Impaired reciprocal regulation between SIRT6 and TGF-ß signaling in fatty liver.

Dysregulated transforming growth factor-beta (TGF-ß) signaling contributes to fibrotic liver disease and hepatocellular cancer (HCC), both of which are associated with fatty liver disease. SIRT6 limits fibrosis by inhibiting TGF-ß signaling through deacetylating SMAD2 and SMAD3 and limits lipogenesis by inhibiting SREBP1 and SREBP2 activity. Here, we showed that, compared to wild-type mice, high-fat diet-induced fatty liver is worse in TGF-ß signaling-deficient mice (SPTBN1+/- ) and the mutant mice had reduced SIRT6 abundance in the liver. Therefore, we hypothesized that altered reciprocal regulation between TGF-ß signaling and SIRT6 contributes to these liver pathologies. We found that deficiency in SMAD3 or SPTBN1 reduced SIRT6 mRNA and protein abundance and impaired TGF-ß induction of SIRT6 transcripts, and that SMAD3 bound to the SIRT6 promoter, suggesting that an SMAD3-SPTBN1 pathway mediated the induction of SIRT6 in response to TGF-ß. Overexpression of SIRT6 in HCC cells reduced the expression of TGF-ß-induced genes, consistent with the suppressive role of SIRT6 on TGF-ß signaling. Manipulation of SIRT6 abundance in HCC cells altered sterol regulatory element-binding protein (SREBP) activity and overexpression of SIRT6 reduced the amount of acetylated SPTBN1 and the abundance of both SMAD3 and SPTBN1. Furthermore, induction of SREBP target genes in response to SIRT6 overexpression was impaired in SPTBN1 heterozygous cells. Thus, we identified a regulatory loop between SIRT6 and SPTBN1 that represents a potential mechanism for susceptibility to fatty liver in the presence of dysfunctional TGF-ß signaling.

TGF-ß Signaling in Liver, Pancreas, and Gastrointestinal Diseases and Cancer.

Genetic alterations affecting transforming growth factor-ß (TGF-ß) signaling are exceptionally common in diseases and cancers of the gastrointestinal system. As a regulator of tissue renewal, TGF-ß signaling and the downstream SMAD-dependent transcriptional events play complex roles in the transition from a noncancerous disease state to cancer in the gastrointestinal tract, liver, and pancreas. Furthermore, this pathway also regulates the stromal cells and the immune system, which may contribute to evasion of the tumors from immune-mediated elimination. Here, we review the involvement of the TGF-ß pathway mediated by the transcriptional regulators SMADs in disease progression to cancer in the digestive system. The review integrates human genomic studies with animal models that provide clues toward understanding and managing the complexity of the pathway in disease and cancer.

Exploring the conformational landscape of protein kinases.

Protein kinases are dynamic enzymes that display complex regulatory mechanisms. Although they possess a structurally conserved catalytic domain, significant conformational dynamics are evident both within a single kinase and across different kinases in the kinome. Here, we highlight methods for exploring this conformational space and its dynamics using kinase domains from ABL1 (Abelson kinase), PKA (protein kinase A), AurA (Aurora A), and PYK2 (proline-rich tyrosine kinase 2) as examples. Such experimental approaches combined with AI-driven methods, such as AlphaFold, will yield discoveries about kinase regulation, the catalytic process, substrate specificity, the effect of disease-associated mutations, as well as new opportunities for structure-based drug design.

Mechanisms and clinical significance of TGF-ß in hepatocellular cancer progression.

Despite progress in treating or preventing viral hepatitis, a leading cause of liver cancer, hepatocellular cancer (HCC) continues to be a major cause of cancer-related deaths globally. HCC is a highly heterogeneous cancer with many genetic alterations common within a patient's tumor and between different patients. This complicates therapeutic strategies. In this review, we highlight the critical role that the Smad-mediated transforming growth factor ß (TGF-ß) pathway plays both in liver homeostasis and in the development and progression of HCC. We summarize the mouse models that have enabled the exploration of the dual nature of this pathway as both a tumor suppressor and a tumor promoter. Finally, we highlight how the insights gained from evaluating pathway activity using transcriptional profiling can be used to stratify HCC patients toward rational therapeutic regimens based on the differences in patients with early or late TGF-ß pathway activity or activated, normal, or inactivated profiles of this key pathway.

Using quantitative immunohistochemistry in patients at high risk for hepatocellular cancer.

Hepatocellular carcinoma (HCC) is the primary form of liver cancer and a major cause of cancer death worldwide. Early detection is key to effective treatment. Yet, early diagnosis is challenging, especially in patients with cirrhosis, who are at high risk of developing HCC. Dysfunction or loss of function of the transforming growth factor ß (TGF-ß) pathway is associated with HCC. Here, using quantitative immunohistochemistry analysis of samples from a multi-institutional repository, we evaluated if differences in TGF-ß receptor abundance were present in tissue from patients with only cirrhosis compared with those with HCC in the context of cirrhosis. We determined that TGFBR2, not TGFBR1, was significantly reduced in HCC tissue compared with cirrhotic tissue. We developed an artificial intelligence (AI)-based process that correctly identified cirrhotic and HCC tissue and confirmed the significant reduction in TGFBR2 in HCC tissue compared with cirrhotic tissue. Thus, we propose that a reduction in TGFBR2 abundance represents a useful biomarker for detecting HCC in the context of cirrhosis and that incorporating this biomarker into an AI-based automated imaging pipeline could reduce variability in diagnosing HCC from biopsy tissue.

Targeting the E3 Ubiquitin Ligase PJA1 Enhances Tumor-Suppressing TGFß Signaling.

RING-finger E3 ligases are instrumental in the regulation of inflammatory cascades, apoptosis, and cancer. However, their roles are relatively unknown in TGFß/SMAD signaling. SMAD3 and its adaptors, such as ß2SP, are important mediators of TGFß signaling and regulate gene expression to suppress stem cell-like phenotypes in diverse cancers, including hepatocellular carcinoma (HCC). Here, PJA1, an E3 ligase, promoted ubiquitination and degradation of phosphorylated SMAD3 and impaired a SMAD3/ß2SP-dependent tumor-suppressing pathway in multiple HCC cell lines. In mice deficient for SMAD3 (Smad3 +/-), PJA1 overexpression promoted the transformation of liver stem cells. Analysis of genes regulated by PJA1 knockdown and TGFß1 signaling revealed 1,584 co-upregulated genes and 1,280 co-downregulated genes, including many implicated in cancer. The E3 ligase inhibitor RTA405 enhanced SMAD3-regulated gene expression and reduced growth of HCC cells in culture and xenografts of HCC tumors, suggesting that inhibition of PJA1 may be beneficial in treating HCC or preventing HCC development in at-risk patients.Significance: These findings provide a novel mechanism regulating the tumor suppressor function of TGFß in liver carcinogenesis.

Secretome profiling identifies neuron-derived neurotrophic factor as a tumor-suppressive factor in lung cancer.

Clinical and preclinical studies show tissue-specific differences in tumorigenesis. Tissue specificity is controlled by differential gene expression. We prioritized genes that encode secreted proteins according to their preferential expression in normal lungs to identify candidates associated with lung cancer. Indeed, most of the lung-enriched genes identified in our analysis have known or suspected roles in lung cancer. We focused on the gene encoding neuron-derived neurotrophic factor (NDNF), which had not yet been associated with lung cancer. We determined that NDNF was preferentially expressed in the normal adult lung and that its expression was decreased in human lung adenocarcinoma and a mouse model of this cancer. Higher expression of NDNF was associated with better clinical outcome of patients with lung adenocarcinoma. Purified NDNF inhibited proliferation of lung cancer cells, whereas silencing NDNF promoted tumor cell growth in culture and in xenograft models. We determined that NDNF is downregulated through DNA hypermethylation near CpG island shores in human lung adenocarcinoma. Furthermore, the lung cancer-related DNA hypermethylation sites corresponded to the methylation sites that occurred in tissues with low NDNF expression. Thus, by analyzing the tissue-specific secretome, we identified a tumor-suppressive factor, NDNF, which is associated with patient outcomes in lung adenocarcinoma.

Focus issue: from egg to egg--cell signaling in germ cells.

In this Focus Issue of Science's STKE, which complements the Science Special Issue on germ cells, we take a closer look at cell signaling in germ cells. STKE highlights the migration of germ cells with an article that describes the different mechanisms controlling primordial germ cell movement and survival in mice and flies. Another article describes a mechanism for mediating plant self-incompatibility through control of the pollen tube, to prevent inappropriate delivery of incompatible sperm to the ovule. A common feature found in each of the organisms discussed, be they animal, insect or plant, is that signals from the surrounding tissues control survival and migration of the germ cells or resulting gametes.

2006: signaling breakthroughs of the year.

With nominations from leading scientists studying cell signaling, the STKE editors compile a list of the year's most important advances. Signaling breakthroughs included molecules and processes both outside cells and inside cells, from channels in the membrane to chromatin in the nucleus. The nominated research ranged from structural and functional revelations to approaches for the global analysis of signaling pathways. Receptors were highlighted with unexpected proteins functioning as receptors, as well as surprising functions for known receptors. This year also brought new insights into the impact of cell signaling on human physiology and disease.

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-ß Superfamily.

We present an integromic analysis of gene alterations that modulate transforming growth factor ß (TGF-ß)-Smad-mediated signaling in 9,125 tumor samples across 33 cancer types in The Cancer Genome Atlas (TCGA). Focusing on genes that encode mediators and regulators of TGF-ß signaling, we found at least one genomic alteration (mutation, homozygous deletion, or amplification) in 39% of samples, with highest frequencies in gastrointestinal cancers. We identified mutation hotspots in genes that encode TGF-ß ligands (BMP5), receptors (TGFBR2, AVCR2A, and BMPR2), and Smads (SMAD2 and SMAD4). Alterations in the TGF-ß superfamily correlated positively with expression of metastasis-associated genes and with decreased survival. Correlation analyses showed the contributions of mutation, amplification, deletion, DNA methylation, and miRNA expression to transcriptional activity of TGF-ß signaling in each cancer type. This study provides a broad molecular perspective relevant for future functional and therapeutic studies of the diverse cancer pathways mediated by the TGF-ß superfamily.

Focus issue: plant communication.

This week's issues of Science and Science's STKE focus on plant signaling with an emphasis on volatile organic compounds. Science emphasizes the chemistry of and information encoded by plant volatiles and how plants, plant pathogens, or humans utilize this aromatic information. Articles and resources at STKE highlight the evolution of olfactory signal transduction, describe the biosynthetic and signaling pathways of the plant hormone jasmonate, and provide an animated overview of how the plant hormone auxin regulates gene expression.

Focus issue: measurement on a small scale.

This week's issues of Science and Science's STKE focus on how instrumentation is advancing investigation of biological questions. Science highlights how advances in detection methods are revealing the chemical aspects of biology, and STKE addresses techniques for single-molecule tracking and approaches to better understanding the interaction of cells with nanoparticles.

Focus issue: signaling lipids.

Membranes are dynamic and specific contributors to cell signaling. Cellular membranes play a key structural role in creating sites for the formation of signaling complexes. Changes in membrane phospholipids can regulate the activity of transmembrane and peripheral membrane proteins. Modification of membrane lipids can result in formation of dynamic signaling molecules. Science's STKE highlights new insights into the roles that lipids and membranes play in cell signaling.

Signal reception and transmission.

From plants to yeast to animals, new pathways and updates to the Database of Cell Signaling highlight how signals received at the surface are transmitted into the cell to mediate complex cellular responses.

Assessing undergraduate laboratory performance.

The lab notebook is one element for assessing student laboratory performance. However, it is also important to be able to communicate research results in a journal article format and a visual poster format. Another key aspect to scientific research is the ability to present a research plan. This article describes four assessment tools that can be used in conjunction with undergraduate lab courses that provide the opportunity for the students to practice each of these essential communication skills.

Differentiation of PC12 cells.

This 3-week-long series of collaborative laboratory exercises explores how to use a cultured cell system (PC12 cells) to study signaling pathways involved in cellular differentiation. The laboratory would be useful in a neurobiology or cell biology course for advanced undergraduate students. The background and details for performing the lab are provided along with suggestions for assessing student performance and understanding.

2005: signaling breakthroughs of the year.

2005 was particularly notable for the range and scope of exciting advances in cell signaling research. Nominations from leading scientists ranged from plant signaling, neurobiology, and immunology to systems biology and structural biology. In plant biology, a new piece added to a long-standing puzzle in auxin signaling was discovered. The exploitation and regulation of RNA in cell signaling was also in the limelight. Intriguing new twists were highlighted in relation to functional and dysfunctional signaling in the brain, calcium-mediated signals, and the innate immune response. Finally, mathematical and statistical analysis of biochemical networks provided new insights into the circuitry of cell signaling pathways.

Daily oxygen rhythms.

The hypoxia response system and circadian clock system are interconnected.

Pseudophosphatase as E3 ubiquitin ligase inhibitor.

The pseudophosphatase STYX prevents the substrate recognition subunit FBXW7 from binding the catalytic E3 ubiquitin ligase complex.

Lysosomes get into the action.

Activity-dependent lysosomal fusion with the plasma membrane stimulates dendrite remodeling.