Preoperative risk factors for 1-year mortality in patients undergoing fenestrated endovascular aortic aneurysm repair in the US Aortic Research Consortium.

BACKGROUND: Early survival (1-year) after elective repair of complex abdominal aortic aneurysms (AAA) or thoracoabdominal aortic aneurysms (TAAA) can be used as an indicator of successful repair and provides a reasonable countermeasure to the annual rupture risk based on diameter. We aimed to identify preoperative factors associated with 1-year mortality after fenestrated or branched endovascular aortic repair (F/BEVAR) and develop a predictive model for 1-year mortality based on patient-specific risk profiles. METHODS: The US-Aortic Research Consortium database was queried for all patients undergoing elective F/BEVAR for complex AAA (cAAA) or TAAA from 2005 to 2022. The primary outcome was 1-year survival based on preoperative risk profile. Multivariable Cox regression was used to determine preoperative variables associated with 1-year mortality overall and by extent of aortic pathology. Logistic regression was performed to build a predictive model for 1-year mortality based on number of risk factors present. RESULTS: A total of 2099 patients met the inclusion criteria for this study (cAAA: n = 709 [34.3%]; type 1-3 TAAA: n = 777 [37.6%]; type 4-5 TAAA: n = 580 [28.1%]). Multivariable Cox regression identified the following significant risk factors associated with 1-year mortality: current smoker, chronic obstructive pulmonary disease, congestive heart failure (CHF), aortic diameter >7 cm, age >75 years, extent 1-3, creatinine >1.7 mg/dL, and hematocrit <36%. When stratified by extent of aortic involvement, multivariable Cox regression revealed risk factors for 1-year mortality in cAAA (CHF maximum aortic diameter >7 cm, hematocrit <36 mg/dL, and current smoking status), type 1-3 TAAA (chronic obstructive pulmonary disease, CHF, and age >75 years), and type 4-5 TAAA (age >75 years, creatinine >1.7 mg/dL, and hematocrit <36 mg/dL). Logistic regression was then used to develop a predictive model for 1-year mortality based on patient risk profile. Appraisal of the model revealed an area under the curve of 0.64 (P < .001), and an observed to expected ratio of 0.85. CONCLUSIONS: This study describes multiple risk factors associated with an increase in 1-year mortality after F/BEVAR. Given that elective repair of cAAA or TAAA is offered to some patients in whom future rupture risk outweighs operative risk, these findings suggest that highly comorbid patients with smaller aneurysms may not benefit from repair. Descriptive and predictive models for 1-year mortality based on patient risk profiles can serve as an adjunct in clinical decision-making when considering elective F/BEVAR.

Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex.

Epigenetic control of gene expression is crucial for maintaining gene regulation. Sin3 is an evolutionarily conserved repressor protein complex mainly associated with histone deacetylase (HDAC) activity. A large number of proteins are part of Sin3/HDAC complexes, and the function of most of these members remains poorly understood. SAP25, a previously identified Sin3A associated protein of 25 kDa, has been proposed to participate in regulating gene expression programs involved in the immune response but the exact mechanism of this regulation is unclear. SAP25 is not expressed in HEK293 cells, which hence serve as a natural knockout system to decipher the molecular functions uniquely carried out by this Sin3/HDAC subunit. Using molecular, proteomic, protein engineering, and interaction network approaches, we show that SAP25 interacts with distinct enzymatic and regulatory protein complexes in addition to Sin3/HDAC. While the O-GlcNAc transferase (OGT) and the TET1 /TET2/TET3 methylcytosine dioxygenases have been previously linked to Sin3/HDAC, in HEK293 cells, these interactions were only observed in the affinity purification in which an exogenously expressed SAP25 was the bait. Additional proteins uniquely recovered from the Halo-SAP25 pull-downs included the SCF E3 ubiquitin ligase complex SKP1/FBXO3/CUL1 and the ubiquitin carboxyl-terminal hydrolase 11 (USP11), which have not been previously associated with Sin3/HDAC. Finally, we use mutational analysis to demonstrate that distinct regions of SAP25 participate in its interaction with USP11, OGT/TETs, and SCF(FBXO3).) These results suggest that SAP25 may function as an adaptor protein to coordinate the assembly of different enzymatic complexes to control Sin3/HDAC-mediated gene expression.

Treatment Location Variation for Chronic Limb-Threatening Ischemia in Patients With Kidney Failure.

INTRODUCTION: End-stage kidney disease (ESKD) is an established risk factor for chronic limb-threatening ischemia (CLTI). Procedural location for ESKD patients has not been well described. This study aims to examine variation in index procedural location in ESKD versus non-ESKD patients undergoing peripheral vascular intervention for CLTI and identify preoperative risk factors for tibial interventions. METHODS: Chronic limb-threatening ischemia (CLTI) patients were identified in the Vascular Quality Initiative (VQI) peripheral vascular intervention dataset. Patient demographics and comorbidities were compared between patients with and without ESKD and those undergoing index tibial versus nontibial interventions. A multivariable logistic regression evaluating risk factors for tibial intervention was conducted. RESULTS: A total of 23,480 procedures were performed on CLTI patients with 13.6% (n = 3154) with ESKD. End-stage kidney disease (ESKD) patients were younger (66.56 ± 11.68 versus 71.66 ± 12.09 y old, P = 0.019), more often Black (40.6 versus 18.6%, P < 0.001), male (61.2 versus 56.5%, P < 0.001), and diabetic (81.8 versus 60.0%, P < 0.001) than non-ESKD patients. Patients undergoing index tibial interventions had higher rates of ESKD (19.4 versus 10.6%, P < 0.001) and diabetes (73.4 versus 57.5%, P < 0.001) and lower rates of smoking (49.9 versus 73.0%, P < 0.001) than patients with nontibial interventions. ESKD (odds ratio (OR) 1.67, 95% confidence interval (CI) 1.52-1.86, P < 0.001), Black race (OR 1.19, 95% CI 1.09-1.30, P < 0.001), and diabetes (OR 1.82, 95% CI 1.71-2.00, P < 0.001) were risk factors for tibial intervention. CONCLUSIONS: Patients with ESKD and CLTI have higher rates of diabetes and tibial disease and lower rates of smoking than non-ESKD patients. Tibial disease was associated with ESKD, diabetes, and Black race.

Distinct states of nucleolar stress induced by anticancer drugs.

Ribosome biogenesis is a vital and highly energy-consuming cellular function occurring primarily in the nucleolus. Cancer cells have an elevated demand for ribosomes to sustain continuous proliferation. This study evaluated the impact of existing anticancer drugs on the nucleolus by screening a library of anticancer compounds for drugs that induce nucleolar stress. For a readout, a novel parameter termed 'nucleolar normality score' was developed that measures the ratio of the fibrillar center and granular component proteins in the nucleolus and nucleoplasm. Multiple classes of drugs were found to induce nucleolar stress, including DNA intercalators, inhibitors of mTOR/PI3K, heat shock proteins, proteasome, and cyclin-dependent kinases (CDKs). Each class of drugs induced morphologically and molecularly distinct states of nucleolar stress accompanied by changes in nucleolar biophysical properties. In-depth characterization focused on the nucleolar stress induced by inhibition of transcriptional CDKs, particularly CDK9, the main CDK that regulates RNA Pol II. Multiple CDK substrates were identified in the nucleolus, including RNA Pol I- recruiting protein Treacle, which was phosphorylated by CDK9 in vitro. These results revealed a concerted regulation of RNA Pol I and Pol II by transcriptional CDKs. Our findings exposed many classes of chemotherapy compounds that are capable of inducing nucleolar stress, and we recommend considering this in anticancer drug development.

Ribosomes are cell structures within a compartment called the nucleolus that are required to make proteins, which are essential for cell function. Due to their uncontrolled growth and division, cancer cells require many proteins and therefore have a particularly high demand for ribosomes. Due to this, some anti-cancer drugs deliberately target the activities of the nucleolus. However, it was not clear if anti-cancer drugs with other targets also disrupt the nucleolus, which may result in side effects. Previously, it had been difficult to study how nucleoli work, partly because in human cells they vary naturally in shape, size, and number. Potapova et al. used fluorescent microscopy to develop a new way of assessing nucleoli based on the location and ratio of certain proteins. These measurements were used to calculate a "nucleolar normality score". Potapova et al. then tested over a thousand anti-cancer drugs in healthy and cancerous human cells. Around 10% of the tested drugs changed the nucleolar normality score when compared to placebo treatment, indicating that they caused nucleolar stress. For most of these drugs, the nucleolus was not the intended target, suggesting that disrupting it was an unintended side effect. Drugs inhibiting proteins called cyclin-dependent kinases caused the most drastic changes in the size and shape of nucleoli, disrupting them completely. These kinases are known to be involved in activating enzymes required for general transcription. Potapova et al. showed that they also are involved in production of ribosomal RNA, revealing an additional role in coordinating ribosome assembly. Taken together, the findings suggest that evaluating the effect of new anti-cancer drugs on the nucleolus could help to develop future treatments with less toxic side effects. The experiments also reveal new avenues for researching how cyclin-dependent kinases control the production of RNA more generally.

Accidental central venous catheter cannulation into aberrant arterial anatomy requiring endovascular intervention.

Central venous catheter placement continues to be an extremely common procedure throughout hospital systems. Although ultrasound guidance can mitigate some placement risks, misplacement of lines into neighboring structures, such as arteries, remains an unfortunate complication. In this report, we will discuss an 83-year-old female with aberrant left subclavian artery and right sided arch, which provided for successful stent graft coverage of arterial injury secondary to accidental subclavian artery cannulation with a central venous catheter with preservation of the right common carotid artery and avoidance of a potentially morbid sternotomy.

Differences in Long-Term Outcomes in End-Stage Kidney Disease Patients with Chronic Limb-Threatening Ischemia.

BACKGROUND: End-stage kidney disease (ESKD) is a risk factor for peripheral arterial disease and major adverse limb events following infra-inguinal bypass. Despite comprising an important patient population, ESKD patients are rarely analyzed as a subgroup and are underrepresented in vascular surgery guidelines. This study aims to compare the long-term outcomes of patients with and without ESKD undergoing endovascular peripheral vascular intervention (PVI) for chronic limb-threatening ischemia (CLTI). METHODS: CLTI patients with and without ESKD from 2007-2020 were identified in the Vascular Quality Initiative PVI dataset. Patients with prior bilateral interventions were excluded. Patients undergoing femoral-popliteal and tibial interventions were included. Mortality, reintervention, amputation, and occlusion rates at 21 months following intervention were examined. Statistical analyses were completed with the t-test, chi-square, and Kaplan-Meier curves. RESULTS: The ESKD cohort was younger (66.4 ± 11.8 vs. 71.6 ± 12.1 years, P < 0.001) with higher rates of diabetes (82.2 vs. 60.9%, P < 0.001) the non-ESKD cohort. Long-term follow-up was available for 58.4% (N = 2,128 procedures) of ESKD patients and 60.8% (N = 13,075 procedures) of non-ESKD patients. At 21 months, ESKD patients had a higher mortality (41.7 vs. 17.4%, P < 0.001) and a higher amputation rate (22.3 vs. 7.1%, P < 0.001); however, they had a lower reintervention rate (13.2 vs. 24.6%, P < 0.001). CONCLUSIONS: CLTI patients with ESKD have worse long-term outcomes at 2 years following PVI than non-ESKD patients. Mortality and amputation are higher with ESKD, while the reintervention rate is lower. Development of guidelines within the ESKD population has the potential to improve limb salvage.

Investigating glycemic control in patients undergoing lower extremity bypass within an enhanced recovery pathway at a single institution.

BACKGROUND: Enhanced recovery pathways (ERPs) aim to lower perioperative stress to facilitate recovery. Limited fasting combined with carbohydrate loading is a common ERP element. The effect of limited fasting has not been elucidated in patients with diabetes. Given the known deleterious effects of poor glycemic control in the perioperative period, such as increased rates of surgical site infection, the associations of preoperative limited fasting with perioperative glycemic control and early outcomes after lower extremity bypass (LEB) were investigated. METHODS: A single institutional retrospective review of patients who underwent infrainguinal LEB from 2016 to 2022 was performed. The ERP was initiated in May 2018. Patients were stratified by diabetes diagnosis and preoperative hemoglobin A1C (HbA1C) levels. Perioperative glycemic control was compared between the limited fasting and traditional fasting patients (nil per os at midnight). Limited fasting was defined as a clear liquid diet until 2 hours before surgery with recommended carbohydrate loading consisting of 400 cc of a clear sports drink (approximately 30 g of carbohydrates). All limited fasting patients were within the ERP. Early perioperative hyperglycemia (EPH) was defined as blood glucose of >180 mg/dL within the first 24 hours of surgery. Perioperative outcomes such as surgical site infection, readmission, reinterventions, and complications were also compared. RESULTS: A total of 393 patients were included (limited fasting patients N = 135; traditional fasting patients N = 258). A trend toward EPH was seen in all limited fasting groups. Evaluating limited fasting within diabetic patients revealed that 74.5% of limited fasting-diabetic patients had EPH compared with 49.6% of traditional fasting-diabetic patients (P = .001). When stratified by the HbA1C level, a significantly higher rate of EPH was seen in the HbA1c >8.0% groups, with 90.5% in the limited fasting patients compared with 67.9% in traditional fasting patients (P = .05). Limited fasting-diabetic patients experience a longer postoperative length of stay at 5.0 days (interquartile range: 3, 9) vs 4.0 days (2, 6) in nondiabetic patients (P = .016). CONCLUSIONS: ERP limited fasting was associated with early perioperative hyperglycemia after LEB, particularly in patients with HbA1C >8.0%. Due to the high prevalence of diabetic patients undergoing LEB under ERP, the role of limited fasting and common glycemic elements of ERP may need to be re-evaluated in this subpopulation.

Serial Capture Affinity Purification and Integrated Structural Modeling of the H3K4me3 Binding and DNA Damage Related WDR76:SPIN1 Complex.

WDR76 is a multifunctional protein involved in many cellular functions. With a diverse and complicated protein interaction network, dissecting the structure and function of specific WDR76 complexes is needed. We previously demonstrated the ability of the Serial Capture Affinity Purification (SCAP) method to isolate specific complexes by introducing two proteins of interest as baits at the same time. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone marker reader that specifically recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to the SCAP analysis of the SPIN1:SPINDOC complex, H3K4me3 was copurified with the WDR76:SPIN1 complex. In combination with crosslinking mass spectrometry, we built an integrated structural model of the complex which revealed that SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Lastly, interaction network analysis of copurifying proteins revealed the potential role of the WDR76:SPIN1 complex in the DNA damage response. Teaser: In contrast to the SPINDOC/SPIN1 complex, analyses reveal that the WDR76/SPIN1 complex interacts with core histones and is involved in DNA damage.

Aortic visceral segment instability is evident following thoracic endovascular aortic repair for acute and subacute type B aortic dissection.

BACKGROUND: Anatomic remodeling within the thoracic aorta following thoracic endovascular aortic repair (TEVAR) for type B aortic dissection (TBAD) has been well documented. However, less is known about the response of the untreated visceral aorta. In the present study, we investigated the visceral aortic behavior after TEVAR for acute or subacute TBAD to identify any associations with the clinical outcomes. METHODS: A multicenter retrospective review was performed of all imaging studies for all patients who had undergone TEVAR for acute (0-14 days) and subacute (14-90 days) nontraumatic TBAD from 2006 to 2020. The cohort was inclusive of those with uncomplicated, high-risk, and complicated (defined in accordance with the Society for Vascular Surgery reporting guidelines) dissections. Centerline aortic measurements of the true and false lumen and total aortic diameter (TAD) were taken at standardized locations relative to the aortic anatomy within each aortic zone (the zones were defined by the Society for Vascular Surgery reporting guidelines). Diameter changes over time were evaluated using repeated measures mixed effects linear growth modeling. Visceral segment instability (VSI) was defined as any growth in the TAD of ≥5 mm within aortic zones 5 through 9. RESULTS: A total of 82 patients were identified. The median length of imaging follow-up was 2.1 years (interquartile range, 0.75-4.5 years), with 15% of the cohort having follow-up >5 years. VSI was present in 55% of the cohort, with an average maximal increase in the TAD of 10.4 ± 6.3 mm during a median follow-up of 2.1 years (interquartile range, 0.75-4.5 years). Approximately one third of the cohort had experienced rapid VSI (growth ≥5 mm in the first year), and 4.8% of the cohort had developed a large paravisceral aortic aneurysm (TAD ≥5 cm) secondary to VSI. Linear growth modeling identified significant predictable growth in the TAD across all visceral zones. Zone 7 had the highest rate of TAD dilation, with a fixed effect estimated rate of 1.3 mm/y (95% confidence interval [CI], 0.23-2.1; P = .022). The preoperative factor most strongly associated with VSI was a cumulative number of zones dissected of six or more (odds ratio, 6.4; 95% CI, 1.07-8.6; P = .041). The odds for aortic reintervention were significantly increased for cases in which VSI led to the development of a paravisceral aortic aneurysm of ≥5 cm (odds ratio, 3.7; 95% CI, 1.1-13; P = .038). CONCLUSIONS: VSI was identified in most patients who had undergone TEVAR for management of acute and subacute TBAD. The preoperative anatomic features such as the dissection extent, rather than the procedural details of graft coverage, might play a more significant role in VSI occurrence. Significant TAD growth had occurred in all visceral segments. These results highlight the importance of lifelong surveillance following TEVAR and identified a subset of patients who might have an increased risk of reintervention.

Perturbation of BRMS1 interactome reveals pathways that impact metastasis.

Breast Cancer Metastasis Suppressor 1 (BRMS1) expression is associated with longer patient survival in multiple cancer types. Understanding BRMS1 functionality will provide insights into both mechanism of action and will enhance potential therapeutic development. In this study, we confirmed that the C-terminus of BRMS1 is critical for metastasis suppression and hypothesized that critical protein interactions in this region would explain its function. Phosphorylation status at S237 regulates BRMS1 protein interactions related to a variety of biological processes, phenotypes [cell cycle (e.g., CDKN2A), DNA repair (e.g., BRCA1)], and metastasis [(e.g., TCF2 and POLE2)]. Presence of S237 also directly decreased MDA-MB-231 breast carcinoma migration in vitro and metastases in vivo. The results add significantly to our understanding of how BRMS1 interactions with Sin3/HDAC complexes regulate metastasis and expand insights into BRMS1's molecular role, as they demonstrate BRMS1 C-terminus involvement in distinct protein-protein interactions.

Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling.

The SNF2 family ATPase Amplified in Liver Cancer 1 (ALC1) is the only chromatin remodeling enzyme with a poly(ADP-ribose) (PAR) binding macrodomain. ALC1 functions together with poly(ADP-ribose) polymerase PARP1 to remodel nucleosomes. Activation of ALC1 cryptic ATPase activity and the subsequent nucleosome remodeling requires binding of its macrodomain to PAR chains synthesized by PARP1 and NAD+ A key question is whether PARP1 has a role(s) in ALC1-dependent nucleosome remodeling beyond simply synthesizing the PAR chains needed to activate the ALC1 ATPase. Here, we identify PARP1 separation-of-function mutants that activate ALC1 ATPase but do not support nucleosome remodeling by ALC1. Investigation of these mutants has revealed multiple functions for PARP1 in ALC1-dependent nucleosome remodeling and provides insights into its multifaceted role in chromatin remodeling.

Driving integrative structural modeling with serial capture affinity purification.

Streamlined characterization of protein complexes remains a challenge for the study of protein interaction networks. Here we describe serial capture affinity purification (SCAP), in which two separate proteins are tagged with either the HaloTag or the SNAP-tag, permitting a multistep affinity enrichment of specific protein complexes. The multifunctional capabilities of this protein-tagging system also permit in vivo validation of interactions using acceptor photobleaching Förster resonance energy transfer and fluorescence cross-correlation spectroscopy quantitative imaging. By coupling SCAP to cross-linking mass spectrometry, an integrative structural model of the complex of interest can be generated. We demonstrate this approach using the Spindlin1 and SPINDOC protein complex, culminating in a structural model with two SPINDOC molecules docked on one SPIN1 molecule. In this model, SPINDOC interacts with the SPIN1 interface previously shown to bind a lysine and arginine methylated sequence of histone H3. Our approach combines serial affinity purification, live cell imaging, and cross-linking mass spectrometry to build integrative structural models of protein complexes.

Differential Complex Formation via Paralogs in the Human Sin3 Protein Interaction Network.

Despite the continued analysis of HDAC inhibitors in clinical trials, the heterogeneous nature of the protein complexes they target limits our understanding of the beneficial and off-target effects associated with their application. Among the many HDAC protein complexes found within the cell, Sin3 complexes are conserved from yeast to humans and likely play important roles as regulators of transcriptional activity. The presence of two Sin3 paralogs in humans, SIN3A and SIN3B, may result in a heterogeneous population of Sin3 complexes and contributes to our poor understanding of the functional attributes of these complexes. Here, we profile the interaction networks of SIN3A and SIN3B to gain insight into complex composition and organization. In accordance with existing data, we show that Sin3 paralog identity influences complex composition. Additionally, chemical cross-linking MS identifies domains that mediate interactions between Sin3 proteins and binding partners. The characterization of rare SIN3B proteoforms provides additional evidence for the existence of conserved and divergent elements within human Sin3 proteins. Together, these findings shed light on both the shared and divergent properties of human Sin3 proteins and highlight the heterogeneous nature of the complexes they organize.

Integrative Modeling of a Sin3/HDAC Complex Sub-structure.

Sin3/HDAC complexes function by deacetylating histones, condensing chromatin, and modulating gene expression. Although components used to build these complexes have been well defined, we still have only a limited understanding of the structure of the Sin3/HDAC subunits assembled around the scaffolding protein SIN3A. To characterize the spatial arrangement of Sin3 subunits, we combined Halo affinity capture, chemical crosslinking, and high-resolution mass spectrometry (XL-MS) to determine intersubunit distance constraints, identifying 66 interprotein and 63 self-crosslinks for 13 Sin3 subunits. Having assessed crosslink authenticity by mapping self-crosslinks onto existing structures, we used distance restraints from interprotein crosslinks to guide assembly of a Sin3 complex substructure. We identified the relative positions of subunits SAP30L, HDAC1, SUDS3, HDAC2, and ING1 around the SIN3A scaffold. The architecture of this subassembly suggests that multiple factors have space to assemble to collectively influence the behavior of the catalytic subunit HDAC1.

Purification and enzymatic assay of class I histone deacetylase enzymes.

The reversible acetylation of histones has a profound influence on transcriptional status. Histone acetyltransferases catalyze the addition of these chemical modifications to histone lysine residues. Conversely, histone deacetylases (HDACs) catalyze the removal of these acetyl groups from histone lysine residues. As modulators of transcription, HDACs have found themselves as targets of several FDA-approved chemotherapeutic compounds which aim to inhibit enzyme activity. The ongoing efforts to develop targeted and isoform-specific HDAC inhibitors necessitates tools to study these modifications and the enzymes that maintain an equilibrium of these modifications. In this chapter, we present an optimized workflow for the isolation of recombinant protein and subsequent assay of class I HDAC activity. We demonstrate the application of this assay by assessing the activities of recombinant HDAC1, HDAC2, and SIN3B. This assay system utilizes readily available reagents and can be used to assess the activity and responsiveness of class I HDAC complexes to HDAC inhibitors.

Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly.

HDAC1 and HDAC2 are components of several corepressor complexes (NuRD, Sin3, CoREST and MiDAC) that regulate transcription by deacetylating histones resulting in a more compact chromatin environment. This limits access of transcriptional machinery to genes and silences transcription. While using an AP-MS approach to map HDAC1/2 protein interaction networks, we noticed that N-terminally tagged versions of HDAC1 and HDAC2 did not assemble into HDAC corepressor complexes as expected, but instead appeared to be stalled with components of the prefoldin-CCT chaperonin pathway. These N-terminally tagged HDACs were also catalytically inactive. In contrast to the N-terminally tagged HDACs, C-terminally tagged HDAC1 and HDAC2 captured complete histone deacetylase complexes and the purified proteins had deacetylation activity that could be inhibited by SAHA (Vorinostat), a Class I/II HDAC inhibitor. This tag-mediated reprogramming of the HDAC1/2 protein interaction network suggests a mechanism whereby HDAC1 is first loaded into the CCT complex by prefoldin to complete folding, and then assembled into active, functional HDAC complexes. Imaging revealed that the prefoldin subunit VBP1 colocalises with nuclear HDAC1, suggesting that delivery of HDAC1 to the CCT complex happens in the nucleus.

A Structured Workflow for Mapping Human Sin3 Histone Deacetylase Complex Interactions Using Halo-MudPIT Affinity-Purification Mass Spectrometry.

Although a variety of affinity purification mass spectrometry (AP-MS) strategies have been used to investigate complex interactions, many of these are susceptible to artifacts because of substantial overexpression of the exogenously expressed bait protein. Here we present a logical and systematic workflow that uses the multifunctional Halo tag to assess the correct localization and behavior of tagged subunits of the Sin3 histone deacetylase complex prior to further AP-MS analysis. Using this workflow, we modified our tagging/expression strategy with 21.7% of the tagged bait proteins that we constructed, allowing us to quickly develop validated reagents. Specifically, we apply the workflow to map interactions between stably expressed versions of the Sin3 subunits SUDS3, SAP30, or SAP30L and other cellular proteins. Here we show that the SAP30 and SAP30L paralogues strongly associate with the core Sin3 complex, but SAP30L has unique associations with the proteasome and the myelin sheath. Next, we demonstrate an advancement of the complex NSAF (cNSAF) approach, in which normalization to the scaffold protein SIN3A accounts for variations in the proportion of each bait capturing Sin3 complexes and allows a comparison among different baits capturing the same protein complex. This analysis reveals that although the Sin3 subunit SUDS3 appears to be used in both SIN3A and SIN3B based complexes, the SAP30 subunit is not used in SIN3B based complexes. Intriguingly, we do not detect the Sin3 subunits SAP18 and SAP25 among the 128 high-confidence interactions identified, suggesting that these subunits may not be common to all versions of the Sin3 complex in human cells. This workflow provides the framework for building validated reagents to assemble quantitative interaction networks for chromatin remodeling complexes and provides novel insights into focused protein interaction networks.

Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer.

Understanding the complexity of cancer biology requires extensive information about the cancer proteome over the course of the disease. The recent advances in mass spectrometry-based proteomics technologies have led to the accumulation of an incredible amount of such proteomic information. This information allows us to identify protein signatures or protein biomarkers, which can be used to improve cancer diagnosis, prognosis and treatment. For example, mass spectrometry-based proteomics has been used in breast cancer research for over two decades to elucidate protein function. Breast cancer is a heterogeneous group of diseases with distinct molecular features that are reflected in tumour characteristics and clinical outcomes. Compared with all other subtypes of breast cancer, triple-negative breast cancer is perhaps the most distinct in nature and heterogeneity. In this review, we provide an introductory overview of the application of advanced proteomic technologies to triple-negative breast cancer research.

SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.

RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down of 12 nuclear and cytoplasmic RBPs followed by quantitative mass spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependent manner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinity precipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONAR identifies 1,923 human, 489 fly, and 745 yeast RBPs, including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins.