The Integration of Proteome-Wide PTM Data with Protein Structural and Sequence Features Identifies Phosphorylations that Mediate 14-3-3 Interactions.

14-3-3s are abundant proteins that regulate essentially all aspects of cell biology, including cell cycle, motility, metabolism, and cell death. 14-3-3s work by docking to phosphorylated Ser/Thr residues on a large network of client proteins and modulating client protein function in a variety of ways. In recent years, aided by improvements in proteomics, the discovery of 14-3-3 client proteins has far outpaced our ability to understand the biological impact of individual 14-3-3 interactions. The rate-limiting step in this process is often the identification of the individual phospho-serines/threonines that mediate 14-3-3 binding, which are difficult to distinguish from other phospho-sites by sequence alone. Furthermore, trial-and-error molecular approaches to identify these phosphorylations are costly and can take months or years to identify even a single 14-3-3 docking site phosphorylation. To help overcome this challenge, we used machine learning to analyze predictive features of 14-3-3 binding sites. We found that accounting for intrinsic protein disorder and the unbiased mass spectrometry identification rate of a given phosphorylation significantly improves the identification of 14-3-3 docking site phosphorylations across the proteome. We incorporated these features, coupled with consensus sequence prediction, into a publicly available web app, called "14-3-3 site-finder". We demonstrate the strength of this approach through its ability to identify 14-3-3 binding sites that do not conform to the loose consensus sequence of 14-3-3 docking phosphorylations, which we validate with 14-3-3 client proteins, including TNK1, CHEK1, MAPK7, and others. In addition, by using this approach, we identify a phosphorylation on A-kinase anchor protein-13 (AKAP13) at Ser2467 that dominantly controls its interaction with 14-3-3.

Effect of delay between nuclear medicine scanning and sentinel node biopsy on outcome in patients with cutaneous melanoma.

BACKGROUND: Sentinel lymph node biopsy (SLNB) is an important staging tool for the management of melanoma. A multicentre study was done to validate previous findings that the timing of lymphoscintigraphy influences the accuracy of SLNB and patient outcomes, particularly survival. METHODS: Data were reviewed on patients undergoing SLNB for melanoma at three centres in the UK and Sweden, examining the effect of timing of SLNB after nuclear medicine scanning. Kaplan-Meier survival analysis was used to assess overall (OS), disease-specific (DSS) and progression-free (PFS) survival, stratified by timing of lymphoscintigraphy. Independent risk factors for survival were identified by Cox multivariable regression analysis. RESULTS: A total of 2270 patients were identified. Median follow-up was 56 months. Univariable analysis showed a 4·2 per cent absolute and 35·5 per cent relative benefit in DSS (hazard ratio 1·36, 95 per cent c.i. 1·05 to 1·74; P = 0·018) for 863 patients whose SLNB was performed up to 12 h after lymphoscintigraphy compared with 1407 patients who had surgery after more than 12 h. There were similar OS and PFS benefits (P = 0·036 and P = 0·022 respectively). Multivariable analysis identified timing of lymphoscintigraphy as an independent predictor of OS (P = 0·017) and DSS (P = 0·030). There was an excess of nodal recurrences as first site of recurrence in the group with delayed surgery (4·5 versus 2·5 per cent; P = 0·008). CONCLUSION: Delaying SLNB beyond 12 h after lymphoscintigraphy with 99 Tc-labelled nanocolloid has a significant negative survival impact in patients with melanoma.

ANTECEDENTES: La biopsia de ganglio centinela (sentinel lymph node biopsy, SLNB) es una técnica importante para la estadificación y tratamiento del melanoma. Se realizó un estudio multicéntrico para validar hallazgos previos según los cuales el momento de la linfogammagrafía (lymphoscintigraphy, LS) influye en la precisión de la SLNB y en los resultados de los pacientes, especialmente en la supervivencia. MÉTODOS: Se revisaron los datos de los pacientes a los que se realizó una SLNB por melanoma en 3 centros en el Reino Unido y Suecia, con especial atención al efecto del período entre la inyección el material radioactivo y la SLNB. Se realizó un análisis de supervivencia mediante el método de Kaplan-Meier para la supervivencia específica de la enfermedad (disease-specific survival, DSS), supervivencia global (overall survival, OS) y supervivencia libre de progresión (progression-free survival, PFS), todas ellas estratificadas por el momento de la LS. Los factores de riesgo independientes para la supervivencia se determinaron mediante un análisis de regresión multivariable de Cox. RESULTADOS: Se incluyeron 2.270 pacientes. La mediana de seguimiento fue de 49 meses. El análisis univariado mostró un beneficio absoluto del 4,2% y relativo del 35,5% (cociente de riesgos instantáneos, hazard ratio, HR: 1,36 (i.c. del 95% 1,05-1,74, P = 0.02)) en la DDS para los pacientes a los que la SLNB se realizó < 12 horas después de la LS (n = 863) en comparación con aquellos realizados > 12 horas (n = 1407). Se detectaron beneficios similares para la OS y la PFS (P = 0,04 y P = 0,02, respectivamente). El análisis multivariable identificó el tiempo entre la LS y la SLNB como un factor independiente de OS (P = 0,017) y DSS (P = 0,03). Hubo un aumento en las recidivas ganglionares como primer sitio de recidiva en el grupo de > 12 horas (2,5% versus 4,5%; P = 0,008). CONCLUSIÓN: Estos datos validan nuestra investigación previa y tienen implicaciones significativas para las unidades de melanoma, en el sentido de que retrasar la SLNB más allá de las 12 horas después de realizar la LS con nanocoloides marcados con Tc99 tiene un impacto negativo significativo en la supervivencia de los pacientes y debe evitarse. Se presenta la hipótesis de que la causa subyacente es la migración temporal del trazador que determina una SLNB incorrecta. .

Microsurgical Reconstructions for Head and Neck Cancers in Elderly Aged >80 Years: An Analysis of Surgical Outcomes and Quality of Life.

BACKGROUND: The rising incidence of primary head and neck (H&N) cancers in the elderly presents a dilemma regarding the appropriateness of complex surgery in this assumed frail age group. With limited data on surgical morbidity, survival, and patient quality of life (QOL), this analysis aimed to broaden the understanding of safety and effectiveness of microsurgical treatment in very elderly H&N cancer patients. METHODS: A prospective database analysis was used to evaluate surgical outcomes (morbidity, survival, and QOL) in all patients aged 80 years and older undergoing microsurgical reconstruction for cutaneous and intra-oral H&N cancers between 2004 and 2014. Outcomes were assessed for their association with surgical, tumour, and patient variables. Comorbidities were categorized by the ACE27 index and postoperative morbidity by the Clavien-Dindo scoring system. QOL was analyzed using the UW-QOLv4. RESULTS: Of 720 microsurgical reconstructions, 96 patients were identified. Median survival was 25 months. The ACE27 index was the only variable significantly associated with survival with a 5-year survival of 59.2 % in the least comorbid group versus 19.7 % in the most comorbid group (p 0.015). ACE-27 showed influence on socioemotional QoL scores. Physical QOL scores were influenced by tumour and operative factors. Patients were found to value physical QOL over socioemotional. CONCLUSIONS: Microsurgical reconstructions are well tolerated in the very elderly patients and should be considered predominantly based on comorbidity. Tumour stage, flap type, and cancer site should still form part of the preoperative counseling due to their implication on postoperative physical function.