulate natural androgen receptor (AR) selection using AR antagonists. Yeast HIS3 gene transactivation was associated with the ligand-induced recruitment of steroid receptor coactivator-1 (SRC-1) by AR mutants, where yeast growth in histidine-free medium was determined as the outcome. This assay is applicable to determine a wide range of clinical AR mutants including those with loss of function relating to androgen insensitivity syndrome (AIS), and those associated with PCa conferring resistance to AR antagonists such as enzalutamide (ENZ), bicalutamide (BIC), and cyproterone acetate (CPA). One clinical AR mutant previously reported to confer ENZ-resistance, F877L, was found to confer partial resistance to CPA as well using designer yeast. Our simple and efficient assay can enable precise one-pot screening of AR mutants, providing a reference for tailored medicine.

Hematopoietic transcription factor GFI1 promotes anchorage independence by sustaining ERK activity in cancer cells.

The switch from anchorage-dependent to anchorage-independent growth is essential for epithelial metastasis. The underlying mechanism, however, is not fully understood. In this study, we identified growth factor independent-1 (GFI1), a transcription factor that drives the transition from adherent endothelial cells to suspended hematopoietic cells during hematopoiesis, as a critical regulator of anchorage independence in lung cancer cells. GFI1 elevated the numbers of circulating and lung-infiltrating tumor cells in xenograft models and predicted poor prognosis of patients with lung cancer. Mechanistically, GFI1 inhibited the expression of multiple adhesion molecules and facilitated substrate detachment. Concomitantly, GFI1 reconfigured the chromatin structure of the RASGRP2 gene and increased its expression, causing Rap1 activation and subsequent sustained ERK activation upon detachment, and this led to ERK signaling dependency in tumor cells. Our studies unveiled a mechanism by which carcinoma cells hijacked a hematopoietic factor to gain anchorage independence and suggested that the intervention of ERK signaling may suppress metastasis and improve the therapeutic outcome of patients with GFI1-positive lung cancer.

Single-domain antibody screening by isPLA-seq.

Single-domain antibody (sdAb) holds the promising strategies for diverse research and translational applications. Here, we describe a method for the adaptation of the in situ proximity ligation assay (isPLA) followed by sequencing (isPLA-seq) to facilitate screening of a high-sensitive, high-throughput sdAb library for a given protein at subcellular and single-cell resolution. Based on the sequence of complementarity-determining region 3 (CDR3), the recombinant sdAb can be produced for in vitro and in vivo utilities. This method provides a general means to identify the functional measure of sdAb and its complementary epitopes and its potential applications to investigate cellular processes.

Autophagic flux in cancer cells at the invasive front in the tumor-stroma border.

Cancer cells at the invasive front directly interact with stromal tissue that provides a microenvironment with mechanical, nutrient, and oxygen supply characteristics distinct from those of intratumoral tissues. It has long been known that cancer cells at the invasive front and cancer cells inside the tumor body exhibit highly differentiated functions and behaviors. However, it is unknown whether cancer cells at different locations exhibit a variety of autophagic flux, an important catabolic process to maintain cellular homeostasis in response to environmental changes. Here, using transmission electron microscopy (TEM), we found that invading cancer cells at the invasive front, which show mesenchymal transcriptomic traits, exhibit higher autophagic flux than cancer cells inside the tumor body in human primary non-small cell lung cancer (NSCLC) tissues. This autophagic feature was further confirmed by a live cell autophagic flux monitoring system combined with a 3D organotypic invasion coculture system. Additionally, the increased autophagic flux endows cancer cells with invasive behavior and positively correlates with the advanced tumor stages and the reduced survival period of lung cancer patients. These findings expand the understanding of autophagic dynamics during cancer invasion.

Molecular basis for recognition of Gly/N-degrons by CRL2ZYG11B and CRL2ZER1.

N-degron pathways are a set of proteolytic systems that target the N-terminal destabilizing residues of substrates for proteasomal degradation. Recently, the Gly/N-degron pathway has been identified as a new branch of the N-degron pathway. The N-terminal glycine degron (Gly/N-degron) is recognized by ZYG11B and ZER1, the substrate receptors of the Cullin 2-RING E3 ubiquitin ligase (CRL2). Here we present the crystal structures of ZYG11B and ZER1 bound to various Gly/N-degrons. The structures reveal that ZYG11B and ZER1 utilize their armadillo (ARM) repeats forming a deep and narrow cavity to engage mainly the first four residues of Gly/N-degrons. The α-amino group of the Gly/N-degron is accommodated in an acidic pocket by five conserved hydrogen bonds. These structures, together with biochemical studies, decipher the molecular basis for the specific recognition of the Gly/N-degron by ZYG11B and ZER1, providing key information for future structure-based chemical probe design.

An infection-induced RhoB-Beclin 1-Hsp90 complex enhances clearance of uropathogenic Escherichia coli.

Host cells use several anti-bacterial pathways to defend against pathogens. Here, using a uropathogenic Escherichia coli (UPEC) infection model, we demonstrate that bacterial infection upregulates RhoB, which subsequently promotes intracellular bacteria clearance by inducing LC3 lipidation and autophagosome formation. RhoB binds with Beclin 1 through its residues at 118 to 140 and the Beclin 1 CCD domain, with RhoB Arg133 being the key binding residue. Binding of RhoB to Beclin 1 enhances the Hsp90-Beclin 1 interaction, preventing Beclin 1 degradation. RhoB also directly interacts with Hsp90, maintaining RhoB levels. UPEC infections increase RhoB, Beclin 1 and LC3 levels in bladder epithelium in vivo, whereas Beclin 1 and LC3 levels as well as UPEC clearance are substantially reduced in RhoB+/- and RhoB-/- mice upon infection. We conclude that when stimulated by UPEC infections, host cells promote UPEC clearance through the RhoB-Beclin 1-HSP90 complex, indicating RhoB may be a useful target when developing UPEC treatment strategies.

Transcriptional coregualtor NUPR1 maintains tamoxifen resistance in breast cancer cells.

To support cellular homeostasis and mitigate chemotherapeutic stress, cancer cells must gain a series of adaptive intracellular processes. Here we identify that NUPR1, a tamoxifen (Tam)-induced transcriptional coregulator, is necessary for the maintenance of Tam resistance through physical interaction with ESR1 in breast cancers. Mechanistically, NUPR1 binds to the promoter regions of several genes involved in autophagy process and drug resistance such as BECN1, GREB1, RAB31, PGR, CYP1B1, and regulates their transcription. In Tam-resistant ESR1 breast cancer cells, NUPR1 depletion results in premature senescence in vitro and tumor suppression in vivo. Moreover, enforced-autophagic flux augments cytoplasmic vacuolization in NUPR1-depleted Tam resistant cells, which facilitates the transition from autophagic survival to premature senescence. Collectively, these findings suggest a critical role for NUPR1 as a transcriptional coregulator in enabling endocrine persistence of breast cancers, thus providing a vulnerable diagnostic and/or therapeutic target for endocrine resistance.

An Integrated Approach for Combinatorial Readout of Dual Histone Modifications by Epigenetic Tandem Domains.

Histone post-translational modifications (HPTMs) serve as signal platforms for recruitment of binding proteins (readers) to regulate gene expression. Accumulated evidence suggests that the intensive distribution of HPTMs may result in crosstalk, which increases or inhibits the recruitment of reader proteins, further altering the functional outcome of HPTMs. Therefore, the comprehensive identification of multiple interactions between combinatorial HPTMs and reading domains is essential to understand the chromatin-templated processes. However, it is still a big challenge to profile these complicated interactions due to various limitations including rather weak, transient and multiple interactions between HPTMs and readers, the high dynamic property of HPTMs as well as the low abundance of reader proteins. Here we developed an integrated approach to profile the complicated interactions between combinatorial HPTMs and dual domains. Based on a combinatorial HPTM peptide library (trimethylation of histone H3 lysine 4 and its neighboring PTMs) and five affinity tag proteins containing tandem-domain probes, histone interactions can be profiled by pull-down assay combined with mass spectrometry analysis. The interactions were further verified by isothermal titration calorimetry and proximity ligation assay, as well as molecular docking. By use of combinatorial HPTMs, we demonstrated that this integrated approach can be successfully utilized for the characterization of multiple interactions between reading domains and combinatorial HPTMs including novel HPTMs with low stoichiometry. Thus, a novel chemical proteomics tool for profiling of multiple PTM-mediated protein-protein interactions was successfully developed and can be adapted for broad biomedical applications.

SPIB promotes anoikis resistance via elevated autolysosomal process in lung cancer cells.

Anoikis (detachment-induced cell death) is a specific type of programmed cell death which occurs in response to the loss of the correct extracellular matrix connections. Anoikis resistance is an important mechanism in cancer invasiveness and metastatic behavior. Autophagy, on the other hand, involves the degradation of damaged organelles and the recycling of misfolded proteins and intracellular components. However, the intersection of these two cellular responses in lung cancer cells has not been extensively studied. Here, we identified that upon matrix deprivation, the lymphocyte lineage-specific Ets transcription factor SPIB was activated and directly enhanced SNAP47 transcription in certain lung cancer cells. Loss of attachment-induced autophagy significantly increased anoikis resistance by SPIB activation. Consistent with this function, SPIB depletion by short hairpin RNA abrogated SNAP47 transcriptional activation upon matrix deprivation. Therefore, these data delineate an important role of SPIB in autophagy-mediated anoikis resistance in lung cancer cells. Accordingly, these findings suggest that manipulating SPIB-regulated pathways in vivo and evaluating the impact of anoikis resistance warrant further investigation. DATABASE: RNA sequencing and ChIP sequencing data are available in Gene Expression Omnibus database under the accession numbers GSE106592 and GSE125561, respectively.

Identification of dual histone modification-binding protein interaction by combining mass spectrometry and isothermal titration calorimetric analysis.

Histone posttranslational modifications (HPTMs) play important roles in eukaryotic transcriptional regulation. Recently, it has been suggested that combinatorial modification codes that comprise two or more HPTMs can recruit readers of HPTMs, performing complex regulation of gene expression. However, the characterization of the multiplex interactions remains challenging, especially for the molecular network of histone PTMs, readers and binding complexes. Here, we developed an integrated method that combines a peptide library, affinity enrichment, mass spectrometry (MS) and bioinformatics analysis for the identification of the interaction between HPTMs and their binding proteins. Five tandem-domain-reader proteins (BPTF, CBP, TAF1, TRIM24 and TRIM33) were designed and prepared as the enriched probes, and a group of histone peptides with multiple PTMs were synthesized as the target peptide library. First, the domain probes were used to pull down the PTM peptides from the library, and then the resulting product was characterized by MS. The binding interactions between PTM peptides and domains were further validated and measured by isothermal titration calorimetry analysis (ITC). Meanwhile, the binding proteins were enriched by domain probes and identified by HPLC-MS/MS. The interaction network of histone PTMs-readers-binding complexes was finally analyzed via informatics tools. Our results showed that the integrated approach combining MS analysis with ITC assay enables us to understand the interaction between the combinatorial HPTMs and reading domains. The identified network of "HPTMs-reader proteins-binding complexes" provided potential clues to reveal HPTM functions and their regulatory mechanisms.

Combination of AAV­mediated NUPR1 knockdown and trifluoperazine induces premature senescence in human lung adenocarcinoma A549 cells in nude mice.

Nuclear protein 1 (NUPR1)/p8, a transcriptional regulator, has the ability to facilitate lung cancer cell survival. Adeno­associated virus (AAV)­based vectors are efficient vehicles for gene transfer and expression. In this study, an AAV­mediated NUPR1 shRNA vector was constructed that effectively inhibited the expression of NUPR1 in a tumor xenograft model derived from lung adenocarcinoma A549 cells. Trifluoperazine (TFP), which is an antipsychotic drug, has the ability to bind to NUPR1 and mimic NUPR1 deficiency in cancer cells. It was also found that the combination of TFP and AAV­mediated NUPR1 shRNA delivery led to significant tumor growth inhibition in nude mice bearing human lung cancer xenografts. Moreover, AAV­mediated NUPR1 shRNA therapy induced premature senescence in vitro and in vivo. Collectively, the findings of this study suggest a putative role for the combination of AAV­NUPR1 shRNA and TFP in lung cancer therapy.

Autophagy and Energy Metabolism.

Autophagy is a lysosome-dependent catabolic process. Both extra- and intra-cellular components are engulfed in autophagic vacuoles and degraded to simple molecules, such as monosaccharides, fatty acids and amino acids. Then, these molecules can be further used to produce ATP through catabolic reactions and/or provide building blocks for the synthesis of essential proteins. Therefore, we consider autophagy a critical and fine-tuned process in maintaining energy homeostasis. The complicated relationships between autophagy and energy metabolism have raised broad interest and have been extensively studied. In this chapter, we summarize the relationships enabling autophagy to control or modulate energy metabolism and allowing metabolic pathways to regulate autophagy. Specifically, we review the correlations between autophagy and energy homeostasis in terms of oxidative phosphorylation, reactive oxygen species in mitochondria, glycolysis, metabolism of glycogen and protein, and so on. An understanding of the role of autophagy in energy homeostasis could help us better appreciate how autophagy determines cell fate under stressful conditions or pathological processes.

Autophagy-Cell Survival and Death.

Autophagy, which is one of the most important ways to maintain cell homeostasis plays an important regulatory role in cell survival and death. Currently, it is agreed that autophagy promotes or inhibits cell death depending on the internal and external environment and cell type. On the one hand, under normal nutritional conditions autophagy regulates cell survival by energy sensing through the main energy sensing cascade kinases. On the other hand, autophagy regulates the process of cell death. mTOR, Beclin 1, caspases, FLIPs, DAPK, and Tp53 play important regulatory roles in autophagy and apoptosis highlighting the crosstalk between the mechanisms underlying the two death modes. However, energy deficiency caused by PARP1 over-activation and DAPK-PKD pathway activation induces necrosis and autophagy, highlighting the interaction between the two pathways. In addition, autophagy regulates cell death through epigenetic regulation such as histone modification. More investigations on the relationship between autophagy and cell death is ongoing. In the future, there will be more challenges in the study of the relationship between autophagy and cell survival and death. As research increasingly focuses on cell death, the relationship between autophagy and existing and newly discovered cell death types is likely to become more complex. The elucidation of the regulatory role of autophagy in cell survival and death requires more research. Some research results are likely to provide hot topics for further investigations on diseases related to cell death disorders and an experimental basis for the targeted regulation of autophagy for specific treatment of diseases.

Glycogen Synthase Kinase-3ß Inhibitor Attenuates Renal Damage Through Regulating Antioxidant and Anti-inflammation in Rat Kidney Transplant With Cold Ischemia Reperfusion.

BACKGROUD: The glycogen synthase kinase-3ß inhibitor thiadiazolidinone derivative 8 (TDZD-8) has been reported to reduce renal ischemia reperfusion (I/R) injury through inhibiting cell damage. However, it is not known whether TDZD-8 could also play a role in protecting the kidney in rat kidney transplantation with renal cold I/R. The aim of the present study was to explore the possible role of TDZD-8 in protecting renal damage in a cold I/R model of rat kidney transplantation. METHODS: The rat model of kidney transplantation with renal cold I/R was established. The renal tissue pathomorphologic changes, renal function, oxidative stress, and inflammatory response were evaluated by detection of a series of indices by hematoxylin and eosin staining, commercial kits, enzyme-linked immunosorbent assay, and spectrophotofluorometry, respectively. RESULTS: Compared with I/R and Graft groups, renal function was significantly improved in TDZD and TDZD-G groups, which were accompanied by the reduction of renal injury, oxidative stress, and inflammation. CONCLUSIONS: These results suggest that preconditioning with glycogen synthase kinase-3ß inhibitor can attenuate kidney transplantation with renal cold I/R through regulating endogenous antioxidant activity and inflammation.