Chemical chaperones reverse early suppression of regulatory circuits during unfolded protein response in B cells from common variable immunodeficiency patients

B cells orchestrate pro-survival and pro-apoptotic inputs during unfolded protein response (UPR) to translate, fold, sort, secrete and recycle immunoglobulins. In common variable immunodeficiency (CVID) patients, activated B cells are predisposed to an overload of abnormally processed, misfolded immunoglobulins. Using highly accurate transcript measurements, we show that expression of UPR genes and immunoglobulin chains differs qualitatively and quantitatively during the first 4 h of chemically induced UPR in B cells from CVID patients and a healthy subject. We tested thapsigargin or tunicamycin as stressors and 4-phenylbutyrate, dimethyl sulfoxide and tauroursodeoxycholic acid as chemical chaperones. We found an early and robust decrease of the UPR upon endoplasmic reticulum (ER) stress in CVID patient cells compared to the healthy control consistent with the disease phenotype. The chemical chaperones increased the UPR in the CVID patient cells in response to the stressors, suggesting that misfolded immunoglobulins were stabilized. We suggest that the AMP-dependent transcription factor alpha branch of the UPR is disturbed in CVID patients, underlying the observed expression behavior.

A protein-centric approach for exome variant aggregation enables sensitive association analysis with clinical outcomes

Somatic mutations are early drivers of tumorigenesis and tumor progression. However, the mutations typically occur at variable positions across different individuals, resulting in the data being too sparse to test meaningful associations between variants and phenotypes. To overcome this challenge, we devised a novel approach called Gene-to-Protein-to-Disease (GPD) which accumulates variants into new sequence units as the degree of genetic assault on structural or functional units of each protein. The variant frequencies in the sequence units were highly reproducible between two large cancer cohorts. Survival analysis identified 232 sequence units in which somatic mutations had deleterious effects on overall survival, including consensus driver mutations obtained from multiple calling algorithms. By contrast, around 76% of the survival predictive units had been undetected by conventional gene-level analysis. We demonstrate the ability of these signatures to separate patient groups according to overall survival, therefore, providing novel prognostic tools for various cancers. GPD also identified sequence units with somatic mutations whose impact on survival was modified by the occupancy of germline variants in the surrounding regions. The findings indicate that a patient's genetic predisposition interacts with the effect of somatic mutations on survival outcomes in some cancers.

Polyubiquitin Chains Linked by Lysine Residue 48 (K48) Selectively Target Oxidized Proteins In Vivo

Aims: Ubiquitin is a highly conserved protein modifier that heavily accumulates during the oxidative stress response. Here, we investigated the role of the ubiquitination system, particularly at the linkage level, in the degradation of oxidized proteins. The function of ubiquitin in the removal of oxidized proteins remains elusive because of the wide range of potential targets and different roles that polyubiquitin chains play. Therefore, we describe in detail the dynamics of the K48 ubiquitin response as the canonical signal for protein degradation. We identified ubiquitin targets and defined the relationship between protein ubiquitination and oxidation during the stress response. Results: Combining oxidized protein isolation, linkage-specific ubiquitination screens, and quantitative proteomics, we found that K48 ubiquitin accumulated at both the early and late phases of the stress response. We further showed that a fraction of oxidized proteins are conjugated with K48 ubiquitin. We identified ∼750 ubiquitinated proteins and ∼400 oxidized proteins that were modified during oxidative stress, and around half of which contain both modifications. These proteins were highly abundant and function in translation and energy metabolism. Innovation and Conclusion: Our work showed for the first time that K48 ubiquitin modifies a large fraction of oxidized proteins, demonstrating that oxidized proteins can be targeted by the ubiquitin/proteasome system. We suggest that oxidized proteins that rapidly accumulate during stress are subsequently ubiquitinated and degraded during the late phase of the response. This delay between oxidation and ubiquitination may be necessary for reprogramming protein dynamics, restoring proteostasis, and resuming cell growth.

Exploiting Interdata Relationships in Next-generation Proteomics Analysis

Mass spectrometry based proteomics and other technologies have matured to enable routine quantitative, system-wide analysis of concentrations, modifications, and interactions of proteins, mRNAs, and other molecules. These studies have allowed us to move toward a new field concerned with mining information from the combination of these orthogonal data sets, perhaps called "integromics." We highlight examples of recent studies and tools that aim at relating proteomic information to mRNAs, genetic associations, and changes in small molecules and lipids. We argue that productive data integration differs from parallel acquisition and interpretation and should move toward quantitative modeling of the relationships between the data. These relationships might be expressed by temporal information retrieved from time series experiments, rate equations to model synthesis and degradation, or networks of causal, evolutionary, physical, and other interactions. We outline steps and considerations toward such integromic studies to exploit the synergy between data sets.

iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery

Computational tools for multiomics data integration have usually been designed for unsupervised detection of multiomics features explaining large phenotypic variations. To achieve this, some approaches extract latent signals in heterogeneous data sets from a joint statistical error model, while others use biological networks to propagate differential expression signals and find consensus signatures. However, few approaches directly consider molecular interaction as a data feature, the essential linker between different omics data sets. The increasing availability of genome-scale interactome data connecting different molecular levels motivates a new class of methods to extract interactive signals from multiomics data. Here we developed iOmicsPASS, a tool to search for predictive subnetworks consisting of molecular interactions within and between related omics data types in a supervised analysis setting. Based on user-provided network data and relevant omics data sets, iOmicsPASS computes a score for each molecular interaction, and applies a modified nearest shrunken centroid algorithm to the scores to select densely connected subnetworks that can accurately predict each phenotypic group. iOmicsPASS detects a sparse set of predictive molecular interactions without loss of prediction accuracy compared to alternative methods, and the selected network signature immediately provides mechanistic interpretation of the multiomics profile representing each sample group. Extensive simulation studies demonstrate clear benefit of interaction-level modeling. iOmicsPASS analysis of TCGA/CPTAC breast cancer data also highlights new transcriptional regulatory network underlying the basal-like subtype as positive protein markers, a result not seen through analysis of individual omics data.

Stem cell-derived cranial and spinal motor neurons reveal proteostatic differences between ALS resistant and sensitive motor neurons

In amyotrophic lateral sclerosis (ALS) spinal motor neurons (SpMN) progressively degenerate while a subset of cranial motor neurons (CrMN) are spared until late stages of the disease. Using a rapid and efficient protocol to differentiate mouse embryonic stem cells (ESC) to SpMNs and CrMNs, we now report that ESC-derived CrMNs accumulate less human (h)SOD1 and insoluble p62 than SpMNs over time. ESC-derived CrMNs have higher proteasome activity to degrade misfolded proteins and are intrinsically more resistant to chemically-induced proteostatic stress than SpMNs. Chemical and genetic activation of the proteasome rescues SpMN sensitivity to proteostatic stress. In agreement, the hSOD1 G93A mouse model reveals that ALS-resistant CrMNs accumulate less insoluble hSOD1 and p62-containing inclusions than SpMNs. Primary-derived ALS-resistant CrMNs are also more resistant than SpMNs to proteostatic stress. Thus, an ESC-based platform has identified a superior capacity to maintain a healthy proteome as a possible mechanism to resist ALS-induced neurodegeneration.

Nucleobindins and encoded peptides: From cell signaling to physiology

Nucleobindins (NUCBs) are DNA and calcium binding, secreted proteins with various signaling functions. Two NUCBs, nucleobindin-1 (NUCB1) and nucleobindin-2 (NUCB2), were discovered during the 1990s. These two peptides are shown to have diverse functions, including the regulation of inflammation and bone formation, among others. In 2006, Oh-I and colleagues discovered that three peptides encoded within the NUCB2 could be processed by prohormone convertases. These peptides were named nesfatin-1, 2 and 3, mainly due to the satiety and fat influencing properties of nesfatin-1. However, it was found that nesfatin-2 and -3 have no such effects. Nesfatin-1, especially its mid-segment, is very highly conserved across vertebrates. Although the receptor(s) that mediate nesfatin-1 effects are currently unknown, it is now considered an endogenous peptide with multiple functions, affecting central and peripheral tissues to regulate metabolism, reproduction, endocrine and other functions. We recently identified a nesfatin-1-like peptide (NLP) encoded within the NUCB1. Like nesfatin-1, NLP suppressed feed intake in mice and fish, and stimulated insulin secretion from pancreatic beta cells. There is considerable evidence available to indicate that nucleobindins and its encoded peptides are multifunctional regulators of cell biology and whole animal physiology. This review aims to briefly discuss the structure, distribution, functions and mechanism of action nucleobindins and encoded peptides.

Abstract P4-01-07: A comprehensive liquid biopsy in patients undergoing neoadjuvant therapy

Background: Precision medicine is revolutionizing breast cancer (BC) care. Comprehensive liquid biopsies are a tool for personalized care in patients with locally advanced breast cancer (LABC). Identifying robust biomarkers as part of a comprehensive liquid biopsy to predict response to treatment is of immense clinical interest.

Methods: After obtaining IRB approval, serial blood samples were collected from patients with LABC undergoing neoadjuvant therapy. Paired biopsies were collected prior to treatment and were sent to Foundation Medicine for next-generation sequencing (NGS). We used a sized-base microfilter technology to capture circulating tumor cells (CTCs) and circulating cancer associated fibroblasts (cCAFs). Patients with one or more CTCs or cCAFs were deemed positive for these tests. Additionally, in collaboration with Foundation Medicine, we extracted circulating tumor DNA (ctDNA) and we analyzed it using the FoundationACT platform. Patients with a detectable genomic alteration in their plasma were considered as having a positive ctDNA test. Our primary objective is to determine if a comprehensive liquid biopsy can serve as a prognostic marker of pathologic complete response (pCR).

Results: For this analysis we describe our findings in the initial blood draw of the first 18 patients enrolled. The mean age is 54 years (38-70). All patients who had their tumors sequenced had a detectable mutation. Consistent with the findings of others, we found TP53 mutations to be the most prevalent at 83.3%. We found that 44% of patients had ctDNA, 68.4% had cCAFs and 78.9% had CTCs. Many patients also had clusters of cells, consisting of one cell type, or co-clusters, consisting of both. 38.9% had CTC clusters, 16.7% had cCAF clusters and 16.7% had co-clusters (CTCs and cCAFs together). Some patients with CTCs did not have cCAFs and vice versa. The number of CTCs and cCAFS did not correlate with stage of disease or receptor status.

Conclusions: We describe a comprehensive liquid biopsy combining a sized-based microfilter technology for CTC and cCAFs identification and the FoundationACT platform for ctDNA analysis is feasible and these biomarkers can be detected in patients with LABC prior to the initiation of neoadjuvant therapy. Our study is accruing rapidly, and we will update our results with the longitudinal collection and the prognostic value of a comprehensive liquid biopsy at the time of the meeting.

Citation Format: Sandoval Leon AC, Medina Saenz K, Miller P, Benson A, Calfa C, Mahtani R, Slingerland J, Perez A, Vogel C, Valdes-Albini F, El-Ashry D, Lippman M. A comprehensive liquid biopsy in patients undergoing neoadjuvant therapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-01-07.

Marie M, Stickney K, VanBuecken D, Vellek B, Webber C, Allen L, Bollyk J, Hilderman N, Ismail H, Lamola S, Sanda S, Vendettuoli H, Tridgell D, Monzavi R, Bock M, Fisher L, Halvorson M, Jeandron D, Kim M, Wood J, Geffner M, Kaufman F, Parkman R, Salazar C, Goland R, Clynes R, Cook S, Freeby M, Pat Gallagher M, Gandica R, Greenberg E, Kurland A, Pollak S, Wolk A, Chan M, Koplimae L, Levine E, Smith K, Trast J, DiMeglio L, Blum J, Evans-Molina C, Hufferd R, Jagielo B, Kruse C, Patrick V, Rigby M, Spall M, Swinney K, Terrell J, Christner L, Ford L, Lynch S, Menendez M, Merrill P, Pescovitz M, Rodriguez H, Alleyn C, Baidal D, Fay S, Gaglia J, Resnick B, Szubowicz S, Weir G, Benjamin R, Conboy D, deManbey A, Jackson R, Jalahej H, Orban T, Ricker A, Wolfsdorf J, Zhang HH, Wilson D, Aye T, Baker B, Barahona K, Buckingham B, Esrey K, Esrey T, Fathman G, Snyder R, Aneja B, Chatav M, Espinoza O, Frank E, Liu J, Perry J, Pyle R, Rigby A, Riley K, Soto A, Gitelman S, Adi S, Anderson M, Berhel A, Breen K, Fraser K, Gerard-Gonzalez A, Jossan P, Lustig R, Moassesfar S, Mugg A, Ng D, Prahalod P, Rangel-Lugo M, Sanda S, Tarkoff J, Torok C, Wesch R, Aslan I, Buchanan J, Cordier J, Hamilton C, Hawkins L, Ho T, Jain A, Ko K, Lee T, Phelps S, Rosenthal S, Sahakitrungruang T, Stehl L, Taylor L, Wertz M, Wong J, Philipson L, Briars R, Devine N, Littlejohn E, Grant T, Gottlieb P, Klingensmith G, Steck A, Alkanani A, Bautista K, Bedoy R, Blau A, Burke B, Cory L, Dang M, Fitzgerald-Miller L, Fouts A, Gage V, Garg S, Gesauldo P, Gutin R, Hayes C, Hoffman M, Ketchum K, Logsden-Sackett N, Maahs D, Messer L, Meyers L, Michels A, Peacock S, Rewers M, Rodriguez P, Sepulbeda F, Sippl R, Steck A, Taki I, Tran BK, Tran T, Wadwa RP, Zeitler P, Barker J, Barry S, Birks L, Bomsburger L, Bookert T, Briggs L, Burdick P, Cabrera R, Chase P, Cobry E, Conley A, Cook G, Daniels J, DiDomenico D, Eckert J, Ehler A, Eisenbarth G, Fain P, Fiallo-Scharer R, Frank N, Goettle H, Haarhues M, Harris S, Horton L, Hutton J, Jeffrrey J, Jenison R, Jones K, Kastelic W, King MA, Lehr D, Lungaro J, Mason K, Maurer H, Nguyen L, Proto A, Realsen J, Schmitt K, Schwartz M, Skovgaard S, Smith J, Vanderwel B, Voelmle M, Wagner R, Wallace A, Walravens P, Weiner L, Westerhoff B, Westfall E, Widmer K, Wright H, Schatz D, Abraham A, Atkinson M, Cintron M, Clare-Salzler M, Ferguson J, Haller M, Hosford J, Mancini D, Rohrs H, Silverstein J, Thomas J, Winter W, Cole G, Cook R, Coy R, Hicks E, Lewis N, Marks J, Pugliese A, Blaschke C, Matheson D, Pugliese A, Sanders-Branca N, Ray Arce LA, Cisneros M, Sabbag S, Moran A, Gibson C, Fife B, Hering B, Kwong C, Leschyshyn J, Nathan B, Pappenfus B, Street A, Boes MA, Peterson Eck S, Finney L, Albright Fischer T, Martin A, Jacqueline Muzamhindo C, Rhodes M, Smith J, Wagner J, Wood B, Becker D, Delallo K, Diaz A, Elnyczky B, Libman I, Pasek B, Riley K, Trucco M, Copemen B, Gwynn D, Toledo F, Rodriguez H, Bollepalli S, Diamond F, Eyth E, Henson D, Lenz A, Shulman D, Raskin P, Adhikari S, Dickson B, Dunnigan E, Lingvay I, Pruneda L, Ramos-Roman M, Raskin P, Rhee C, Richard J, Siegelman M, Sturges D, Sumpter K, White P, Alford M, Arthur J, Aviles-Santa ML, Cordova E, Davis R, Fernandez S, Fordan S, Hardin T, Jacobs A, Kaloyanova P, Lukacova-Zib I, Mirfakhraee S, Mohan A, Noto H, Smith O, Torres N, Wherrett D, Balmer D, Eisel L, Kovalakovska R, Mehan M, Sultan F, Ahenkorah B, Cevallos J, Razack N, Jo Ricci M, Rhode A, Srikandarajah M, Steger R, Russell WE, Black M, Brendle F, Brown A, Moore D, Pittel E, Robertson A, Shannon A, Thomas JW, Herold K, Feldman L, Sherwin R, Tamborlane W, Weinzimer S, Toppari J, Kallio T, Kärkkäinen M, Mäntymäki E, Niininen T, Nurmi B, Rajala P, Romo M, Suomenrinne S, Näntö-Salonen K, Simell O, Simell T, Bosi E, Battaglia M, Bianconi E, Bonfanti R, Grogan P, Laurenzi A, Martinenghi S, Meschi F, Pastore M, Falqui L, Teresa Muscato M, Viscardi M, Bingley P, Castleden H, Farthing N, Loud S, Matthews C, McGhee J, Morgan A, Pollitt J, Elliot-Jones R, Wheaton C, Knip M, Siljander H, Suomalainen H, Colman P, Healy F, Mesfin S, Redl L, Wentworth J, Willis J, Farley M, Harrison L, Perry C, Williams F, Mayo A, Paxton J, Thompson V, Volin L, Fenton C, Carr L, Lemon E, Swank M, Luidens M, Salgam M, Sharma V, Schade D, King C, Carano R, Heiden J, Means N, Holman L, Thomas I, Madrigal D, Muth T, Martin C, Plunkett C, Ramm C, Auchus R, Lane W, Avots E, Buford M, Hale C, Hoyle J, Lane B, Muir A, Shuler S, Raviele N, Ivie E, Jenkins M, Lindsley K, Hansen I, Fadoju D, Felner E, Bode B, Hosey R, Sax J, Jefferies C, Mannering S, Prentis R, She J, Stachura M, Hopkins D, Williams J, Steed L, Asatapova E, Nunez S, Knight S, Dixon P, Ching J, Donner T, Longnecker S, Abel K, Arcara K, Blackman S, Clark L, Cooke D, Plotnick L, Levin P, Bromberger L, Klein K, Sadurska K, Allen C, Michaud D, Snodgrass H, Burghen G, Chatha S, Clark C, Silverberg J, Wittmer C, Gardner J, LeBoeuf C, Bell P, McGlore O, Tennet H, Alba N, Carroll M, Baert L, Beaton H, Cordell E, Haynes A, Reed C, Lichter K, McCarthy P, McCarthy S, Monchamp T, Roach J, Manies S, Gunville F, Marosok L, Nelson T, Ackerman K, Rudolph J, Stewart M, McCormick K, May S, Falls T, Barrett T, Dale K, Makusha L, McTernana C, Penny-Thomas K, Sullivan K, Narendran P, Robbie J, Smith D, Christensen R, Koehler B, Royal C, Arthur T, Houser H, Renaldi J, Watsen S, Wu P, Lyons L, House B, Yu J, Holt H, Nation M, Vickers C, Watling R, Heptulla R, Trast J, Agarwal C, Newell D, Katikaneni R, Gardner C, Del A, Rio A, Logan H, Collier C, Rishton G, Whalley A, Ali S, Ramtoola T, Quattrin L, Mastrandea A, House M, Ecker C, Huang C, Gougeon J, Ho D, Pacuad D, Dunger J, May C, O’Brien C, Acerini B, Salgin A, Thankamony R, Williams J, Buse G, Fuller M, Duclos J, Tricome H, Brown D, Pittard D, Bowlby A, Blue T, Headley S, Bendre K, Lewis K, Sutphin C, Soloranzo J, Puskaric H, Madison M, Rincon M, Carlucci R, Shridharani B, Rusk E, Tessman D, Huffman H, Abrams B, Biederman M, Jones V, Leathers W, Brickman P, Petrie D, Zimmerman J, Howard L, Miller R, Alemzadeh D, Mihailescu R, Melgozza-Walker N, Abdulla C, Boucher-Berry D, Ize-Ludlow R, Levy C, Swenson, Brousell N, Crimmins D, Edler T, Weis C, Schultz D, Rogers D, Latham C, Mawhorter C, Switzer W, Spencer P, Konstantnopoulus S, Broder J, Klein L, Knight L, Szadek G, Welnick B, Thompson R, Hoffman A, Revell J, Cherko K, Carter E, Gilson J, Haines G, Arthur B, Bowen W, Zipf P, Graves R, Lozano D, Seiple K, Spicer A, Chang J, Fregosi J, Harbinson C, Paulson S, Stalters P, Wright D, Zlock A, Freeth J, Victory H, Maheshwari A, Maheshwari T, Holmstrom J, Bueno R, Arguello J, Ahern L, Noreika V, Watson S, Hourse P, Breyer C, Kissel Y, Nicholson M, Pfeifer S, Almazan J, Bajaj M, Quinn K, Funk J, McCance E, Moreno R, Veintimilla A, Wells J, Cook S, Trunnel J, Henske S, Desai K, Frizelis F, Khan R, Sjoberg K, Allen P, Manning G, Hendry B, Taylor S, Jones W, Strader M, Bencomo T, Bailey L, Bedolla C, Roldan C, Moudiotis B, Vaidya C, Anning S, Bunce S, Estcourt E, Folland E, Gordon C, Harrill J, Ireland J, Piper L, Scaife K, Sutton S, Wilkins M, Costelloe J, Palmer L, Casas C, Miller M, Burgard C, Erickson J, Hallanger-Johnson P, Clark W, Taylor A, Lafferty S, Gillett C, Nolan M, Pathak L, Sondrol T, Hjelle S, Hafner J, Kotrba R, Hendrickson A, Cemeroglu T, Symington M, Daniel Y, Appiagyei-Dankah D, Postellon M, Racine L, Kleis K, Barnes S, Godwin H, McCullough K, Shaheen G, Buck L, Noel M, Warren S, Weber S, Parker I, Gillespie B, Nelson C, Frost J, Amrhein E, Moreland A, Hayes J, Peggram J, Aisenberg M, Riordan J, Zasa E, Cummings K, Scott T, Pinto A, Mokashi K, McAssey E, Helden P, Hammond L, Dinning S, Rahman S, Ray C, Dimicri S, Guppy H, Nielsen C, Vogel C, Ariza L, Morales Y, Chang R, Gabbay L, Ambrocio L, Manley R, Nemery W, Charlton P, Smith L, Kerr B, Steindel-Kopp M, Alamaguer D, Liljenquist G, Browning T, Coughenour M, Sulk E, Tsalikan M, Tansey J, Cabbage N. Identical and Nonidentical Twins: Risk and Factors Involved in Development of Islet Autoimmunity and Type 1 Diabetes

OBJECTIVE

There are variable reports of risk of concordance for progression to islet autoantibodies and type 1 diabetes in identical twins after one twin is diagnosed. We examined development of positive autoantibodies and type 1 diabetes and the effects of genetic factors and common environment on autoantibody positivity in identical twins, nonidentical twins, and full siblings.

RESEARCH DESIGN AND METHODS

Subjects from the TrialNet Pathway to Prevention Study (N = 48,026) were screened from 2004 to 2015 for islet autoantibodies (GAD antibody [GADA], insulinoma-associated antigen 2 [IA-2A], and autoantibodies against insulin [IAA]). Of these subjects, 17,226 (157 identical twins, 283 nonidentical twins, and 16,786 full siblings) were followed for autoantibody positivity or type 1 diabetes for a median of 2.1 years.

RESULTS

At screening, identical twins were more likely to have positive GADA, IA-2A, and IAA than nonidentical twins or full siblings (all P < 0.0001). Younger age, male sex, and genetic factors were significant factors for expression of IA-2A, IAA, one or more positive autoantibodies, and two or more positive autoantibodies (all P ≤ 0.03). Initially autoantibody-positive identical twins had a 69% risk of diabetes by 3 years compared with 1.5% for initially autoantibody-negative identical twins. In nonidentical twins, type 1 diabetes risk by 3 years was 72% for initially multiple autoantibody-positive, 13% for single autoantibody-positive, and 0% for initially autoantibody-negative nonidentical twins. Full siblings had a 3-year type 1 diabetes risk of 47% for multiple autoantibody-positive, 12% for single autoantibody-positive, and 0.5% for initially autoantibody-negative subjects.

CONCLUSIONS

Risk of type 1 diabetes at 3 years is high for initially multiple and single autoantibody-positive identical twins and multiple autoantibody-positive nonidentical twins. Genetic predisposition, age, and male sex are significant risk factors for development of positive autoantibodies in twins.

Site-Specific K63 Ubiquitinomics Provides Insights into Translation Regulation under Stress

During oxidative stress, K63-linked polyubiquitin chains modify a variety of proteins including ribosomes. Knowledge of the precise sites of K63 ubiquitin is key to understand its function during the response to stress. To identify the sites of K63 ubiquitin, we developed a new mass spectrometry based method that quantified >1100 K63 ubiquitination sites in yeast that responded to oxidative stress induced by H₂O₂. We determined that under stress, K63 ubiquitin-modified proteins were involved in several cellular functions including ion transport, protein trafficking, and translation. The most abundant ubiquitin sites localized to the head of the 40S subunit of the ribosome, modified assembled polysomes, and affected the binding of translation factors. The results suggested a new pathway of post-initiation control of translation during oxidative stress and illustrated the importance of high-resolution mapping of noncanonical ubiquitination events.

EBprotV2: A Perseus Plugin for Differential Protein Abundance Analysis of Labeling-Based Quantitative Proteomics Data

We present EBprotV2, a Perseus plugin for peptide-ratio-based differential protein abundance analysis in labeling-based proteomics experiments. The original version of EBprot models the distribution of log-transformed peptide-level ratios as a Gaussian mixture of differentially abundant proteins and nondifferentially abundant proteins and computes the probability score of differential abundance for each protein based on the reproducible magnitude of peptide ratios. However, the fully parametric model can be inflexible, and its R implementation is time-consuming for data sets containing a large number of peptides (e.g., >100 000). The new tool built in the C++ language is not only faster in computation time but also equipped with a flexible semiparametric model that handles skewed ratio distributions better. We have also developed a Perseus plugin for EBprotV2 for easy access to the tool. In addition, the tool now offers a new submodule (MakeGrpData) to transform label-free peptide intensity data into peptide ratio data for group comparisons and performs differential abundance analysis using mixture modeling. This approach is especially useful when the label-free data have many missing peptide intensity data points.

New insights into the cellular temporal response to proteostatic stress

Maintaining a healthy proteome involves all layers of gene expression regulation. By quantifying temporal changes of the transcriptome, translatome, proteome, and RNA-protein interactome in cervical cancer cells, we systematically characterize the molecular landscape in response to proteostatic challenges. We identify shared and specific responses to misfolded proteins and to oxidative stress, two conditions that are tightly linked. We reveal new aspects of the unfolded protein response, including many genes that escape global translation shutdown. A subset of these genes supports rerouting of energy production in the mitochondria. We also find that many genes change at multiple levels, in either the same or opposing directions, and at different time points. We highlight a variety of putative regulatory pathways, including the stress-dependent alternative splicing of aminoacyl-tRNA synthetases, and protein-RNA binding within the 3’ untranslated region of molecular chaperones. These results illustrate the potential of this information-rich resource.

Integration of large-scale multi-omic datasets: a protein-centric view

Innovative mass spectrometry-based proteomics has enabled routine measurements of protein abundance, localization, interactions, and modifications, covering unique aspects of gene expression regulation and function. It is now time to move from isolated analyses of these datasets toward true integration of proteomics with other data types to gain insights from the interactions and interdependencies of biomolecules. When combined with genomic or transcriptomic data, proteomics expands genome annotation to identify variant or missing genes. Dynamic proteomic measurements can move analysis from predominantly concentration-based framework to that of synthesis and degradation of proteins. Proteomic data from thousands of cancer patients can foster identification of novel pathogenic mutations via detection of protein sequence changes that lead to dysregulated pathways in various tumors. Such comprehensive efforts can exploit the synergy arising from large and complex datasets to advance virtually every field of biology.

Implications of Nondifferential Misclassification on Estimates of Attributable Risk

Objectives: Only the effects of isolated nondifferential misclassification of exposure or disease on the estimates of attributable risk have been discussed in the literature. The aim of this paper is to broaden the spectrum of scenarios for which implications of misclassification are available.

Methods: For this purpose, a matrix-based approach allowing a comprehensive, unified analysis of various structures of misclassification is introduced. The relative bias or – in the situation of covariate misclassification – the relative adjustment are presented for the different misclassification scenarios.

Results: Under nondifferential misclassification of exposure or disease, the attributable risk is biased towards the null with the only exception of perfect sensitivity of exposure classification or perfect specificity of disease classification both leading to an unbiased attributable risk. From these two marginal effects, the consequences of simultaneous nondifferential independent misclassification of exposure and disease on the attributable risk are derived in the matrix-based approach. Misclassification of a dichotomous covariate leads to partial adjustment.

Conclusions: To a large extent, the results for the attributable risk are in accordance with the well-known results for the relative risk. The algebraic differences between the two risk measures, however, make it necessary to repeat the methodological considerations for the attributable risk.

PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes

PTMscape predicts PTM sites using descriptors of sequence and physico-chemical microenvironment, and tests enrichment of single or pairs of PTMs in protein domains.

While tandem mass spectrometry can detect post-translational modifications (PTM) at the proteome scale, reported PTM sites are often incomplete and include false positives. Computational approaches can complement these datasets by additional predictions, but most available tools use prediction models pre-trained for single PTM type by the developers and it remains a difficult task to perform large-scale batch prediction for multiple PTMs with flexible user control, including the choice of training data. We developed an R package called PTMscape which predicts PTM sites across the proteome based on a unified and comprehensive set of descriptors of the physico-chemical microenvironment of modified sites, with additional downstream analysis modules to test enrichment of individual or pairs of PTMs in protein domains. PTMscape is flexible in the ability to process any major modifications, such as phosphorylation and ubiquitination, while achieving the sensitivity and specificity comparable to single-PTM methods and outperforming other multi-PTM tools. Applying this framework, we expanded proteome-wide coverage of five major PTMs affecting different residues by prediction, especially for lysine and arginine modifications. Using a combination of experimentally acquired sites (PSP) and newly predicted sites, we discovered that the crosstalk among multiple PTMs occur more frequently than by random chance in key protein domains such as histone, protein kinase, and RNA recognition motifs, spanning various biological processes such as RNA processing, DNA damage response, signal transduction, and regulation of cell cycle. These results provide a proteome-scale analysis of crosstalk among major PTMs and can be easily extended to other types of PTM.

Abstract P6-11-03: A phase 2 open-label study of lucitanib in patients (pts) with FGF aberrant metastatic breast cancer (MBC)

BACKGROUND: Lucitanib is a potent, oral antiangiogenic tyrosine kinase inhibitor of Vascular Endothelial Growth Factor Receptors 1-3 (VEGFR1-3), Platelet-Derived Growth Factor Receptors alpha and beta (PDGFRα/β), and Fibroblast Growth Factor Receptors 1-3 (FGFR1-3). FGF aberrancies (amplification of FGFR1,or 11q[amplicon containing FGF ligands 3, 4, and 19]), are genomic alterations observed in over 20% of breast cancer pts and promote cancer proliferation and survival.

METHODS: MBC pts who had received at least 1 metastatic line of therapy were randomized 1:1 to 10 or 15 mg QD of lucitanib. Stratification was based on local assessment of FGF aberrancy; pts with both FGFR1 and 11q-amplified tumors were stratified as FGFR1 amplified. Central confirmation of FGFR1 or 11q amplification was done using Abbott FISH probes (FGFR1 or 11q copy number ≥ 6 and a ratio of FGFR1 or 11q to centromere ≥ 2). Investigator-assessed progression-free survival (PFS) was the primary endpoint. Secondary endpoints included objective response rate (ORR) per RECIST 1.1, disease control rate (DCR), duration of response (DR), and incidence of treatment-emergent adverse events (TEAE).

RESULTS: Enrollment completed in 3/2016; 178 pts that received at least 1 dose of lucitanib are included in this analysis (baseline characteristics in Table 1). Due to grade 3 hypertension in the 15 mg group (46% vs 37% in 10 mg group), enrollment to the 15 mg group was halted. Overall, most pts (97%) experienced at least 1 TEAE, with the most frequently (≥ 30%) occurring events being hypertension (73%), fatigue (48%), nausea (43%), hypothyroidism (40%), and headache (33%). Grade ≥ 3 TEAEs occurred in 66% of pts, with hypertension as the most frequent event (40%) followed by proteinuria and hyponatremia (both 6%). AEs were manageable with dose interruption or reduction, with approximately 8% of pts ending treatment due to an AE. Current median PFS is 3.5 mos (95% CI 2.8-4.6; range 0.62-12.95) and 2.6 mos (95% CI 1.8-2.9; range 0.82-18.87) respectively for the 10 mg and 15 mg treatment groups. No differences in clinical activity were observed by treatment group, FGF aberrancy, hormone receptor or HER2 status. Of the 168 evaluable pts, confirmed ORR was 3%; overall DCR was 27% (32% for pts in the 10 mg group compared to 20% for the 15 mg group); overall mean (standard deviation) DR of 3.3 (1.8) mos.

Baseline Characteristics 10 mg QD15 mg QD N=109N=69Age (years)Median5653Range27-8227-80SexFemale109 (100%)67 (97%)Male02 (3%)ECOG PSmissing5 (5%)2 (3%)051 (47%)30 (43%)153 (49%)37 (54%)Number of prior anticancer therapies in the metastatic setting&gt; 332 (29%)21 (30%)3-648 (44%)32 (46%)&gt; 629 (27%)16 (23%)Endocrine/HER2 statusmissing7 (6%)1 (1%)ER+ or PR+74 (68%)50 (73%)HER2+12 (11%)7 (10%)TNBC16 (15%)11 (16%)FGFR aberrancyFGFR1 amplified54 (49%)29 (42%)11q amplified31 (28%)24 (35%)FGFR1 and 11q amplified13 (12%)9 (13%)FGFR1 and 11q non-amplified11 (10%)7 (10%)

CONCLUSION: At 10 mg QD, lucitanib has modest activity with manageable toxicity in this heavily pretreated pt population. Future clinical development for lucitanib may focus on alternative biomarkers to identify sensitive tumors and rational combinations with other anti-cancer drugs.

Citation Format: Mayer IA, Arteaga CL, Nanda R, Miller KD, Jhaveri K, Brufsky AM, Rugo H, Yardley DA, Vahdat LT, Sadeghi S, Audeh MW, Rolfe L, Litten J, Knox A, Raponi M, Tankersley C, Isaacson J, Wride K, Morganstern DE, Vogel C, Connolly RM, Gradishar WJ, Patel R, Pusztai L, Abu-Khalaf M. A phase 2 open-label study of lucitanib in patients (pts) with FGF aberrant metastatic breast cancer (MBC) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-11-03.

The relationship between maternal self-efficacy, compliance and outcome in a trial of vitamin D supplementation in pregnancy

In a randomised controlled trial of vitamin D during pregnancy, we demonstrated that women with lower self-efficacy were more likely to experience practical problems with taking the trial medication and that this was associated with lower compliance and achieved 25(OH)-vitamin D concentrations.

INTRODUCTION

The relationship between self-efficacy (the belief that one can carry out a behaviour), compliance with study protocol and outcome was explored within a randomised, double-blind, placebo-controlled trial of vitamin D supplementation in pregnancy.

METHODS

In the Maternal Vitamin D Osteoporosis Study (MAVIDOS) trial, women with circulating plasma 25(OH)-vitamin D of 25-100 nmol/l in early pregnancy were randomised to either 1000 IU cholecalciferol/day or matched placebo from 14 weeks until delivery. Circulating 25(OH)-vitamin D concentrations were assessed at 14 and 34 weeks' gestation. A sequential sub-sample completed Schwarzer's General Self-Efficacy Scale at 14 and 34 weeks and the Problematic Experiences of Therapy Scale at 34 weeks. Women were interviewed about their experiences of the trial and interview transcripts analysed thematically.

RESULTS

In 203 women, those with higher self-efficacy were less likely to experience practical problems taking the study medication (odds ratio (OR) 0.81 (95 % confidence interval (CI) 0.69-0.95), p = 0.01). Over half reported practical problems associated with poorer compliance with the protocol requiring women to take the medication daily. Compliance in women who experienced practical problems was 94 % compared with 98 % for those with no problems (p < 0.001). Poorer compliance was also associated with lower concentrations of 25(OH)-D in late pregnancy in the treatment group (β = 0.54 nmol/l (95 % CI 0.18-0.89), p = 0.003). Thematic analysis suggested common difficulties were remembering to take the medication every day and swallowing the large capsules.

CONCLUSIONS

These findings suggest that differences in self-efficacy influence trial outcomes. Such information may help clinicians anticipate responses to routine vitamin D supplementation in pregnancy and identify those who may need more support to comply.

TRIAL REGISTRATION

ISRCTN82927713, registered 11/04/2008.