Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group

BACKGROUND

The use of next-generation sequencing technologies has enabled the rapid identification of non-synonymous somatic mutations in cancer cells. Neoantigens are mutated peptides derived from somatic mutations not present in normal tissues that may result in the presentation of tumour-specific peptides capable of eliciting antitumour T-cell responses. Personalised neoantigen-based cancer vaccines and adoptive T-cell therapies have been shown to prime host immunity against tumour cells and are under clinical trial development. However, the optimisation and standardisation of neoantigen identification, as well as its delivery as immunotherapy are needed to increase tumour-specific T-cell responses and, thus, the clinical efficacy of current cancer immunotherapies.

METHODS

In this recommendation article, launched by the European Society for Medical Oncology (ESMO), we outline and discuss the available framework for neoantigen prediction and present a systematic review of the current scientific evidence.

RESULTS

A number of computational pipelines for neoantigen prediction are available. Most of them provide peptide major histocompatibility complex (MHC) binding affinity predictions, but more recent approaches incorporate additional features like variant allele fraction, gene expression, and clonality of mutations. Neoantigens can be predicted in all cancer types with high and low tumour mutation burden, in part by exploiting tumour-specific aberrations derived from mutational frameshifts, splice variants, gene fusions, endogenous retroelements and other tumour-specific processes that could yield more potently immunogenic tumour neoantigens. Ongoing clinical trials will highlight those cancer types and combinations of immune therapies that would derive the most benefit from neoantigen-based immunotherapies.

CONCLUSIONS

Improved identification, selection and prioritisation of tumour-specific neoantigens are needed to increase the scope of benefit from cancer vaccines and adoptive T-cell therapies. Novel pipelines are being developed to resolve the challenges posed by high-throughput sequencing and to predict immunogenic neoantigens.

Chromatin network markers of leukemia

MOTIVATION

The structure of chromatin impacts gene expression. Its alteration has been shown to coincide with the occurrence of cancer. A key challenge is in understanding the role of chromatin structure (CS) in cellular processes and its implications in diseases.

RESULTS

We propose a comparative pipeline to analyze CSs and apply it to study chronic lymphocytic leukemia (CLL). We model the chromatin of the affected and control cells as networks and analyze the network topology by state-of-the-art methods. Our results show that CSs are a rich source of new biological and functional information about DNA elements and cells that can complement protein-protein and co-expression data. Importantly, we show the existence of structural markers of cancer-related DNA elements in the chromatin. Surprisingly, CLL driver genes are characterized by specific local wiring patterns not only in the CS network of CLL cells, but also of healthy cells. This allows us to successfully predict new CLL-related DNA elements. Importantly, this shows that we can identify cancer-related DNA elements in other cancer types by investigating the CS network of the healthy cell of origin, a key new insight paving the road to new therapeutic strategies. This gives us an opportunity to exploit chromosome conformation data in healthy cells to predict new drivers.

AVAILABILITY AND IMPLEMENTATION

Our predicted CLL genes and RNAs are provided as a free resource to the community at https://life.bsc.es/iconbi/chromatin/index.html.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A systematic review and trial sequential analysis of intravenous vs. oral peri-operative paracetamol

Postoperative pain might be different after intravenous vs. oral paracetamol. We systematically reviewed randomised controlled trials in patients >15 years that compared intravenous with oral paracetamol for postoperative pain. We identified 14 trials with 1695 participants. There was inconclusive evidence for an effect of route of paracetamol administration on postoperative pain at 0–2 h (734 participants), 2–6 h (766 participants), 6–24 h (1115 participants) and >24 h (248 participants), with differences in standardised mean (95%CI) pain scores for intravenous vs. oral of −0.17 (−0.45 to 0.10), −0.09 (−0.24 to 0.06), 0.06 (−0.12 to 0.23) and 0.03 (−0.22 to 0.28), respectively. Trial sequential analyses suggested that a total of 3948 participants would be needed to demonstrate a meaningful difference in pain or its absence at 0–2 h. There were no differences in secondary outcomes. Intravenous paracetamol is more expensive than oral paracetamol. Substitution of oral paracetamol in half the patients given intravenous paracetamol in our hospital would save around £ 38,711 (€ 43,960 or US$ 47,498) per annum.

Women's interest in a personal breast cancer risk assessment and lifestyle advice at NHS mammography screening

Background

Although mortality from breast cancer is declining, incidence continues to increase and is often detected at routine NHS screening. Most middle aged and older women in England attend for screening every 3 years. Assessing their personal breast cancer risk and providing preventative lifestyle advice could help to further reduce breast cancer incidence.

Methods

A cross-sectional, self-complete postal survey measured attendees' interest in having a personal risk assessment, expected impact on screening attendance, knowledge of associations between lifestyle and breast cancer and preferred ways of accessing preventative lifestyle advice.

Results

A total of 1803/4948 (36.4%) completed questionnaires were returned. Most participants (93.7%) expressed interest in a personal risk assessment and 95% (1713/1803) believed it would make no difference or encourage re-attendance. Two-thirds (1208/1803) associated lifestyle with breast cancer, but many were unaware of specific risks such as weight gain, obesity, alcohol consumption and physical inactivity. NHS sourced advice was expected to be more credible than other sources, and booklets, brief counselling or an interactive website were most preferred for accessing this.

Conclusions

Attendees appear to welcome an intervention that would facilitate more proactive clinical and lifestyle prevention and address critical research gaps in breast cancer prevention and early detection.

Abstract P3-13-03: Multicenter clinical trial of percutaneous laser ablation for early stage primary breast cancer. Results of 49 cases with radiographic and pathological correlation

Introduction: Percutaneous laser ablation of early stage primary breast cancer remains investigational. A multicenter, international clinical trial (NCT01478438) was completed to determine feasibility of this technique.

Methods: Patients with a single focus of biopsy proven infiltrating ductal carcinoma measuring 20 mm or less by pre-ablation MRI were treated by image-guided percutaneous laser ablation. A laser diode source (805 nominal nanometer wavelength) was used to perform the thermal ablation. Thermal sensors placed at the periphery of the tumor measured achievement of predefined temperature levels, indicating successful ablation. The patients were evaluated by post-ablation mammogram, ultrasound and MRI at 4 weeks post-ablation, after which they underwent surgical excision. Pathology specimens were evaluated by hematoxylin & eosin, CK 8/18, Ki-67 and estrogen receptor staining.

Results: Forty-nine of the 61 enrolled patients (ages 42-77, mean age 64 years) undergoing percutaneous laser ablation have finished protocol analysis and are reported in this series. Ablation was considered complete by the treating physician in all cases. The mean tumor size was 11.3 mm. The mean laser time was 15.7 minutes. There were no serious adverse events. Seven patients (14%) reported mild adverse events (pain, blisters, lump). Post-ablation cell viability was determined by MRI and by changes in CK 8/18, Ki67 and estrogen receptor staining. A post-ablation discordance between MRI and pathology was found in evaluation of 4 patients (8%). Three patients (6%) were considered "false negative" with a post-ablation residual tumor burden of less than 2mm which was not detected by MRI. One patient (2%) had a complete pathologic ablation but positive MRI ("false positive"). One patient (2%) had adjacent residual DCIS, visible in retrospect on the pre-ablation MRI and was considered a screening failure. Eight patients (16%) were found to have residual invasive cancer by both post-ablation MRI and pathologic analysis. Complete ablation was confirmed in 36 patients (73%) when evaluated by both post-ablation MRI and pathologic analysis.

Conclusion: Percutaneous laser ablation holds promise as an alternative to lumpectomy in the treatment of early stage breast cancer. There is a strong correlation (92%) between findings on post-ablation MRI and changes in CK 8/18, Ki67 and estrogen receptor staining in this series. Additional trials are necessary to determine the long-term curative potential of this technique.

Citation Format: Schwartzberg BS, Abdelatif OMA, Lewin JM, Bernard JM, Brehm JL, Bu-Ali HM, Cawthorn SJ, Chen-Seeto M, Feldman SM, Govindarajulu S, Jones LI, Juette A, Kavia S, Maganini RO, Pain SJ, Shere MH, Shriver CD, Smith SG, Valencia A, Whitacre EB, Whitney R. Multicenter clinical trial of percutaneous laser ablation for early stage primary breast cancer. Results of 49 cases with radiographic and pathological correlation. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-13-03.

[Evolution of the intake and nutritional status of zinc, iron and copper in women undergoing bariatric surgery until the second year after surgery]

INTRODUCTION

Bariatric surgery allows a significant reduction in weight and improvement of comorbidities associated with obesity in the long term, but it can also adversely affect the nutritional status of some micronutrients.

OBJECTIVES

To evaluate changes in intake and parameters of nutritional status of zinc, iron and copper in patients undergoing Roux-en-Y gastric bypass (GBP) or sleeve gastrectomy (SG), until the second postoperative year.

METHODS

We prospectively studied 45 women undergoing GBP or SG (mean age 35.2 ± 8.4 years, mean BMI 39.8 ± 4.0 kg/m²), every 6 months We measured intake and status indications nutritional zinc, iron and copper, and annually evaluated body composition. The contribution of minerals through supplements represented twice the recommended intake for a healthy woman in patients undergoing GT and three times for GBP.

RESULTS

20 women underwent GBP and 25 SG. In both groups there was a significant reduction in weight and body fat percentage, which was maintained until the second postoperative year. Women who have had a greater commitment GBP nutritional status of zinc, iron and copper, that patients undergoing SG.

CONCLUSIONS

Gastric bypass Roux-Y produces a greater commitment of nutritional status of zinc, iron and copper sleeve gastrectomy. It should evaluate whether administration of supplementation fractional improve the absorption of these nutrients.

[Alopecia in women with severe and morbid obesity who undergo bariatric surgery]

INTRODUCTION

Bariatric surgery leads to a significant body weigh reduction although it is associated to a higher risk of presenting some nutritional deficiencies. A common complication, little studied and mainly related to zinc deficiency is alopecia.

OBJECTIVES

To compare the nutritional status of zinc, iron, copper, selenium and protein-visceral in women with different degrees of hair loss at 6 months after gastric bypass or tubular gastrectomy.

METHODS

The patients were categorized into two groups according to the degree of hair loss: group 1 or mild loss (n = 42) and group 2 or severe hair loss (n = 45). Zinc, iron, copper, and selenium, as well as the indicators of the nutritional status of zinc, iron, copper, and proteinvisceral were assessed before and after 6 months of the surgery.

RESULTS

In both groups there was a significant body weight reduction at 6 months post-surgery (-38.9% ± 16.4%). Patients in group 1 presented a significantly higher intake of zinc (20.6 ± 8.1 vs. 17.1 ± 7.7 mg/d) and iron (39.7 ± 35.9 vs. 23.8 ± 21.3 mg/d.), and lower compromise in the nutritional status of zinc and iron than group 2. However, patients in group 2 had lower compromise in the nutritional status of copper. There were no differences regarding the plasma concentrations of albumin.

CONCLUSIONS

The patients having lower hair loss at six months after surgery had higher zinc and iron intake and lower compromise of the nutritional status of both minerals.

Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study

The Dictionary of Interacting Proteins (DIP) (Xenarios et al., 2000) is a large repository of protein interactions: its March 2000 release included 2379 protein pairs whose interactions have been detected by experimental methods. Even if many of these correspond to poorly characterized proteins, the result of massive yeast two-hybrid screenings, as many as 851 correspond to interactions detected using direct biochemical methods.

We used information retrieval technology to search automatically for sentences in Medline abstracts that support these 851 DIP interactions. Surprisingly, we found correspondence between DIP protein pairs and Medline sentences describing their interactions in only 30% of the cases. This low coverage has interesting consequences regarding the quality of annotations (references) introduced in the database and the limitations of the application of information extraction (IE) technology to Molecular Biology. It is clear that the limitation of analyzing abstracts rather than full papers and the lack of standard protein names are difficulties of considerably more importance than the limitations of the IE methodology employed. A positive finding is the capacity of the IE system to identify new relations between proteins, even in a set of proteins previously characterized by human experts. These identifications are made with a considerable degree of precision.

This is, to our knowledge, the first large scale assessment of IE capacity to detect previously known interactions: we thus propose the use of the DIP data set as a biological reference to benchmark IE systems.

Intragastric balloon and multidisciplinary team

BACKGROUND

The intragastric balloon is widely used for weight reduction in obese patients, but results are variable. We describe our results enhancing the importance of a Multidisciplinary Team (MT) taking part in the treatment.

METHODS

A retrospective review was done concerning a total of 119 balloons , placed in 116 patients, under endoscopic control and conscious sedation, from May 2001 until August 2006. 49 patients were prepared and recommended to be followed by a MT in a physical unit, at least every 15 days during 6 months. 67 were indicated and followed by other colleagues, without MT. Removal was performed 6 months later.

RESULTS

Concerning our 49 patients, mean age was 38, 1 years, 31 female and 18 males, with BMI ranged between 32 and 63, average of 42. The average decrease of weight excess was 31, 85% (-4, 45-80, 4%), and the BMI diminished 5,3 points (from 13,6 to gain of 0,9). The treatment failed in 34,6 % of our patients -including 4 patients lost of follow-up (8, 16%)-, compared with 53, 8% of patients without structured MT for selection and follow-up. Physical exercise enhanced markedly the results with 45, 8% of excess of weight loss in women and 39, 7% in males, compared with 14, 6 and 15, 6% in patients who didn't follow the program. The weight loss was mostly fat mass, 89,9% in men and 75,6% in women.- The results maintenance was obtained in 40% of patients one year later. There were no major complications; one balloon had to be removed at 3 weeks because of intolerance, another at 5 months because of gastroesophageal reflux.

CONCLUSIONS

BIB is an effective help to achieve a short term weight loss in obese patients; nevertheless, good and long lasting results will depend on the modification of life style obtained by a multidisciplinary approach.

Wnt signaling pathway is epigenetically regulated by methylation of Wnt antagonists in acute myeloid leukemia

Activation of the Wnt signaling pathway has been implicated recently in the pathogenesis of leukemia. We studied the function of epigenetic regulation of the Wnt pathway and its prognostic relevance in acute myelogenous leukemia (AML). We used a methylation-specific polymerase chain reaction approach to analyze the promoter methylation status of a panel of Wnt antagonists including sFRP1, sFRP2, sFRP4, sFRP5, DKK1 and DKK3. Aberrant methylation of Wnt antagonists was detected in four AML cell lines and in up to 64% of AML marrow samples. Treatment of the cell lines with 5-aza-2'-deoxycytidine induced reexpression of methylated Wnt antagonists and inactivation of the Wnt pathway by downregulating the Wnt pathway genes cyclin D1, TCF1 and LEF1 and reducing nuclear localization of beta-catenin. In a subgroup of patients 60 years and younger with newly diagnosed AML and intermediate-risk cytogenetics, abnormal methylation of Wnt antagonists was associated with decreased 4-year relapse-free survival (28 vs 61%, respectively, P=0.03). Our results indicate a function of the epigenetic regulation of the Wnt pathway in predicting relapse in a subgroup of AML patients.

[Physical activity and bariatric surgery]

Obesity is a very serious problem at the 21st Century essentially affecting developed countries. It may be considered a pandemicity. Among predisposing factors for obesity here are, on the one hand, the new feeding habits with fat-and carbohydrate-rich pre-cooked foods, and in the other hand sedentary lifestyle due to occidental society lifestyles. Although obesity is considered a chronic disease, it would really represent a normal and physiologic adaptation mechanism to an "obesogenic" environment. Bariatric surgery represents a solution for morbid obesity when all the other conservative measures have failed, achieving the modification of nutritional habits and nutrients absorption. However, it is paramount to modify lifestyle concerning sedentary lifestyle. Individualized exercise monitoring offers the advantage of motivating and rejection to exercise. It is necessary to study and assess the efficacy of aerobic and anaerobic physical activity at both pre-surgical preparation and further course of these patients.

FireDB--a database of functionally important residues from proteins of known structure

The FireDB database is a databank for functional information relating to proteins with known structures. It contains the most comprehensive and detailed repository of known functionally important residues, bringing together both ligand binding and catalytic residues in one site. The platform integrates biologically relevant data filtered from the close atomic contacts in Protein Data Bank crystal structures and reliably annotated catalytic residues from the Catalytic Site Atlas. The interface allows users to make queries by protein, ligand or keyword. Relevant biologically important residues are displayed in a simple and easy to read manner that allows users to assess binding site similarity across homologous proteins. Binding site residue variations can also be viewed with molecular visualization tools. The database is available at

Empirical limits for template-based protein structure prediction: the CASP5 example

Most protein structure prediction methods use templates to assist in the construction of protein models. In this paper, we analyse the current state of template-based modelling approaches and reach an estimate of the empirical limits of these methods. Our analysis show that current prediction methods are already reaching these empirical accuracy limits in the easier cases, where finding a close homologue to the native target structure is not a problem. However, we find that even in the absence of alignment errors and using optimal templates, template-based methods have intrinsic limitations, suggesting that other methodologies, such as ab initio procedures, must be used if accuracy is ultimately to be improved.

A CLN5 mutation causing an atypical neuronal ceroid lipofuscinosis of juvenile onset

Three related patients from Colombia presented with a juvenile-onset neuronal ceroid lipofuscinosis. Electron microscopy of one case showed condensed fingerprint profiles, and genetic analyses identified a novel missense mutation in CLN5. The authors demonstrate the existence of pathogenic CLN5 mutations outside northern Europe and that mutations in this gene can lead to an atypical late-onset neuronal ceroid lipofuscinosis disease, in addition to the late infantile form first described in Finland.

Role of ionic fluxes in the apoptotic cell death of cultured cerebellar granule neurons

Cultured cerebellar granule neurons (CGC) increase survival in a medium containing 25 mM KCl (K25), and they die apoptotically when cultures are treated with staurosporine (St) or are transferred to a 5-mM KCl containing medium (K5). Apoptotic CGC show nuclear condensation and caspase-3 activation. Cell death induced by these conditions was partially prevented when cultures were maintained under alkaline conditions, which also induced a marked reduction of the caspase-3 activation. The acidification of the medium further increased cell death induced by both stimuli. Cultures transferred to K5 suffered an immediate intracellular alkalinization that remained constant during the time K5 was present. In contrast, St did not modify cytosolic pH at any of the evaluated times. On the other hand, DIDS, furosemide, and bumetanide prevented CGC death induced by K5 and St. Other drugs such as amiloride, EIPA, tamoxifen, NEM, or NPPB did not modify cell death induced by these conditions. Both DIDS and bumetanide markedly inhibited the processing and activation of caspase-3, and DIDS prevented the nuclear condensation induced by K5 and St. These findings suggest that pH is a condition that could contribute to the modulation of cell death induced by some stimuli and that other ions, such as potassium, could have a role in the initial phase of apoptotic death of CGC.

A new ATP-binding fold in actin, hexokinase and Hsc70

One of a cell biologist's favourite occupations is to discover the proteins that perform newly described functions in the cell. Very often lately, this has resulted in the identification of protein families whose related amino acid sequences reflect similar functions, but can proteins with totally unrelated sequences have similar structures and functions? In this review, Ken Holmes, Chris Sander and Alfonso Valencia describe the structural similarities between three well-known proteins that have no readily detectable primary sequence similarities but for which X-ray crystallography has revealed very similar structures. A comparison of their structures provides insights into their common mechanisms of action and into protein evolution, and has been used to detect related proteins in sequence data bases.

A neural network approach to evaluate fold recognition results

Fold recognition techniques assist the exploration of protein structures, and web-based servers are part of the standard set of tools used in the analysis of biochemical problems. Despite their success, current methods are only able to predict the correct fold in a relatively small number of cases. We propose an approach that improves the selection of correct folds from among the results of two methods implemented as web servers (SAMT99 and 3DPSSM). Our approach is based on the training of a system of neural networks with models generated by the servers and a set of associated characteristics such as the quality of the sequence-structure alignment, distribution of sequence features (sequence-conserved positions and apolar residues), and compactness of the resulting models. Our results show that it is possible to detect adequate folds to model 80% of the sequences with a high level of confidence. The improvements achieved by taking into account sequence characteristics open the door to future improvements by directly including such factors in the step of model generation. This approach has been implemented as an automatic system LIBELLULA, available as a public web server at http://www.pdg.cnb.uam.es/servers/libellula.html.

Effect of montelukast added to inhaled budesonide on control of mild to moderate asthma

BACKGROUND

Proinflammatory leukotrienes, which are not completely inhibited by inhaled corticosteroids, may contribute to asthmatic problems [corrected]. A 16 week multicentre, randomised, double blind, controlled study was undertaken to study the efficacy of adding oral montelukast, a leukotriene receptor antagonist, to a constant dose of inhaled budesonide.

METHODS

A total of 639 patients aged 18-70 years with forced expiratory volume in 1 second (FEV(1)) > or =55% predicted and a minimum predefined level of asthma symptoms during a 2 week placebo run in period were randomised to receive montelukast 10 mg (n=326) or placebo (n=313) once daily for 16 weeks. All patients received a constant dose of budesonide (400-1600 microg/day) by Turbuhaler throughout the study.

RESULTS

Mean FEV(1) at baseline was 81% predicted. The median percentage of asthma exacerbation days was 35% lower (3.1% v 4.8%; p=0.03) and the median percentage of asthma free days was 56% higher (66.1% v 42.3%; p=0.001) in the montelukast group than in the placebo group. Patients receiving concomitant treatment with montelukast had significantly (p<0.05) fewer nocturnal awakenings and significantly (p<0.05) greater improvements in beta agonist use and morning peak expiratory flow rate (PEFR).

CONCLUSIONS

For patients with mild airway obstruction and persistent asthma symptoms despite budesonide treatment, concomitant treatment with montelukast significantly improves asthma control.