A global S. cerevisiae small ubiquitin-related modifier (SUMO) system interactome.

The small ubiquitin-related modifier (SUMO) system has been implicated in a number of biological functions, yet the individual components of the SUMO machinery involved in each of these activities were largely unknown. Here we report the first global SUMO system interactome. Using affinity purification coupled with mass spectrometry, we identify >450 protein-protein interactions surrounding the SUMO E2, Siz type E3s and SUMO-specific proteases in budding yeast. Exploiting this information-rich resource, we validate several Siz1- and Siz2-specific substrates, identify a nucleoporin required for proper Ulp1 localization, and uncover important new roles for Ubc9 and Ulp2 in the maintenance of ribosomal DNA.

IgA and IgG hypogammaglobulinemia in Waldenström's macroglobulinemia.

BACKGROUND: Hypogammaglobulinemia is common in Waldenström's macroglobulinemia. The etiology of this finding remains unclear, but it has been speculated to be based on tumor-induced suppression of the 'uninvolved' immunoglobulin production DESIGN AND METHODS: We evaluated the incidence of IgA and IgG hypogammaglobulinemia in 207 untreated patients with Waldenström's macroglobulinemia and investigated the associated clinicopathological findings and impact of therapy. We also sequenced eight genes (AICDA, BTK, CD40, CD154, NEMO, TACI, SH2D1A, UNG) implicated in immunoglobulin deficiency in 19 Waldenström's macroglobulinemia patients with IgA and/or IgG hypogammaglobulinemia. RESULTS: At baseline 63.3%, 58.0% and 49.3% of the 207 patients had abnormally low serum levels of IgA, IgG, or both. No association between IgA and IgG hypogammaglobulinemia and disease burden, serum IgM levels, beta(2)-microglobulin, International Prognostic Scoring System score, or incidence of recurrent infections was observed, although the presence of adenopathy and/or splenomegaly was associated with a lower incidence of hypogammaglobulinemia. Lower IgA and IgG levels were associated with disease progression in patients managed with a 'watch and wait' strategy. IgA and/or IgG levels remained abnormally low despite response to treatment, including complete remissions. A missense mutation in the highly conserved catalytic site of UNG was observed in a patient with hypogammaglobulinemia, warranting further study of this pathway in Waldenström's macroglobulinemia. CONCLUSIONS: IgA and IgG hypogammaglobulinemia is common in Waldenström's macroglobulinemia and persists despite therapeutic intervention and response. IgA and IgG hypogammaglobulinemia does not predict the risk of recurrent infections in patients with Waldenström's macroglobulinemia, although lower levels of serum IgA and IgG are associated with disease progression in Waldenström's macroglobulinemia patients being managed with a 'watch and wait' strategy.

Raw data for the identification of SUMOylated proteins in S. cerevisiae subjected to two types of osmotic shock, using affinity purification coupled with mass spectrometry.

The small ubiquitin-related modifier (SUMO) "stress response" (SSR) is a poorly understood evolutionarily conserved phenomenon in which steady-state SUMO conjugate levels are dramatically increased in response to environmental stresses. Here we describe the data acquired using affinity-purification coupled with mass spectrometry to identify proteins that are SUMOylated in response to two different types of osmotic stress, 1 M sorbitol and 1 M KCl. The mass spectrometry dataset described here has been uploaded to the MassIVE repository with ID: MSV000078739, and consists of 32 raw MS files acquired in data-dependent mode on a Thermo Q-Exactive instrument. iProphet-processed MS/MS search results and associated SAINT scores are also included as a reference. These data are discussed and interpreted in "The S. cerevisiae SUMO stress response is a conjugation-deconjugation cycle that targets the transcription machinery", by Lewicki et al. in the Journal of Proteomics, 2014 [1].

The S. cerevisiae SUMO stress response is a conjugation-deconjugation cycle that targets the transcription machinery.

The small ubiquitin-related modifier (SUMO) "stress response" (SSR) is a poorly understood evolutionarily conserved phenomenon in which steady-state SUMO conjugate levels are dramatically increased in response to environmental stresses. Here we characterize Saccharomyces cerevisiae SSR kinetics in response to several different types of stress, demonstrate that SSR activation and inactivation do not require protein synthesis or proteasome-dependent degradation, and establish that the SSR is effected primarily by the Siz1 E3 ligase and inactivated by the SUMO-specific protease Ulp2. Affinity purification coupled with mass spectrometry identifies the primary hyperosmotic SSR targets as components of the TFIID and mediator complexes, Pol II-associated mRNA maturation factors, chromatin remodeling proteins, and the transcriptional co-repressor Tup1-Cyc8. Consistent with these findings, our data also suggest that ongoing transcription (but not translation) is required to activate the SSR. The SSR thus does not appear to be directly linked to the stress itself, but likely represents a synchronized wave of sumoylation that occurs as a consequence of the large-scale, coordinated changes in the transcriptional program in response to environmental stress. BIOLOGICAL SIGNIFICANCE: SUMO is a ubiquitin-like protein with a number of important biological functions. Increased levels of sumoylation are associated with a number of human diseases, and previous reports have described an evolutionarily conserved "SUMO stress response" (SSR), in which SUMO conjugate levels are markedly increased in response to environmental stresses. However, the connection between cellular stress and sumoylation has remained poorly understood. Here we conduct the first in-depth characterization of the S. cerevisiae SSR. The SUMO system components required to effect it are identified, and SSR kinetics in response to different types of environmental stresses are established. Using mass spectrometry, we identify the principle osmotic shock-associated SSR targets as components of the basal transcription machinery, transcriptional regulators and chromatin remodeling complexes. Consistent with these data, we also observe that the sumoylation of SSR targets is dependent upon, and thus appears to be coupled with, transcription. Together, our data suggest that the SSR is not responsive to environmental stress per se, but more likely reflects a synchronized, transcription-coupled wave of sumoylation that accompanies the rapid, global re-programming of transcription in response to stress. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.

Global analysis of SUMO chain function reveals multiple roles in chromatin regulation.

Like ubiquitin, the small ubiquitin-related modifier (SUMO) proteins can form oligomeric "chains," but the biological functions of these superstructures are not well understood. Here, we created mutant yeast strains unable to synthesize SUMO chains (smt3(allR)) and subjected them to high-content microscopic screening, synthetic genetic array (SGA) analysis, and high-density transcript profiling to perform the first global analysis of SUMO chain function. This comprehensive assessment identified 144 proteins with altered localization or intensity in smt3(allR) cells, 149 synthetic genetic interactions, and 225 mRNA transcripts (primarily consisting of stress- and nutrient-response genes) that displayed a >1.5-fold increase in expression levels. This information-rich resource strongly implicates SUMO chains in the regulation of chromatin. Indeed, using several different approaches, we demonstrate that SUMO chains are required for the maintenance of normal higher-order chromatin structure and transcriptional repression of environmental stress response genes in budding yeast.

Family history of non-hematologic cancers among Waldenstrom macroglobulinemia patients: a preliminary study.

BACKGROUND: Little is known about the epidemiology and etiology of Waldenstrom macroglobulinemia (WM). Despite several studies of the relation between family history and B-cell disorders and WM, family history of non-hematologic cancers has not been systematically investigated. We thus examined associations of family history of breast, colorectal, lung, ovarian, and prostate cancers with WM. METHODS: All probands aged 20-79 years with bone marrow biopsy-confirmed diagnosis of WM between May 1, 1999 and January 1, 2010 at the Bing Center for Waldenstrom Macroglobulinemia were eligible for inclusion in our analysis. We reviewed medical records for eligible probands to determine family history of cancer (defined as a cancer diagnosis for ≥1 first-degree relative(s) of the proband). Using expected values constructed from the United States National Health Interview Survey, we estimated age- and race-standardized rate ratios (RRs) for family history of breast, colorectal, lung, ovarian, and prostate cancers by WM subtype. RESULTS: Family history of prostate cancer had the largest overall rate ratio (RR=1.4, 95% confidence limits [CL]: 1.1, 1.7), and among sporadic cases, family history of prostate and breast cancer had the largest rate ratios (prostate: RR=1.3, 95% CL: 1.1, 1.7; breast: RR=1.3, 95% CL: 1.2, 1.6). CONCLUSION: Our study suggests that it may be worthwhile to pursue these associations in a case-control study with uniform selection and data collection for cases and controls, and at least some record-based information on family history.

Associated malignancies in patients with Waldenström's macroglobulinemia and their kin.

We examined the incidence of other malignancies in 924 Waldenström's Macroglobulinemia (WM) patients and their kin. A total of 225 (24.3%) patients had ≥1 additional malignancy, with 63% predating the WM diagnosis. The most common gender-adjusted malignancies were prostate (9.4%), breast (8.0%), non-melanoma skin (7.1%), hematologic (2.8%), melanoma (2.2%), lung (1.4%) and thyroid 1.1%). Among hematologic malignancies, all 13 cases of diffuse large B-cell lymphoma and 4 cases of acute myelogenous leukemia were diagnosed after WM, and were therapy-related. Familial WM subgroup analysis showed a higher incidence of prostate cancer (P=.046) in sporadic WM patients, while patients with familial WM had a higher incidence of lung cancer (P=.0043). An increased incidence of myeloid leukemias (P<.0001) was reported among kin of familial WM patients. These data reveal specific cancer associations with WM, and provide a basis for exploratory studies aimed at delineating a common genetic basis. Additionally, these studies suggest specific cancer clustering based on familial predisposition to WM.