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BACKGROUND: Initial learning curves are potentially shorter in robotic-assisted surgery (RAS) than in conventional laparoscopic surgery (LS). There is little evidence to support this claim. Furthermore, there is limited evidence how skills from LS transfer to RAS. METHODS: A randomized controlled, assessor blinded crossover study to compare how RAS naïve surgeons (n = 40) performed linear-stapled side-to-side bowel anastomoses in an in vivo porcine model with LS and RAS. Technique was rated using the validated anastomosis objective structured assessment of skills (A-OSATS) score and the conventional OSATS score. Skill transfer from LS to RAS was measured by comparing the RAS performance of LS novices and LS experienced surgeons. Mental and physical workload was measured with the NASA-task load index (NASA-Tlx) and the Borg-scale. OUTCOMES: In the overall cohort, there were no differences between RAS and LS for surgical performance (A-OSATS, time, OSATS). Surgeons that were naïve in both LS and RAS had significantly higher A-OSATS scores in RAS (Mean (Standard deviation (SD)): LS: 48.0 ± 12.1; RAS: 52.0 ± 7.5); p = 0.044) mainly deriving from better bowel positioning (LS: 8.7 ± 1.4; RAS: 9.3 ± 1.0; p = 0.045) and closure of enterotomy (LS: 12.8 ± 5.5; RAS: 15.6 ± 4.7; p = 0.010). There was no statistically significant difference in how LS novices and LS experienced surgeons performed in RAS [Mean (SD): novices: 48.9 ± 9.0; experienced surgeons: 55.9 ± 11.0; p = 0.540]. Mental and physical demand was significantly higher after LS. CONCLUSION: The initial performance was improved for RAS versus LS for linear stapled bowel anastomosis, whereas workload was higher for LS. There was limited transfer of skills from LS to RAS.
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Procedimentos Cirúrgicos do Sistema Digestório , Laparoscopia , Procedimentos Cirúrgicos Robóticos , Animais , Anastomose Cirúrgica , Competência Clínica , Estudos Cross-Over , Laparoscopia/métodos , Procedimentos Cirúrgicos Robóticos/métodos , Suínos , Humanos , CirurgiõesRESUMO
BACKGROUND: The aim of this study was to assess the transferability of surgical skills for the laparoscopic hernia module between the serious game Touch Surgery™ (TS) and the virtual reality (VR) trainer Lap Mentor™. Furthermore, this study aimed to collect validity evidence and to discuss "sources of validity evidence" for the findings using the laparoscopic inguinal hernia module on TS. METHODS: In a randomized crossover study, medical students (n = 40) in their clinical years performed laparoscopic inguinal hernia modules on TS and the VR trainer. TS group started with "Laparoscopic Inguinal Hernia Module" on TS (phase 1: Preparation, phase 2: Port Placement and Hernia Repair), performed the module first in training, then in test mode until proficiency was reached. VR group started with "Inguinal Hernia Module" on the VR trainer (task 1: Anatomy Identification, task 2: Incision and Dissection) and also performed the module until proficiency. Once proficiency reached in the first modality, the groups performed the other training modality until reaching proficiency. Primary endpoint was the number of attempts needed to achieve proficiency for each group for each task/phase. RESULTS: Students starting with TS needed significantly less attempts to reach proficiency for task 1 on the VR trainer than students who started with the VR trainer (TS = 2.7 ± 0.6 vs. VR = 3.2 ± 0.7; p = 0.028). No significant differences for task 2 were observed between groups (TS = 2.3 ± 1.1 vs. VR = 2.1 ± 0.8; p = 0.524). For both phases on TS, no significant skill transfer from the VR trainer to TS was observed. Aspects of validity evidence for the module on TS were collected. CONCLUSION: The results show that TS brought additional benefit to improve performances on the VR trainer for task 1 but not for task 2. Skill transfer from the VR trainer to TS could not be shown. VR and TS should thus be used in combination with TS first in multimodal training to ensure optimal training conditions.
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Hérnia Inguinal , Cirurgiões , Realidade Virtual , Competência Clínica , Simulação por Computador , Estudos Cross-Over , Hérnia Inguinal/cirurgia , Laparoscopia , Estudantes de Medicina , Cirurgiões/educação , Jogos de Vídeo , Humanos , Masculino , Feminino , Adulto JovemRESUMO
BACKGROUND: Anastomotic suturing is the Achilles heel of pancreatic surgery. Especially in laparoscopic and robotically assisted surgery, the pancreatic anastomosis should first be trained outside the operating room. Realistic training models are therefore needed. METHODS: Models of the pancreas, small bowel, stomach, bile duct, and a realistic training torso were developed for training of anastomoses in pancreatic surgery. Pancreas models with soft and hard textures, small and large ducts were incrementally developed and evaluated. Experienced pancreatic surgeons (n = 44) evaluated haptic realism, rigidity, fragility of tissues, and realism of suturing and knot tying. RESULTS: In the iterative development process the pancreas models showed high haptic realism and highest realism in suturing (4.6 ± 0.7 and 4.9 ± 0.5 on 1-5 Likert scale, soft pancreas). The small bowel model showed highest haptic realism (4.8 ± 0.4) and optimal wall thickness (0.1 ± 0.4 on -2 to +2 Likert scale) and suturing behavior (0.1 ± 0.4). The bile duct models showed optimal wall thickness (0.3 ± 0.8 and 0.4 ± 0.8 on -2 to +2 Likert scale) and optimal tissue fragility (0 ± 0.9 and 0.3 ± 0.7). CONCLUSION: The biotissue training models showed high haptic realism and realistic suturing behavior. They are suitable for realistic training of anastomoses in pancreatic surgery which may improve patient outcomes.
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Procedimentos Cirúrgicos do Sistema Digestório , Laparoscopia , Humanos , Técnicas de Sutura , Laparoscopia/educação , Anastomose Cirúrgica , Pâncreas/cirurgia , Competência ClínicaRESUMO
SUMMARY: The detection and prediction of true neoantigens is of great importance for the field of cancer immunotherapy. Wesearched the literature for proposed neoantigen features and integrated them into a toolbox called NEOantigen Feature toolbOX (NeoFox). NeoFox is an easy-to-use Python package that enables the annotation of neoantigen candidates with 16 neoantigen features. AVAILABILITY AND IMPLEMENTATION: NeoFox is freely available as an open source Python package released under the GNU General Public License (GPL) v3 license at https://github.com/TRON-Bioinformatics/neofox. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Antígenos de Neoplasias , Software , Antígenos de Neoplasias/análise , Biologia ComputacionalRESUMO
BACKGROUND: A recent RCT has shown that routine intraoperative drain placement after pancreatoduodenectomy (PD) is not necessary. The aim was to confirm this in real-world conditions. METHODS: A propensity score-matched (PSM) analysis of patients with and without drainage after PD or distal pancreatectomy (DP) at a high-volume centre was undertaken. Main outcomes were complications and duration of hospital stay. Multivariable regression analysis was used to assessed which factors led to intraoperative drainage after the standard was changed from drain to no drain. RESULTS: Of 377 patients who underwent PD, 266 were included in PSM analysis. No drain was associated with fewer major complications (42 (31.6 per cent) versus 62 (46.6 per cent); P = 0.017), shorter duration of hospital stay (mean(s.d.) 14.7(8.5) versus 19.6(14.9) days; P = 0.001), and required fewer interventional drain placements (8.4 versus 19.8 per cent; P = 0.013). In PSM analysis after DP (112 patients), no drainage was associated with fewer clinically relevant postoperative pancreatic fistulas (9 versus 18 per cent; P = 0.016), fewer overall complications (mean(s.d.) comprehensive complication index score 15.9(15.4) versus 24.8(20.4); P = 0.012), and a shorter hospital stay (9.3(7.0) versus 13.5(9.9) days; P = 0.011). Multivisceral resection (OR 2.80, 95 per cent c.i. 1.10 to 7.59; P = 0.034) and longer operating times (OR 1.56, 1.04 to 2.36; P = 0.034) influenced the choice to place a drain after PD. Greater blood loss was associated with drainage after DP (OR 1.14, 1.02 to 1.30; P = 0.031). CONCLUSION: Standard pancreatic resections can be performed safely without drainage. Surgeons were more reluctant to omit drainage after complex pancreatic resections.
Pancreatic surgery has traditionally relied on the use of drains placed during surgery that should facilitate outflow of fluids from the operating site. This principle has recently been challenged by specially designed studies showing that patients who do not receive a drain may have fewer complications. The present study has demonstrated that these results also apply to routine clinical settings outside the constraints of surgical trials.
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Drenagem , Complicações Pós-Operatórias , Humanos , Pancreatectomia , Fístula Pancreática/etiologia , Pancreaticoduodenectomia/efeitos adversos , Complicações Pós-Operatórias/etiologia , Pontuação de PropensãoRESUMO
Communication between individuals via molecules, termed chemosignaling, is widespread among animal and plant species. However, we lack knowledge on the specific functions of the substances involved for most systems. The femoral gland is an organ that secretes a waxy substance involved in chemical communication in lizards. Although the lipids and volatile substances secreted by the femoral glands have been investigated in several biochemical studies, the protein composition and functions of secretions remain completely unknown. Applying a proteomic approach, we provide the first attempt to comprehensively characterize the protein composition of femoral gland secretions from the Galápagos marine iguana. Using samples from several organs, the marine iguana proteome was assembled by next-generation sequencing and MS, resulting in 7513 proteins. Of these, 4305 proteins were present in the femoral gland, including keratins, small serum proteins, and fatty acid-binding proteins. Surprisingly, no proteins with discernible roles in partner recognition or inter-species communication could be identified. However, we did find several proteins with direct associations to the innate immune system, including lysozyme C, antileukoproteinase (ALP), pulmonary surfactant protein (SFTPD), and galectin (LGALS1) suggesting that the femoral glands function as an important barrier to infection. Furthermore, we report several novel anti-microbial peptides from the femoral glands that show similar action against Escherichia coli and Bacillus subtilis such as oncocin, a peptide known for its effectiveness against Gram-negative pathogens. This proteomics data set is a valuable resource for future functional protein analysis and demonstrates that femoral gland secretions also perform functions of the innate immune system.
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Anti-Infecciosos/metabolismo , Anti-Infecciosos/farmacologia , Iguanas/metabolismo , Sistema Imunitário/metabolismo , Imunidade Inata , Proteoma/metabolismo , Transcriptoma , Animais , Apoproteínas/genética , Apoproteínas/metabolismo , Bacillus subtilis/efeitos dos fármacos , Encéfalo/metabolismo , Fatores Quimiotáticos/genética , Fatores Quimiotáticos/metabolismo , Equador , Endopeptidases/genética , Endopeptidases/metabolismo , Escherichia coli/efeitos dos fármacos , Galectinas/genética , Galectinas/metabolismo , Coração/fisiologia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Iguanas/genética , Iguanas/imunologia , Imunidade Inata/genética , Pulmão/metabolismo , Muramidase/genética , Muramidase/metabolismo , Músculos/metabolismo , Miocárdio/metabolismo , Especificidade de Órgãos , Proteoma/genética , Proteoma/imunologia , Proteômica , Proteínas Associadas a Surfactantes Pulmonares/genética , Proteínas Associadas a Surfactantes Pulmonares/metabolismo , Pele/metabolismo , Espectrometria de Massas em Tandem , Transcriptoma/genéticaRESUMO
Heart development relies on PTMs that control cardiomyocyte proliferation, differentiation and cardiac morphogenesis. We generated a map of phosphorylation sites during the early stages of cardiac postnatal development in mice; we quantified over 10,000 phosphorylation sites and 5000 proteins that were assigned to different pathways. Analysis of mitochondrial proteins led to the identification of PGC-1- and ERR-induced regulator in muscle 1 (PERM1), which is specifically expressed in skeletal muscle and heart tissue and associates with the outer mitochondrial membrane. We demonstrate PERM1 is subject to rapid changes mediated by the UPS through phosphorylation of its PEST motif by casein kinase 2. Ablation of Perm1 in mice results in reduced protein expression of lipin-1 accompanied by accumulation of specific phospholipid species. Isolation of Perm1-deficient mitochondria revealed significant downregulation of mitochondrial transport proteins for amino acids and carnitines, including SLC25A12/13/29/34 and CPT2. Consistently, we observed altered levels of various lipid species, amino acids, and acylcarnitines in Perm1-/- mitochondria. We conclude that the outer mitochondrial membrane protein PERM1 regulates homeostasis of lipid and amino acid metabolites in mitochondria.
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Proteínas de Membrana/metabolismo , Membranas Mitocondriais/metabolismo , Proteínas Musculares/metabolismo , Miocárdio/metabolismo , Fosfoproteínas/metabolismo , Proteômica , Animais , Coração/embriologia , Metabolismo dos Lipídeos , Camundongos , Camundongos Knockout , Mitocôndrias Cardíacas/genética , Mitocôndrias Cardíacas/metabolismo , Proteínas Musculares/genética , Organogênese/genética , Proteômica/métodosRESUMO
Heat shock protein 90 (HSP90) stabilizes many client proteins, including the BCR-ABL1 oncoprotein. BCR-ABL1 is the hallmark of chronic myeloid leukemia (CML) in which treatment-free remission (TFR) is limited, with clinical and economic consequences. Thus, there is an urgent need for novel therapeutics that synergize with current treatment approaches. Several inhibitors targeting the N-terminal domain of HSP90 are under investigation, but side effects such as induction of the heat shock response (HSR) and toxicity have so far precluded their US Food and Drug Administration approval. We have developed a novel inhibitor (aminoxyrone [AX]) of HSP90 function by targeting HSP90 dimerization via the C-terminal domain. This was achieved by structure-based molecular design, chemical synthesis, and functional preclinical in vitro and in vivo validation using CML cell lines and patient-derived CML cells. AX is a promising potential candidate that induces apoptosis in the leukemic stem cell fraction (CD34+CD38-) as well as the leukemic bulk (CD34+CD38+) of primary CML and in tyrosine kinase inhibitor (TKI)-resistant cells. Furthermore, BCR-ABL1 oncoprotein and related pro-oncogenic cellular responses are downregulated, and targeting the HSP90 C terminus by AX does not induce the HSR in vitro and in vivo. We also probed the potential of AX in other therapy-refractory leukemias. Therefore, AX is the first peptidomimetic C-terminal HSP90 inhibitor with the potential to increase TFR in TKI-sensitive and refractory CML patients and also offers a novel therapeutic option for patients with other types of therapy-refractory leukemia because of its low toxicity profile and lack of HSR.
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Antineoplásicos/farmacologia , Proteínas de Choque Térmico HSP90/antagonistas & inibidores , Proteínas de Choque Térmico HSP90/química , Resposta ao Choque Térmico/efeitos dos fármacos , Mesilato de Imatinib/farmacologia , Domínios e Motivos de Interação entre Proteínas , Inibidores de Proteínas Quinases/farmacologia , Multimerização Proteica , Animais , Antineoplásicos/química , Sítios de Ligação , Biomarcadores Tumorais , Ciclo Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Modelos Animais de Doenças , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Proteínas de Fusão bcr-abl/antagonistas & inibidores , Proteínas de Fusão bcr-abl/química , Proteínas de Choque Térmico HSP90/metabolismo , Humanos , Mesilato de Imatinib/química , Leucemia Mielogênica Crônica BCR-ABL Positiva/tratamento farmacológico , Leucemia Mielogênica Crônica BCR-ABL Positiva/metabolismo , Camundongos , Modelos Moleculares , Conformação Molecular , Estrutura Molecular , Ligação Proteica , Inibidores de Proteínas Quinases/química , Multimerização Proteica/efeitos dos fármacos , Análise Espectral , Relação Estrutura-Atividade , Ensaios Antitumorais Modelo de XenoenxertoRESUMO
T-cell proliferation and generation of protective memory during chronic infections depend on Interleukin-7 (IL-7) availability and receptivity. Regulation of IL-7 receptor (IL-7R) expression and signalling are key for IL-7-modulated T-cell functions. Aberrant expression of soluble (s) and membrane-associated (m) IL-7R molecules is associated with development of autoimmunity and immune failure in acquired immune deficiency syndrome (AIDS) patients. Here we investigated the role of IL-7/IL-7R on T-cell immunity in human tuberculosis. We performed two independent case-control studies comparing tuberculosis patients and healthy contacts. This was combined with follow-up examinations for a subgroup of tuberculosis patients under therapy and recovery. Blood plasma and T cells were characterised for IL-7/sIL-7R and mIL-7R expression, respectively. IL-7-dependent T-cell functions were determined by analysing STAT5 phosphorylation, antigen-specific cytokine release and by analysing markers of T-cell exhaustion and inflammation. Tuberculosis patients had lower soluble IL-7R (p < 0.001) and higher IL-7 (p < 0.001) plasma concentrations as compared to healthy contacts. Both markers were largely independent and aberrant expression normalised during therapy and recovery. Furthermore, tuberculosis patients had lower levels of mIL-7R in T cells caused by post-transcriptional mechanisms. Functional in vitro tests indicated diminished IL-7-induced STAT5 phosphorylation and impaired IL-7-promoted cytokine release of Mycobacterium tuberculosis-specific CD4+ T cells from tuberculosis patients. Finally, we determined T-cell exhaustion markers PD-1 and SOCS3 and detected increased SOCS3 expression during therapy. Only moderate correlation of PD-1 and SOCS3 with IL-7 expression was observed. We conclude that diminished soluble IL-7R and increased IL-7 plasma concentrations, as well as decreased membrane-associated IL-7R expression in T cells, reflect impaired T-cell sensitivity to IL-7 in tuberculosis patients. These findings show similarities to pathognomonic features of impaired T-cell functions and immune failure described in AIDS patients.
Assuntos
Linfócitos T CD4-Positivos/imunologia , Interleucina-7/sangue , Receptores de Interleucina-7/sangue , Tuberculose/imunologia , Adulto , Idoso , Estudos de Casos e Controles , Feminino , Humanos , Interleucina-7/genética , Interleucina-7/imunologia , Masculino , Pessoa de Meia-Idade , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/fisiologia , Fosforilação , Receptores de Interleucina-7/genética , Receptores de Interleucina-7/imunologia , Fator de Transcrição STAT5/genética , Fator de Transcrição STAT5/imunologia , Proteína 3 Supressora da Sinalização de Citocinas/genética , Proteína 3 Supressora da Sinalização de Citocinas/imunologia , Tuberculose/microbiologia , Adulto JovemRESUMO
Skeletal muscles are composed of heterogeneous collections of fibers with different metabolic profiles. With varied neuronal innervation and fiber-type compositions, each muscle fulfils specific functions and responds differently to stimuli and perturbations. We assessed individual fibers by mass spectrometry to dissect protein changes after loss of neuronal innervation due to section of the sciatic nerve in mice. This proteomics approach enabled us to quantify â¼600 proteins per individual soleus and EDL (extensor digitorum longus) muscle fiber. Expression of myosin heavy chain (MyHC) in individual fibers enabled clustering of specific fiber types; comparison of fibers from control and denervated muscles with the same MyHC expression revealed restricted regulation of a total of 240 proteins in type-I, -IIa, or -IIb fibers 7 days after denervation. The levels of several mitochondrial and proteasomal proteins were significantly altered, indicating rapid adaption of metabolic processes after denervation. Furthermore, we observed fiber-type-specific regulation of proteins involved in calcium ion binding and transport, such as troponins, parvalbumin, and ATP2A2, indicating marked remodeling of muscle contractility after denervation. This study provides novel insight into how different muscle fiber types remodel their proteomes during muscular atrophy.
Assuntos
Fibras Musculares de Contração Rápida/metabolismo , Fibras Musculares Esqueléticas/metabolismo , Fibras Musculares de Contração Lenta/metabolismo , Proteoma/metabolismo , Proteômica/métodos , Animais , Camundongos Endogâmicos C57BL , Proteínas Mitocondriais/metabolismo , Contração Muscular , Denervação Muscular , Proteínas Musculares/metabolismo , Músculo Esquelético/inervação , Músculo Esquelético/metabolismo , Atrofia Muscular/metabolismo , Atrofia Muscular/fisiopatologia , Cadeias Pesadas de Miosina/metabolismo , Complexo de Endopeptidases do Proteassoma/metabolismoRESUMO
BACKGROUND: Endometrioid adenocarcinoma of the uterus and ovarian endometrioid carcinoma share many morphological and molecular features. Differentiation between simultaneous primary carcinomas and ovarian metastases of an endometrial cancer may be very challenging but is essential for prognostic and therapeutic considerations. CASE PRESENTATION: In the present case study of a 33 year-old patient we used targeted amplicon next-generation re-sequencing for clarifying the origin of synchronous endometrioid cancer of the corpus uteri and the left ovary. The patient developed a metachronous lung metastasis of an endometrioid adenocarcinoma four years after hyster- and adnexectomy, vaginal brachytherapy and treatment with the synthetic steroid tibolone. Removal of the metastasis and megestrol treatment for seven years led to a complete remission. A total of 409 genes from the Ampliseq Comprehensive Cancer Panel (Ion Torrent, Thermo Fisher) were analysed by next generation sequencing and mutations in 10 genes, including ARID1A, CTNNB1, PIK3CA and PTEN were identified and confirmed by Sanger sequencing. Primary endometrial as well as ovarian cancer showed an identical mutational profile, suggesting the presence of an ovarian metastasis of the endometrial cancer, rather than a simultaneous endometrial and ovarian cancer. The metachronous lung metastasis showed a different mutational profile compared to the primary cancer. Immunohistochemical staining of the corresponding proteins suggested that the tumour development was driven by alterations in the protein function rather than by changes of the protein abundance in the cell. CONCLUSIONS: Our results have demonstrated next generation sequencing as a valuable tool in the differentiation of synchronous primary tumours and metastases, which has an important impact on the clinical decision making process. Similar to breast cancer, targeted therapies based on mutational tumour profiling will become increasingly important in endometrial and ovarian cancer. In summary, our results support the usage of next generation sequencing as a supplementary diagnostic tool, assisting in personalized precision medicine.
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Biomarcadores Tumorais/genética , Neoplasias do Endométrio/patologia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Neoplasias Pulmonares/secundário , Mutação/genética , Neoplasias Primárias Múltiplas/patologia , Neoplasias Ovarianas/secundário , Adulto , Análise Mutacional de DNA , Neoplasias do Endométrio/genética , Feminino , Humanos , Neoplasias Pulmonares/genética , Neoplasias Primárias Múltiplas/genética , Neoplasias Ovarianas/genética , PrognósticoRESUMO
Ras is a molecular switch cycling between an active, GTP-bound and an inactive, GDP-bound state. Mutations in Ras, mostly affecting the off-switch, are found in many human tumours. Recently, it has been shown that K-Ras 4B is targeted by lysine acetylation at K104. Based on results obtained for an acetylation mimetic Ras mutant (K104Q), it was hypothesised that K104-acetylation might interfere with its oncogenicity by impairing SOS-catalysed guanine-nucleotide exchange. We prepared site-specifically K104-acetylated K-Ras 4B and the corresponding oncogenic mutant protein G12V using the genetic-code expansion concept. We found that SOS-catalysed nucleotide exchange, also of allosterically activated SOS, was neither affected by acetylation of K104 in wildtype K-Ras 4B nor in the G12V mutant, suggesting that glutamine is a poor mimetic for acetylation at this site. In vitro, the lysine-acetyltransferases CBP and p300 were able to acetylate both, wildtype and G12V K-Ras 4B. In addition to K104 we identified further acetylation sites in K-Ras 4B, including K147, within the important G5/SAK-motif. However, the intrinsic and the SOS-catalysed nucleotide exchange was not affected by K147-acetylation of K-Ras 4B. Finally, we show that Sirt2 and HDAC6 do neither deacetylate K-Ras 4B if acetylated at K104 nor if acetylated at K147 in vitro.
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Lisina/metabolismo , Processamento de Proteína Pós-Traducional , Proteínas Proto-Oncogênicas p21(ras)/química , Proteínas Proto-Oncogênicas p21(ras)/metabolismo , Acetilação , Regulação Alostérica , Sequência de Aminoácidos , Animais , Biocatálise , Humanos , Modelos Moleculares , Mutação , Conformação Proteica , Proteínas Proto-Oncogênicas p21(ras)/genética , Proteínas Son Of Sevenless/metabolismoRESUMO
Cancer immunotherapy has witnessed rapid advancement in recent years, with a particular focus on neoantigens as promising targets for personalized treatments. The convergence of immunogenomics, bioinformatics, and artificial intelligence (AI) has propelled the development of innovative neoantigen discovery tools and pipelines. These tools have revolutionized our ability to identify tumor-specific antigens, providing the foundation for precision cancer immunotherapy. AI-driven algorithms can process extensive amounts of data, identify patterns, and make predictions that were once challenging to achieve. However, the integration of AI comes with its own set of challenges, leaving space for further research. With particular focus on the computational approaches, in this article we have explored the current landscape of neoantigen prediction, the fundamental concepts behind, the challenges and their potential solutions providing a comprehensive overview of this rapidly evolving field.
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Antígenos de Neoplasias , Inteligência Artificial , Imunoterapia , Neoplasias , Medicina de Precisão , Humanos , Neoplasias/terapia , Neoplasias/imunologia , Medicina de Precisão/métodos , Antígenos de Neoplasias/imunologia , Imunoterapia/métodos , Biologia Computacional/métodos , AnimaisRESUMO
Motivation: Neoantigens are promising targets for cancer immunotherapies and might arise from alternative splicing. However, detecting tumor-specific splicing is challenging because many non-canonical splice junctions identified in tumors also appear in healthy tissues. To increase tumor-specificity, we focused on splicing caused by somatic mutations as a source for neoantigen candidates in individual patients. Results: We developed the tool splice2neo with multiple functionalities to integrate predicted splice effects from somatic mutations with splice junctions detected in tumor RNA-seq and to annotate the resulting transcript and peptide sequences. Additionally, we provide the tool EasyQuant for targeted RNA-seq read mapping to candidate splice junctions. Using a stringent detection rule, we predicted 1.7 splice junctions per patient as splice targets with a false discovery rate below 5% in a melanoma cohort. We confirmed tumor-specificity using independent, healthy tissue samples. Furthermore, using tumor-derived RNA, we confirmed individual exon-skipping events experimentally. Most target splice junctions encoded neoepitope candidates with predicted major histocompatibility complex (MHC)-I or MHC-II binding. Compared to neoepitope candidates from non-synonymous point mutations, the splicing-derived MHC-I neoepitope candidates had lower self-similarity to corresponding wild-type peptides. In conclusion, we demonstrate that identifying mutation-derived, tumor-specific splice junctions can lead to additional neoantigen candidates to expand the target repertoire for cancer immunotherapies. Availability and implementation: The R package splice2neo and the python package EasyQuant are available at https://github.com/TRON-Bioinformatics/splice2neo and https://github.com/TRON-Bioinformatics/easyquant, respectively.
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Previous studies showed that the neoantigen candidate load is an imperfect predictor of immune checkpoint blockade (ICB) efficacy. Further studies provided evidence that the response to ICB is also affected by the qualitative properties of a few or even single candidates, limiting the predictive power based on candidate quantity alone. Here, we predict ICB efficacy based on neoantigen candidates and their neoantigen features in the context of the mutation type, using Multiple-Instance Learning via Embedded Instance Selection (MILES). Multiple instance learning is a type of supervised machine learning that classifies labeled bags that are formed by a set of unlabeled instances. MILES performed better compared with neoantigen candidate load alone for low-abundant fusion genes in renal cell carcinoma. Our findings suggest that MILES is an appropriate method to predict the efficacy of ICB therapy based on neoantigen candidates without requiring direct T cell response information.
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Introduction: The cell line MC38 is a commonly used murine model for colorectal carcinoma. It has a high mutational burden, is sensitive to immune checkpoint immunotherapy and endogenous CD8+ T cell responses against neoantigens have been reported. Methods: Here, we re-sequenced exomes and transcriptomes of MC38 cells from two different sources, namely Kerafast (originating from NCI/NIH, MC38-K) and the Leiden University Medical Center cell line collection (MC38-L), comparing the cell lines on the genomic and transcriptomic level and analyzing their recognition by CD8+ T cells with known neo-epitope specificity. Results: The data reveals a distinct structural composition of MC38-K and MC38-L cell line genomes and different ploidies. Further, the MC38-L cell line harbored about 1.3-fold more single nucleotide variations and small insertions and deletions than the MC38-K cell line. In addition, the observed mutational signatures differed; only 35.3% of the non-synonymous variants and 5.4% of the fusion gene events were shared. Transcript expression values of both cell lines correlated strongly (p = 0.919), but we found different pathways enriched in the genes that were differentially upregulated in the MC38-L or MC38-K cells, respectively. Our data show that previously described neoantigens in the MC38 model such as Rpl18mut and Adpgkmut were absent in the MC38-K cell line resulting that such neoantigen-specific CD8+ T cells recognizing and killing MC38-L cells did not recognize or kill MC38-K cells. Conclusion: This strongly indicates that at least two sub-cell lines of MC38 exist in the field and underlines the importance of meticulous tracking of investigated cell lines to obtain reproducible results, and for correct interpretation of the immunological data without artifacts. We present our analyses as a reference for researchers to select the appropriate sub-cell line for their own studies.
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Neoplasias Colorretais , Transcriptoma , Humanos , Animais , Camundongos , Linfócitos T CD8-Positivos , Linhagem Celular Tumoral , MutaçãoRESUMO
Somatic mutations in cancer cells can generate tumour-specific neoepitopes, which are recognized by autologous T cells in the host. As neoepitopes are not subject to central immune tolerance and are not expressed in healthy tissues, they are attractive targets for therapeutic cancer vaccines. Because the vast majority of cancer mutations are unique to the individual patient, harnessing the full potential of this rich source of targets requires individualized treatment approaches. Many computational algorithms and machine-learning tools have been developed to identify mutations in sequence data, to prioritize those that are more likely to be recognized by T cells and to design tailored vaccines for every patient. In this Review, we fill the gaps between the understanding of basic mechanisms of T cell recognition of neoantigens and the computational approaches for discovery of somatic mutations and neoantigen prediction for cancer immunotherapy. We present a new classification of neoantigens, distinguishing between guarding, restrained and ignored neoantigens, based on how they confer proficient antitumour immunity in a given clinical context. Such context-based differentiation will contribute to a framework that connects neoantigen biology to the clinical setting and medical peculiarities of cancer, and will enable future neoantigen-based therapies to provide greater clinical benefit.
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Vacinas Anticâncer , Neoplasias , Antígenos de Neoplasias/genética , Humanos , Imunoterapia , Neoplasias/genética , Neoplasias/terapia , Linfócitos TRESUMO
After one year of absence, the 18th Annual Meeting of the Association for Cancer Immunotherapy (CIMT), Europe's cancer immunotherapy meeting, took place virtually from 10 to 12 May 2021. Over 850 academic and clinical professionals from 30 countries met to discuss the recent advancements in cancer immunotherapy and the current progress in COVID19-related research. This meeting report summarizes the highlights of CIMT2021.
Assuntos
COVID-19 , Neoplasias , Humanos , Imunoterapia , Neoplasias/terapia , Microambiente TumoralRESUMO
Cancer-associated gene fusions are a potential source for highly immunogenic neoantigens, but the lack of computational tools for accurate, sensitive identification of personal gene fusions has limited their targeting in personalized cancer immunotherapy. Here we present EasyFuse, a machine learning computational pipeline for detecting cancer-specific gene fusions in transcriptome data obtained from human cancer samples. EasyFuse predicts personal gene fusions with high precision and sensitivity, outperforming previously described tools. By testing immunogenicity with autologous blood lymphocytes from patients with cancer, we detected pre-established CD4+ and CD8+ T cell responses for 10 of 21 (48%) and for 1 of 30 (3%) identified gene fusions, respectively. The high frequency of T cell responses detected in patients with cancer supports the relevance of individual gene fusions as neoantigens that might be targeted in personalized immunotherapies, especially for tumors with low mutation burden.
Assuntos
Antígenos de Neoplasias , Neoplasias , Antígenos de Neoplasias/genética , Linfócitos T CD8-Positivos , Fusão Gênica , Humanos , Imunoterapia , Neoplasias/genética , Neoplasias/terapiaRESUMO
Heat shock proteins 90 (Hsp90) are promising therapeutic targets due to their involvement in stabilizing several aberrantly expressed oncoproteins. In cancerous cells, Hsp90 expression is elevated, thereby exerting antiapoptotic effects, which is essential for the malignant transformation and tumor progression. Most of the Hsp90 inhibitors (Hsp90i) under investigation target the ATP binding site in the N-terminal domain of Hsp90. However, adverse effects, including induction of the prosurvival resistance mechanism (heat shock response or HSR) and associated dose-limiting toxicity, have so far precluded their clinical approval. In contrast, modulators that interfere with the C-terminal domain (CTD) of Hsp90 do not inflict HSR. Since the CTD dimerization of Hsp90 is essential for its chaperone activity, interfering with the dimerization process by small-molecule protein-protein interaction inhibitors is a promising strategy for anticancer drug research. We have developed a first-in-class small-molecule inhibitor (5b) targeting the Hsp90 CTD dimerization interface, based on a tripyrimidonamide scaffold through structure-based molecular design, chemical synthesis, binding mode model prediction, assessment of the biochemical affinity, and efficacy against therapy-resistant leukemia cells. 5b reduces xenotransplantation of leukemia cells in zebrafish models and induces apoptosis in BCR-ABL1+ (T315I) tyrosine kinase inhibitor-resistant leukemia cells, without inducing HSR.