Genomic profiling, or molecular profiling of the tumor, is becoming a key component of therapeutic decision making in clinical oncology, and is typically carried out via next generation sequencing. However, the interpretation of the results and evaluation of rationale for targeting the uncovered alterations is challenging and requires a deep understanding of cancer biology, genetics, genomics and oncology. Multidisciplinary molecular tumor boards represent a promising strategy in the facilitation of molecularly-informed therapeutic decisions, and usually consist of specialists with various fields of expertise. To effectively communicate the biological and clinical significance of genomic findings, as well as to make molecular tumor board discussions more productive, we developed and implemented evidence blocks into case discussions in our center. We found that this approach facilitated clinicians' understanding of the results of genomic profiling, and resulted in shorter yet more efficient case discussions within the molecular tumor board. Here, we discuss our experience with evidence blocks and how their implementation influenced the molecular tumor board practice.
With the increased use of gene expression profiling for personalized oncology, optimized RNA sequencing (RNA-seq) protocols and algorithms are necessary to provide comparable expression measurements between exome capture (EC)-based and poly-A RNA-seq. Here, we developed and optimized an EC-based protocol for processing formalin-fixed, paraffin-embedded samples and a machine-learning algorithm, Procrustes, to overcome batch effects across RNA-seq data obtained using different sample preparation protocols like EC-based or poly-A RNA-seq protocols. Applying Procrustes to samples processed using EC and poly-A RNA-seq protocols showed the expression of 61% of genes (N = 20,062) to correlate across both protocols (concordance correlation coefficient > 0.8, versus 26% before transformation by Procrustes), including 84% of cancer-specific and cancer microenvironment-related genes (versus 36% before applying Procrustes; N = 1,438). Benchmarking analyses also showed Procrustes to outperform other batch correction methods. Finally, we showed that Procrustes can project RNA-seq data for a single sample to a larger cohort of RNA-seq data. Future application of Procrustes will enable direct gene expression analysis for single tumor samples to support gene expression-based treatment decisions.
Gene Expression Profiling , RNA , Humans , Tissue Fixation/methods , Gene Expression Profiling/methods , RNA/genetics , Sequence Analysis, RNA/methods , Machine Learning
Colorectal cancer (CRC) is currently one of the most common tumor types diagnosed worldwide. In the early stages, the disease responds well to surgical and chemotherapeutic treatment, but in the later stages when therapeutic options are exhausted, comprehensive genomic profiling can guide further treatment decisions. We present the case of a 46-year-old man of Ashkenazi Jewish ancestry who was diagnosed with KRAS-mutated metastatic colorectal cancer. After surgery and progression on standard FOLFOX/FOLFIRI + bevacizumab therapy, as well as on Trifluridine/Tipiracil, comprehensive genomic profiling was performed with the hope of expanding therapeutic options. Following comprehensive tumor molecular profiling via NGS, a discussion of the case was discussed at the local molecular tumor board in order to determine further treatment strategy. An activating variant of KRAS and PIK3CA, FLT3 and SRC amplification and damaging TP53 and APC variants were discarded by MTB as potential targetable biomarkers. The BRCA2 p.S1415fs*4 founder frameshift variant was of interest and the patient was included in the clinical trial investigating the efficacy of a PARP inhibitor talazoparib. Unfortunately, the disease progression was detected within one month of talazoparib treatment and the patient died during the 8th cycle of FOLFIRI + bevacizumab therapy rechallenge.
Despite the existence of effective first and second line therapy options for patients with colorectal cancer, heavily treated patients have limited additional therapies. Genomic profiling is a promising tool for guiding subsequent treatment selection. Here, we describe the results of treating a colorectal cancer patient with molecularly-matched therapy based on the results of genomic profiling. The patient received a combination of afatinib and bevacizumab due to the presence of ERRFI1 variant. To our knowledge, this is the first report on the effect of EGFR inhibitors in patients with ERRFI1-altered RAS/BRAF wild-type colorectal adenocarcinoma.
Microsatellite instability (MSI) is one of the most important molecular characteristics of a tumor, which occurs among various tumor types. In this review article, we examine the molecular characteristics of MSI tumors, both sporadic and Lynch-associated. We also overview the risks of developing hereditary forms of cancer and potential mechanisms of tumor development in patients with Lynch syndrome. Additionally, we summarize the results of major clinical studies on the efficacy of immune checkpoint inhibitors for MSI tumors and discuss the predictive role of MSI in the context of chemotherapy and checkpoint inhibitors. Finally, we briefly discuss some of the underlying mechanisms causing therapy resistance in patients treated with immune checkpoint inhibitors.
This study is one of the first attempts to assess CeO2 nanoparticles as a nanoplatform for radiopharmaceuticals with radionuclides. The process of functionalization using a bifunctional azacrown ligand is described, and the resulting conjugates are characterized by IR and Raman spectroscopy. Their complexes with 207Bi show a high stability in medically relevant media, thus encouraging the further study of these conjugates in vivo as potential combined radiopharmaceuticals.
In this paper, we propose and use a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure using external force actions. A molecular dynamics manipulator (MD manipulator) is a controlled MDS type. As an example, the applicability of the developed algorithm for assembling peptide nanotubes (PNT) from linear phenylalanine (F or Phe) chains of different chirality is presented. The most adequate regimes for the formation of nanotubes of right chirality D from the initial L-F and nanotubes of left chirality L of their initial dipeptides D-F modes were determined. We use the method of a mixed (vector-scalar) product of the vectors of the sequence of dipole moments of phenylalanine molecules located along the nanotube helix to calculate the magnitude and sign of chirality of self-assembled helical phenylalanine nanotubes, which shows the validity of the proposed approach. As result, all data obtained correspond to the regularity of the chirality sign change of the molecular structures with a hierarchical complication of their organization.
In this study we consider the features of spatial-structure formation in proteins and their application in bioengineering. Methods for the quantitative assessment of the chirality of regular helical and irregular structures of proteins are presented. The features of self-assembly of phenylalanine (F) into peptide nanotubes (PNT), which form helices of different chirality, are also analyzed. A method is proposed for calculating the magnitude and sign of the chirality of helix-like peptide nanotubes using a sequence of vectors for the dipole moments of individual peptides.
Using ferrocenecarboxylic acid (FcCO2H) and triethanolamine (H3tea) as ligands, the isostructural heterotrimetallic complexes [LnIII2CrIII2(OH)2(FcCO2)4(NO3)2(Htea)2]·2MePh·2THF (Ln = Tb (1), Dy (2), Ho (3), Er (4), and Y (5); Fc = (η5-C5H4)(η5-C5H5)Fe; H3tea = N(CH2CH2OH)3) were obtained. In all of the complexes which possess a defective dicubane structure, two doubly deprotonated triethanolamine ligands chelate the chromium ions. However, during the synthesis of 1, an isomeric complex 1a in which Tb3+ is chelated by triethanolamine as a tetradentate ligand, was also isolated as a few single crystals. Magnetic susceptibility measurements revealed dominant antiferromagnetic interactions in the {LnIII2CrIII2} cores of 1-4 leading to the formation of complexes with an uncompensated magnetic moment, while weak Cr-Cr ferromagnetic interactions were detected in the Y analogue. Complexes 1, 2, and 3 exhibit single-molecule magnet properties dominated by an Orbach-type relaxation mechanism with magnetization reversal barriers (Δ/kB) estimated around 54, 75, and 47 K, respectively. The Dy complex exhibits a magnetization hysteresis in an applied magnetic field at temperatures below 4 K. Thermolysis of the complexes was studied by TGA and DSC techniques; the final products obtained under an air atmosphere contain mixed oxide Cr0.75Fe1.25O3 and heterotrimetallic oxide LnCr1-xFexO3 (with x ≈ 0.75) phases.
We prepared and studied two similar series of Er and Yb thiocyanates, involving [Ln(H2O)5(NCS)3]·H2O (1Er, 1Yb) as well as the molecular and ionic complexes with 2,2'-bipyridine (bpy) and 1,10-phenantroline (phen), [Ln(H2O)(bpy)2(NCS)3]·0.5(bpy)·H2O (2Er, 2Yb), [Ln(H2O)(phen)2(NCS)3]·phen·0.5H2O (3Er, 3Yb), [Hbpy][Ln(bpy)2(NCS)4]·H2O (4Er, 4Yb) and [Hphen][Ln(phen)2(NCS)4] (5Er, 5Yb). All the complexes were found to exhibit the properties of field-induced single-molecule magnets. For 1Yb, the effective value of the energy barrier for magnetization reversal, Δeff/kB, equals to 50 K, which is among the highest ones currently known for molecular SMMs based on Yb3+. The obtained data are discussed involving essential structural features of the complexes, namely the configuration of the Ln environment, i.e. its composition and geometry as well as mutual distribution of different donating centers. To the best of our knowledge, this work also involves experimental investigation of the largest and thus sufficiently representative series of similar mononuclear SMMs based on Er and Yb within one study.
