Processing Machinery Research Articles

Miniature Inverted-repeat Transposable Elements Drive Rapid MicroRNA Diversification in Angiosperms.

MicroRNAs (miRNAs) are fast evolving endogenous small RNAs that regulate organism function and behavior in both animals and plants. Although models for de novo miRNA biogenesis have been proposed, the genomic mechanisms driving swift diversification of the miRNA repertoires in plants remain elusive. Here, by comprehensively analyzing 21 phylogenetically representative plant species, ranging from green algae to angiosperms, we systematically identified de novo miRNA events associated with 8,649 miRNA loci. We found that 399 (4.6%), 466 (5.4%), and 1,402 (16.2%) miRNAs were derived from inverted gene duplication events, long terminal repeats of retrotransposons, and miniature inverted-repeat transposable elements (MITEs), respectively. Among the miRNAs of these origins, MITEs, especially those belonging to the Mutator, Tc1/Mariner, and PIF/Harbinger superfamilies, were the predominant genomic source for de novo miRNAs in the 15 examined angiosperms but not in the six non-angiosperms. Our data further illustrated a transposition-transcription process by which MITEs are converted into new miRNAs (termed MITE-miRNAs) whereby properly sized MITEs are transcribed and therefore become potential substrates for the miRNA processing machinery by transposing into introns of active genes. By analyzing the 58,038 putative target genes for the 8,095 miRNAs, we found that the target genes of MITE-miRNAs were preferentially associated with response to environmental stimuli such as temperature, suggesting that MITE-miRNAs are pertinent to plant adaptation. Collectively, these findings demonstrate that molecular conversion of MITEs is a genomic mechanism leading to rapid and continuous changes to the miRNA repertoires in angiosperm.

Integrasi ANP dan TOPSIS dalam Pemilihan Strategi Pemasaran yang Optimal

Creating a competitive advantage by providing value to customers has become a major focus in the formulation of marketing strategies. Making a good marketing strategy, companies can maximize the company's internal strengths and minimize existing weaknesses. CV ABC is a company engaged in the manufacture and supply of agricultural machinery, plantation machinery, fishery machinery, food processing tools and machinery and laboratory equipment. This research process uses the multi-criteria decision-making method Analytic Network Process (ANP) to determine the weight of the importance of the marketing resource evaluation criteria, as well as the TOPSIS method to obtain the best and ideal marketing strategy. The purpose of this research is to determine the optimal marketing strategy to be applied to the company. Therefore, this study uses the ANP method to obtain the relative weight of each criterion based on the respondents' subjective assessment of the company in CV ABC. To assess each marketing strategy, the TOPSIS method is used to rank the best and most ideal marketing strategies applied in the company. Based on the ANP results obtained, there are five criteria that are considered important in determining marketing strategies, these criteria are the ability to relate to customers (0,423), Reputation and Competition (0,208), Human Resource Assets (0,142), Market Innovation Ability (0,140), and Managerial Ability (0,088). The results of the ranking show that the differentiation strategy is the optimal marketing strategy for CV ABC.

MM-210 Targeting Proteasome-Dependent Antigen Presentation to Enhance T Cell–Mediated Tumor Killing

Cancer immunotherapy has emerged as a leading strategy in the war on cancer; however, only a minority of patients exhibit maximal benefits and durable responses. Proteasomes are central components of the proteolytic processing machinery required to generate antigenic peptides presented by MHC class I molecules to cytotoxic T lymphocytes (CTLs). Since cancer cells downregulate the generation and presentation of antigenic peptides to escape anti-tumor immunity, we hypothesized that proteasomal generation of antigenic peptides could be pharmacologically enhanced to increase tumor antigen presentation and enhance CTL-mediated tumor lysis. We performed a cell-based, high-throughput screen (HTS) using ~3,400 FDA-approved drugs and bioactive molecules to identify agents that increased proteasomal peptide-hydrolyzing activity. We then determined whether "hits" identified in the HTS also increased the presentation of a specific MHC class I antigen, SIINFEKL, which is derived from chicken ovalbumin. We engineered a T cell that specifically expresses a T-cell receptor (TCR) that recognizes SIINFEKL. Tumor cells were pre-treated with hits identified in the HTS, most notably the histone deacetylase (HDAC6) inhibitors Tubastatin A and ACY-1215, and then incubated with the engineered T cells to determine the effect on T cell-mediated tumor lysis. We found that Tubastatin A and ACY-1215 potently increased proteasome activity in the cell-based assay. We employed the lymphoma cell line EG.7-ova that constitutively expresses the chicken ovalbumin gene. Proteasomal degradation of ovalbumin generates a peptide, SIINFEKL, that is presented at the tumor surface complexed with the MHC class I molecule. Treatment of EG. 7-ova cells with HDAC6 inhibitors enhanced the presentation of the SIINFEKL:MHC class I complex nearly 3-fold. CTLs were then engineered to express a TCR that specifically recognizes SIINFEKL. When EG.7-ova cells were pre-treated with HDAC6 inhibitors and then co-cultured with SIINFEKL-restricted CTLs, tumor lysis was also increased up to 3-fold. Western blotting showed that treatment of MM cells with HDAC6 inhibitors increased immunoproteasome levels and catalytic activity. Taken together, our results endorse a paradigm-shifting approach to exploit pharmacologics that enhance the proteasomal generation of tumor antigens as an anti-myeloma strategy. Pharmacologic modulation of proteasome activity potently stimulates the presentation of tumor antigens and represents an actionable approach to trigger anti-myeloma immunity.

204. THE TUMOUR IMMUNE MICROENVIRONMENT IN OESOPHAGEAL ADENOCARCINOMA HAS PROGNOSTIC SIGNIFICANCE

Abstract Oesophageal adenocarcinoma (OAC) is a deadly disease with an increasing incidence globally. Treatment outcomes with traditional therapy have largely plateaued and responses to immunotherapy are modest at best, necessitating the need for better biomarker driven selection. We aimed to unravel the tumour neoantigen landscape and immune microenvironment in OAC patients to aid improved patient selection and inform novel immunotherapy trials. To characterise the tumour immune microenvironment and neoantigen landscape of OACs, we performed DNA sequencing (n = 117) and RNA sequencing (n = 115) on biopsies taken at pre-treatment endoscopy. Using expression-based computational methods we analysed transcriptomic data to profile infiltration levels of 28 immune cell populations and their functional orientation, as well as stromal signatures and immune checkpoint molecules. TCGA data was used for as a validation cohort. Tumour neoantigens were predicted using the pVAC-Seq pipeline. Using an immune based classification based on the tumour microenvironment composition, we identified three distinct phenotypes; immune-enriched (IE), heterogeneously-infiltrated (HI), and immune-cold (IC). The IE group showed improved survival compared to both HI and IC, with HI showing the worst survival. The HI-group showed no difference in stromal scores to the IE group, but showed significantly decreased adaptive-immune cell infiltration, indicating that an immunosuppressive stromal compartment may be driving outcomes for these patients. No difference was seen in total or quality neoantigen load between groups, but high correlation with antigen processing machinery is seen. Our analysis expands the knowledge of the relatively unknown tumour immune microenvironment of OAC. We have identified three immune TME-phenotypes with prognostic utility with current standard of care therapies; which may also act as potential immunotherapy biomarkers. This is being explored further in ongoing immune microenvironment research and will guide future translational studies.

Temporal reproduction: A paradigm indicating a 3-s time window.

The experimental paradigm of temporal reproduction has provided unique insights into the temporal machinery of cognitive processes. Both behavioral observations and electrophysiological methods with this paradigm indicate a time window of some 3 s.

End9: an early-passage cell line defective in master HLA-I transcriptional coordinators

Disruption in the HLA class I (HLA-I), β2-microglobulin (β2M) and/or Antigen Processing and Presentation Machinery (APPM) structural genes is believed to favor tumor immune escape, whereas purely regulatory mutants are few and poorly characterized. The endometrial carcinoma End9 was the extreme HLA-I/APPM-low outlier in a panel of >100 early-passage tumor cell lines established in culture by us from essentially all major tumor histotypes. The defect arose in vivo, was retained in culture, and remained stable for >100 passages. End9 was found to express no constitutive or IFN-responsive HLA-A, -B, -F, and-G, little HLA-C and β2m, ‘normal‘ HLA-E, and barely detectable TAP, tapasin, LMP2, LMP7, ERAP1 and ERAP2, as evaluated by protein and nucleic acid biochemistry. Lacking evidence for genomic damage, we used a reporter construct to assess the 3 major upstream HLA-I regulatory boxes (EnhA, ISRE and SXY), and attempted phenotypic rescue by transduction with missing trans-acting function(s). The NF-KB:EnhA interplay was apparently conserved, whereas the ISRE and SXY modules were simultaneously shut off due to (a) a complete JAK1 absence, (b) a physiological lack of CIITA, and (c) an epigenetic (5-Azacitidine-reversible) suppression of an intact (as per sequencing) NLRC5. The near-zero HLA-I/APPM phenotype of End9 highlighted several features of HLA-I regulation, including: (a) SXY-independent HLA-C transcription; (b) subordination of the EnhA and ISRE boxes (IFN and TNFα responsiveness) to promoter opening by CIITA/NLRC5; and (c) marginal HLA-I/APPM transactivation by residual NLRC5 at baseline and even upon >100X overexpression. End9 is the first regulatory mutant defective in a hierarchically high set of transacting functions operating upstream to most HLA-I/APPM members, resulting in a trophoblast-like, presumably immunoevasive phenotype. The defect involves NLRC5 but NLRC5 refractoriness implies a shortage of other transcriptional co-activators, making End9 a suitable recipient for complementation cloning to discover novel HLA-A/-B/APPM master coordinators.

Sequestering the 5'-cap for viral RNA packaging.

Many viruses evolved mechanisms for capping the 5'-ends of their plus-strand RNAs as a means of hijacking the eukaryotic messenger RNA (mRNA) splicing/translation machinery. Although capping is critical for replication, the RNAs of these viruses have other essential functions including their requirement to be packaged as either genomes or pre-genomes into progeny viruses. Recent studies indicate that human immunodeficiency virus type-1 (HIV-1) RNAs are segregated between splicing/translation and packaging functions by a mechanism that involves structural sequestration of the 5'-cap. Here, we examined studies reported for other viruses and retrotransposons that require both selective packaging of their RNAs and 5'-RNA capping for host-mediated translation. Our findings suggest that viruses and retrotransposons have evolved multiple mechanisms to control 5'-cap accessibility, consistent with the hypothesis that removal or sequestration of the 5' cap enables packageable RNAs to avoid capture by the cellular RNA processing and translation machinery.

Assembly of the immunoproteasome in cDC2 allows for cross-presentation of antigens under stimulatory conditions in vivo

Dendritic cells are major initiators of immune responses, but are also responsible for the maintenance of peripheral T cell tolerance. A critical decision for induction of immune activation or immune tolerance is dependent on the activation status of DCs, which could be induced by the presence of diverse pathogens. For the recognition of pathogen associated molecular patterns (PAMPs) DCs express pattern recognition receptors (PRR), such as Toll-like receptors (TLR), or C-type lectin receptors (CLR). Previously, we have demonstrated, that steady-state DC subpopulations are specialized regarding processing and presentation of captured antigens. Therefore, DCs tightly control and direct activation of different T cell responses. Here, we investigated how TLR-mediated activation of murine cDC1 and cDC2 DCs influences the expression of molecules involved in the MHC class I antigen processing machinery. We provide evidence that activation of cDC2 DCs induces upregulation of Calreticulin, Calnexin, Erap1, ERp57, TAP1, TAP2, and Tapasin under certain immunostimulatory conditions in vivo. Importantly, delivery of targeted antigens to cDC2 DCs in combination with specific TLR-ligands allowed for cross-presentation and activation of CD8+ T cells in wildtype but also BATF3-/-(missing cDC1 DCs) mice in vivo. Moreover, the complete knock out of the three immunoproteasome subunits (β1i, β2i, β5i) hindered the cross-presentation of antigens by cDC2, but not cDC1 DCs. Our findings suggest that DCs harbor a strong flexibility in counteracting infections and tumor development if they are appropriately stimulated.

Soluble T cell receptor-based immunotherapies empowered by large scale HLA ligandomics

Immunocore focuses on the development of T cell receptor (TCR)-based bispecifics for immunotherapy. Soluble, affinity-enhanced, TCR-based molecules are engineered to target peptides presented on the cell surface in complex with Human Leucocyte Antigen (HLA) molecules (peptide:HLA). Essential to our platform is the identification and validation of peptide:HLA targets, achieved by mass spectrometry (MS). We have particularly focussed on characterizing the immunopeptidome of the most frequent allele, HLA-A*02:01. HLA complexes are isolated from immortalized cancer cells and tumour tissues by affinity purification using various HLA-restriction specific antibodies. HLA peptides, eluted under acidic conditions, are fractionated by reverse phase liquid chromatography and analysed by LC-MS/MS. Mass spectra, searched using PEAKS, are integrated with gene expression and HLA typing data in an in-house database. Fully validated target peptides are used to clonally expand HLA-peptide specific T cells. Isolated TCRs are engineered into soluble molecules (mTCRs) whose affinity is enhanced using phage display technology. Our HLA peptidomic workflow combines novel biochemical techniques with high resolution mass spectrometry and extensive data integration to maximise the depth of the HLA ligandome. Our combined findings across hundreds of cancer cell lines provides peptide information on all protein coding genes, with the very low novelty rate observed in tissue material suggesting that the processing machinery of in vitro model systems accurately represent the tissue environment. Our Immune mobilising monoclonal T cell receptors Against Cancer molecules (ImmTAC®) are generated by coupling high-affinity mTCRs with an anti-CD3 scFv domain to redirect polyclonal T cell responses toward cancer cells. Immunocore has three ImmTAC molecules in clinical trials with our lead candidate, IMCgp100, entered in pivotal trials as a monotherapy for the treatment of patients with metastatic uveal melanoma (NCT03070392, clinicaltrials.gov). Our cell line-based HLA-A*02:01peptide atlas represents a comprehensive resource for effective design of TCR-based immunotherapeutics for cancer treatment.

Investigating the MHC Class II-Restricted Processing Landscape of HIV-1 Antigens

Robust HIV-specific CD4 T cell (TCD4+) responses are associated with decreased viral load, increased antibody neutralization breadth, and a slower progression to AIDS, and should therefore be considered in HIV vaccine development. TCD4+ are activated by antigen-derived peptides displayed in complex with MHCII on the surface of antigen presenting cells (APC). According to the classical model, internalized antigens are processed and loaded onto MHCII in late endosomal compartments. However, alternative mechanisms, such as endogenous processing, have been described. Endogenous processing occurs when virally-derived antigens produced within infected APCs are proteolyzed and loaded onto MHCII by a network of intracellular pathways. The contribution of these alternative processing pathways is not insignificant: our laboratory has shown that endogenous processing drives the vast majority of the in vivo TCD4+ response to influenza virus. The relative contributions of these pathways to the HIV-specific TCD4+ response, however, are unknown. Furthermore, our understanding of the cell types that act as APCs during HIV-1 infection is incomplete. For example, TCD4+, which transiently express MHCII and costimulatory molecules upon activation and are HIV host cells, might act in this capacity. To this end, we have assessed the processing and presentation capabilities of key cell types, including dendritic cells and macrophages. We observe significant heterogeneity in the processing of HIV-1 proteins by these cells. In addition, we found that activated TCD4+ express several components of the antigen processing machinery and are able to present antigen derived from a live HIV-1 infection. Future work is aimed at identifying the underlying machinery involved in this presentation, with the long-term goal of informing rational HIV-1 vaccine design.

Nuclear m6 A reader YTHDC1 suppresses proximal alternative polyadenylation sites by interfering with the 3' processing machinery.

N6-methyladenosine (m6 A) and alternative polyadenylation (APA) are important regulators of gene expression in eukaryotes. Recently, it was found that m6 A is closely related to APA. However, the molecular mechanism of this new APA regulation remains elusive. Here, we show that YTHDC1, a nuclear m6 A reader, can suppress proximal APA sites and produce longer 3' UTR transcripts by binding to their upstream m6 A sites. YTHDC1 can directly interact with the 3' end processing factor FIP1L1 and interfere with its ability to recruit CPSF4. Binding to the m6 A sites can promote liquid-liquid phase separation of YTHDC1 and FIP1L1, which may play an important role in their interaction and APA regulation. Collectively, YTHDC1 as an m6 A "reader" links m6 A modification with pre-mRNA 3' end processing, providing a new mechanism for APA regulation.

Moisture‐dependent engineering properties of underutilized browntop millet (unhulled and hulled) and characterization of milled flour

AbstractBrowntop millet is an underutilized indigenous cereal crop. It is termed as the nutricereal due to its superiority in terms of nutritional quality. The current study attempted to investigate the effect of moisture content (10%–27%) on properties such as physical, mechanical, aerodynamic, and textural properties of unhulled and hulled browntop millet to uncover the gaps in developing the efficient primary processing machinery. In addition, we investigated the impact of milling on the biochemical, functional, color, structural, and powder flow properties of browntop millet flour. The results revealed that as the moisture content increased, the principle dimensions, 1000 grain weight, terminal velocity, angle of repose, and static coefficient of friction were linearly increased. In the same moisture content range, characteristics such as true density, bulk density, porosity, and hardness displayed an inverse trend. Milling showed a substantial (p < 0.05) influence on the nutritional, functional and color parameters. FTIR spectra and X‐ray diffraction patterns demonstrated a slight change in functional groups and a slight decrease in starch crystallinity respectively. All three millet flours were cohesive. These flours, however, exhibited a positive correlation with bulk density and a negative correlation with wall friction and effective internal friction angles as the principle consolidating stress increased.Practical ApplicationMillets are a globally significant food crop with major economic influence in developing nations. They are one of the most significant drought‐resistant crops, and a good source of health‐promoting complex carbohydrates, dietary fiber, phenolic compounds, and phytochemicals. Despite of their high nutritional superiority and environmental friendliness, production and consumption have declined over the years. The significant factor contributing to this decline is the lack of machinery or equipment available to process on a commercial and residential scale after harvest. The knowledge of the measured properties will encourage researchers to develop and modernize equipment used for destoning, grading, sorting, separation, dehulling, and conveying. The measured nutritional, mineral, functional, structural, and powder flow properties of milled browntop millet fractions will help develop a new product. So that millet can be used to its full potential.

Ionizing Radiation Drives Key Regulators of Antigen Presentation and a Global Expansion of the Immunopeptidome

Little is known about the pathways regulating MHC antigen presentation and the identity of treatment-specific T cell antigens induced by ionizing radiation. For this reason, we investigated the radiation-specific changes in the colorectal tumor cell proteome. We found an increase in DDX58 and ZBP1 protein expression, two nucleic acid sensing molecules likely involved in induction of the dominant interferon response signature observed after genotoxic insult. We further observed treatment-induced changes in key regulators and effector proteins of the antigen processing and presentation machinery. Differential regulation of MHC allele expression was further driving the presentation of a significantly broader MHC-associated peptidome postirradiation, defining a radiation-specific peptide repertoire. Interestingly, treatment-induced peptides originated predominantly from proteins involved in catecholamine synthesis and metabolic pathways. A nuanced relationship between protein expression and antigen presentation was observed where radiation-induced changes in proteins do not correlate with increased presentation of associated peptides. Finally, we detected an increase in the presentation of a tumor-specific neoantigen derived from Mtch1. This study provides new insights into how radiation enhances antigen processing and presentation that could be suitable for the development of combinatorial therapies. Data are available via ProteomeXchange with identifier PXD032003.

U1 snRNP proteins promote proximal alternative polyadenylation sites by directly interacting with 3' end processing core factors.

In eukaryotic cells, both alternative splicing and alternative polyadenylation (APA) play essential roles in the gene regulation network. U1 small ribonucleoprotein particle (U1 snRNP) is a major component of spliceosome, and U1 snRNP complex can suppress proximal APA sites through crosstalking with 3' end processing factors. However, here we show that both knockdown and overexpression of SNRPA, SNRPC, SNRNP70, and SNRPD2, the U1 snRNP proteins, promote the usage of proximal APA sites at the transcriptome level. SNRNP70 can drive the phase transition of PABPN1 from droplet to aggregate, which may reduce the repressive effects of PABPN1 on the proximal APA sites. Additionally, SNRNP70 can also promote the proximal APA sites by recruiting CPSF6, suggesting that the function of CPSF6 on APA is related with other RNA-binding proteins and cell context-dependent. Consequently, these results reveal that, on the contrary to U1 snRNP complex, the free proteins of U1 snRNP complex can promote proximal APA sites through the interaction with 3' end processing machinery.

Fip1 is a multivalent interaction scaffold for processing factors in human mRNA 3' end biogenesis.

3' end formation of most eukaryotic mRNAs is dependent on the assembly of a ~1.5 MDa multiprotein complex, that catalyzes the coupled reaction of pre-mRNA cleavage and polyadenylation. In mammals, the cleavage and polyadenylation specificity factor (CPSF) constitutes the core of the 3' end processing machinery onto which the remaining factors, including cleavage stimulation factor (CstF) and poly(A) polymerase (PAP), assemble. These interactions are mediated by Fip1, a CPSF subunit characterized by high degree of intrinsic disorder. Here, we report two crystal structures revealing the interactions of human Fip1 (hFip1) with CPSF30 and CstF77. We demonstrate that CPSF contains two copies of hFip1, each binding to the zinc finger (ZF) domains 4 and 5 of CPSF30. Using polyadenylation assays we show that the two hFip1 copies are functionally redundant in recruiting one copy of PAP, thereby increasing the processivity of RNA polyadenylation. We further show that the interaction between hFip1 and CstF77 is mediated via a short motif in the N-terminal 'acidic' region of hFip1. In turn, CstF77 competitively inhibits CPSF-dependent PAP recruitment and 3' polyadenylation. Taken together, these results provide a structural basis for the multivalent scaffolding and regulatory functions of hFip1 in 3' end processing.

Notch1 Induces Defective Epithelial Surfactant Processing and Pulmonary Fibrosis.

Rationale: Although type II alveolar epithelial cells (AEC2s) are chronically injured in idiopathic pulmonary fibrosis (IPF), they contribute to epithelial regeneration in IPF. Objectives: We hypothesized that Notch signaling may contribute to AEC2 proliferation, dedifferentiation characterized by loss of surfactant processing machinery, and lung fibrosis in IPF. Methods: We applied microarray analysis, kinome profiling, flow cytometry, immunofluorescence analysis, western blotting, quantitative PCR, and proliferation and surface activity analysis to study epithelial differentiation, proliferation, and matrix deposition invitro (AEC2 lines, primary murine/human AEC2s), ex vivo (human IPF-derived precision-cut lung slices), and invivo (bleomycin and pepstatin application, Notch1 [Notch receptor 1] intracellular domain overexpression). Measurements and Main Results: We document here extensive SP-B and -C (surfactant protein-B and -C) processing defects in IPF AEC2s, due to loss of Napsin A, resulting in increased intra-alveolar surface tension and alveolar collapse and induction of endoplasmic reticulum stress in AEC2s. In vivo pharmacological inhibition of Napsin A results in the development of AEC2 injury and overt lung fibrosis. We also demonstrate that Notch1 signaling is already activated early in IPF and determines AEC2 fate by inhibiting differentiation (reduced lamellar body compartment, reduced capacity to process hydrophobic SP) and by causing increased epithelial proliferation and development of lung fibrosis, putatively via altered JAK (Janus kinase)/Stat (signal transducer and activator of transcription) signaling in AEC2s. Conversely, inhibition of Notch signaling in IPF-derived precision-cut lung slices improved the surfactant processing capacity of AEC2s and reversed fibrosis. Conclusions: Notch1 is a central regulator of AEC2 fate in IPF. It induces alveolar epithelial proliferation and loss of Napsin A and of surfactant proprotein processing, and it contributes to fibroproliferation.

Tumor Antigenicity and a Pre-Existing Adaptive Immune Response in Advanced BRAF Mutant Colorectal Cancers.

Simple SummaryBRAF mutant metastatic CRCs (BRAF-mCRCs) are considered a unique clinical entity characterized by a dismal prognosis and that do not respond efficiently to both standard chemotherapy and to orally selective inhibitors of BRAFV600E. In this study, the gene expression profiles of 89 immunotherapy-naïve BRAF-CRCs were generated using the PanCancer IO 360 gene expression panel to improve the knowledge of the mechanisms involved in tumor-suppressive immune functions in BRAF-mCRCs. A significant fraction of BRAF-mCRCs shows a hot/inflamed profile and may be potential candidates for responding to immunotherapy. Only a partial overlap between these hot signatures and the presence of microsatellite instability (MSI) was observed, demonstrating that MSI tumors showed a not differential expression of MHC Class I antigen presentation pathway compared with microsatellite-stable tumors. The analysis of gene expression profiles is a promising strategy both for immune profiling of primary tumors before any treatment and for following the evolution of metastatic disease during therapy.The main hypothesis of this study is that gene expression profiles (GEPs) integrating both tumor antigenicity and a pre-existing adaptive immune response can be used to generate distinct immune-related signatures of BRAF mutant colorectal cancers (BRAF-CRCs) to identify actionable biomarkers predicting response to immunotherapy. GEPs of 89 immunotherapy-naïve BRAF-CRCs were generated using the Pan-Cancer IO 360 gene expression panel and the NanoString nCounter platform and were correlated with microsatellite instability (MSI) status and with CD8+ tumor-infiltrating lymphocyte (TIL) content. Hot/inflamed profiles were found in 52% of all cases, and high scores of Tumor Inflammation Signature were observed in 42% of the metastatic BRAF-CRCs. A subset of MSI tumors showed a cold profile. Antigen Processing Machinery (APM) signature was not differentially expressed in MSI tumors compared with MSS cases. By contrast, the APM signature was significantly upregulated in CD8+ BRAF-CRCs versus CD8− tumors. Our study demonstrates that a significant fraction of BRAF-CRCs may be a candidate for immunotherapy and that the simultaneous analysis of MSI status and CD8+ TIL content increases accuracy in identifying patients who can potentially benefit from immune checkpoint inhibitors. GEPs may be very useful in expanding the spectrum of patients with BRAF-CRCs who can benefit from immune checkpoint blockade.

A Study on the Optimal Flexible Job-Shop Scheduling with Sequence-Dependent Setup Time Based on a Hybrid Algorithm of Improved Quantum Cat Swarm Optimization

Multi-item and small-lot-size production modes lead to frequent setup, which involves significant setup times and has a substantial impact on productivity. In this study, we investigated the optimal flexible job-shop scheduling problem with a sequence-dependent setup time. We built a mathematical model with the optimal objective of minimization of the maximum completion time (makespan). Considering the process sequence, which is influenced by setup time, processing time, and machine load limitations, first, processing machinery is chosen based on machine load and processing time, and then processing tasks are scheduled based on setup time and processing time. An improved quantum cat swarm optimization (QCSO) algorithm is proposed to solve the problem, a quantum coding method is introduced, the quantum bit (Q-bit) and cat swarm algorithm (CSO) are combined, and the cats are iteratively updated by quantum rotation angle position; then, the dynamic mixture ratio (MR) value is selected according to the number of algorithm iterations. The use of this method expands our understanding of space and increases operation efficiency and speed. Finally, the improved QCSO algorithm and parallel genetic algorithm (PGA) are compared through simulation experiments. The results show that the improved QCSO algorithm has better results, and the robustness of the algorithm is improved.

Cancer Immunotherapy: Diverse Approaches and Obstacles.

Cancer immunotherapy approaches have progressed significantly during the last decade due to the significant improvement of our understanding of immunologic evasion of malignant cells. Depending on the type, stage, and grade of cancer, distinct immunotherapy approaches are being designed and recommended; each is different in efficacy and adverse effects. Malignant cells can adopt multiple strategies to alter the normal functioning of the immune system in recognizing and eliminating them. These strategies include secreting different immunosuppressive factors, polarizing tumor microenvironment cells to immunosuppressive ones, and interfering with the normal function of the antigen processing machinery (APM). In this context, careful evaluation of immune surveillance has led to a better understanding of the roles of cytokines, including IL-2, IL-12, IL-15, interferon-α (IFN-α), tumor necrosis factor-α (TNF-α), and transforming growth factor-β (TGF-β) in cancer formation and their potential application in cancer immunotherapy. Additionally, monoclonal antibodies (mAbs), adoptive cell therapy approaches, immune checkpoint blockade, and cancer vaccines also play significant roles in cancer immunotherapy. Moreover, the development of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/CAS9) as an outstanding genome editing tool resolved many obstacles in cancer immunotherapy. In this regard, this review aimed to investigate the impacts of different immunotherapy approaches and their potential roles in the current and future roads of cancer treatment. Whatever the underlying solution for treating highly malignant cancers is, it seems that solving the question is nowhere near an achievement unless the precise cooperation of basic science knowledge with our translational experience.

Displacement flows in rotating pipes

<h2>Abstract</h2> Displacement flows frequently occur in natural phenomena and industrial applications, e.g., in lung airways, oil well cementing, coating and cleaning of processing machinery. We study experimentally and numerically the effects of a pipe axial rotation on buoyant miscible flows in inclined pipes, while considering three cases of progressively increasing complexity: (i) Newtonian exchange flows (Lyu et al., 2020), (ii) Newtonian displacement flows (Lyu & Taghavi, 2018), and (iii) viscoplastic displacement flows (Lyu & Taghavi, 2020). We show how the flow dynamics is governed by an elegant balance among the characteristic velocities of the flow. We demonstrate that increasing the pipe rotation speed induces transverse mixing and results in a complete removal of the displaced fluid by the displacing fluid, above a critical rotation speed. Our findings offer insights on how to improve displacement efficiency using rotational motion.