Integrated imaging probe and bispecific antibody development enables in vivo targeting of glypican-3-expressing hepatocellular carcinoma.

Glypican-3 (GPC3) is a proteoglycan with high sensitivity and specificity for hepatocellular carcinoma (HCC). We describe the integrated development and validation of a GPC3-targeting optical imaging probe and T-cell redirecting antibody (TRAB) as a theranostic strategy for the detection and treatment of HCC. A novel TRAB targeting GPC3 on HCC tumor cells and the CD3 T-cell receptor as well as a distinct GPC3-specific optical imaging probe were developed from a short peptide. The efficacy of GPC3/CD3 TRAB was evaluated in vitro using interferon-γ release and calcein-AM assays. Patient-derived xenografts (PDX) were used to assess the in vivo efficacy of GPC3/CD3 TRAB and the GPC3 imaging probe for the detection of GPC3+ HCC. GPC3/CD3 TRAB caused a dose-dependent escalation in interferon-γ release from inactive peripheral blood T-cells (P = 0.001) and higher tumor-cell lysis (P = 0.01) compared to controls in vitro. Intratumorally injected GPC3/CD3 TRAB resulted in significant prolongation of tumor doubling time in the GPC3+ PDX mice, with an associated reduction of tumor fluorescent signal from the HiLyte 488- conjugated GPC3 specific peptide on optical imaging. HCC cell targeting using a GPC3/CD3 TRAB derived from a small peptide resulted in effective T-cell activation and induction of a cytotoxic response toward GPC3+ HCC tumor cells both in vitro and in vivo. GPC3-specific optical imaging enabled the detection of the GPC3+ HCC cells and noninvasive monitoring of tumor response to adoptive immunotherapy. The integrated development of a targeted therapeutic and molecular imaging probe provides a novel paradigm for developing cancer theranostics.

HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search.

Recent analyses of public microbial genomes have found over a million biosynthetic gene clusters, the natural products of the majority of which remain unknown. Additionally, GNPS harbors billions of mass spectra of natural products without known structures and biosynthetic genes. We bridge the gap between large-scale genome mining and mass spectral datasets for natural product discovery by developing HypoRiPPAtlas, an Atlas of hypothetical natural product structures, which is ready-to-use for in silico database search of tandem mass spectra. HypoRiPPAtlas is constructed by mining genomes using seq2ripp, a machine-learning tool for the prediction of ribosomally synthesized and post-translationally modified peptides (RiPPs). In HypoRiPPAtlas, we identify RiPPs in microbes and plants. HypoRiPPAtlas could be extended to other natural product classes in the future by implementing corresponding biosynthetic logic. This study paves the way for large-scale explorations of biosynthetic pathways and chemical structures of microbial and plant RiPP classes.

NPvis: An Interactive Visualizer of Peptidic Natural Product-MS/MS Matches.

Peptidic natural products (PNPs) represent a medically important class of secondary metabolites that includes antibiotics, anti-inflammatory and antitumor agents. Advances in tandem mass spectra (MS/MS) acquisition and in silico database search methods have enabled high-throughput PNP discovery. However, the resulting spectra annotations are often error-prone and their validation remains a bottleneck. Here, we present NPvis, a visualizer suitable for the evaluation of PNP-MS/MS matches. The tool interactively maps annotated spectrum peaks to the corresponding PNP fragments and allows researchers to assess the match correctness. NPvis accounts for the wide chemical diversity of PNPs that prevents the use of the existing proteomics visualizers. Moreover, NPvis works even if the exact chemical structure of the matching PNP is unknown. The tool is available online and as a standalone application. We hope that it will benefit the community by streamlining PNP data analysis and validation.

Transarterial Embolization Modulates the Immune Response within Target and Nontarget Hepatocellular Carcinomas in a Rat Model.

Background Transarterial embolization (TAE) is the most common treatment for hepatocellular carcinoma (HCC); however, there remain limited data describing the influence of TAE on the tumor immune microenvironment. Purpose To characterize TAE-induced modulation of the tumor immune microenvironment in a rat model of HCC and identify factors that modulate this response. Materials and Methods TAE was performed on autochthonous HCCs induced in rats with use of diethylnitrosamine. CD3, CD4, CD8, and FOXP3 lymphocytes, as well as programmed cell death protein ligand-1 (PD-L1) expression, were examined in three cohorts: tumors from rats that did not undergo embolization (control), embolized tumors (target), and nonembolized tumors from rats that had a different target tumor embolized (nontarget). Differences in immune cell recruitment associated with embolic agent type (tris-acryl gelatin microspheres [TAGM] vs hydrogel embolics) and vascular location were examined in rat and human tissues. A generalized estimating equation model and t, Mann-Whitney U, and χ2 tests were used to compare groups. Results Cirrhosis-induced alterations in CD8, CD4, and CD25/CD4 lymphocytes were partially normalized following TAE (CD8: 38.4%, CD4: 57.6%, and CD25/CD4: 21.1% in embolized liver vs 47.7% [P = .02], 47.0% [P = .01], and 34.9% [P = .03], respectively, in cirrhotic liver [36.1%, 59.6%, and 4.6% in normal liver]). Embolized tumors had a greater number of CD3, CD4, and CD8 tumor-infiltrating lymphocytes relative to controls (191.4 cells/mm2 vs 106.7 cells/mm2 [P = .03]; 127.8 cells/mm2 vs 53.8 cells/mm2 [P < .001]; and 131.4 cells/mm2 vs 78.3 cells/mm2 [P = .01]) as well as a higher PD-L1 expression score (4.1 au vs 1.9 au [P < .001]). A greater number of CD3, CD4, and CD8 lymphocytes were found near TAGM versus hydrogel embolics (4.1 vs 2.0 [P = .003]; 3.7 vs 2.0 [P = .01]; and 2.2 vs 1.1 [P = .03], respectively). The number of lymphocytes adjacent to embolics differed based on vascular location (17.9 extravascular CD68+ peri-TAGM cells vs 7.0 intravascular [P < .001]; 6.4 extravascular CD68+ peri-hydrogel embolic cells vs 3.4 intravascular [P < .001]). Conclusion Transarterial embolization-induced dynamic alterations of the tumor immune microenvironment are influenced by underlying liver disease, embolic agent type, and vascular location. © RSNA, 2022 Online supplemental material is available for this article. See also the editorials by Kennedy et al and by White in this issue.

Nerpa: A Tool for Discovering Biosynthetic Gene Clusters of Bacterial Nonribosomal Peptides.

Microbial natural products are a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class of natural products that include antibiotics, immunosuppressants, and anticancer agents. Recent breakthroughs in natural product discovery have revealed the chemical structure of several thousand NRPs. However, biosynthetic gene clusters (BGCs) encoding them are known only for a few hundred compounds. Here, we developed Nerpa, a computational method for the high-throughput discovery of novel BGCs responsible for producing known NRPs. After searching 13,399 representative bacterial genomes from the RefSeq repository against 8368 known NRPs, Nerpa linked 117 BGCs to their products. We further experimentally validated the predicted BGC of ngercheumicin from Photobacterium galatheae via mass spectrometry. Nerpa supports searching new genomes against thousands of known NRP structures, and novel molecular structures against tens of thousands of bacterial genomes. The availability of these tools can enhance our understanding of NRP synthesis and the function of their biosynthetic enzymes.

Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery.

Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs.

De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments.

Cyclic and branch cyclic peptides (cyclopeptides) represent a class of bioactive natural products that include many antibiotics and anti-tumor compounds. Despite the recent advances in metabolomics analysis, still little is known about the cyclopeptides in the human gut and their possible interactions due to a lack of computational analysis pipelines that are applicable to such compounds. Here, we introduce CycloNovo, an algorithm for automated de novo cyclopeptide analysis and sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms, to identify cyclopeptides in spectral datasets. CycloNovo reconstructed 32 previously unreported cyclopeptides (to the best of our knowledge) in the human gut and reported over a hundred cyclopeptides in other environments represented by various spectra on Global Natural Products Social Molecular Network (GNPS). https://github.com/bbehsaz/cyclonovo.

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.

NPS: scoring and evaluating the statistical significance of peptidic natural product-spectrum matches.

MOTIVATION: Peptidic natural products (PNPs) are considered a promising compound class that has many applications in medicine. Recently developed mass spectrometry-based pipelines are transforming PNP discovery into a high-throughput technology. However, the current computational methods for PNP identification via database search of mass spectra are still in their infancy and could be substantially improved. RESULTS: Here we present NPS, a statistical learning-based approach for scoring PNP-spectrum matches. We incorporated NPS into two leading PNP discovery tools and benchmarked them on millions of natural product mass spectra. The results demonstrate more than 45% increase in the number of identified spectra and 20% more found PNPs at a false discovery rate of 1%. AVAILABILITY AND IMPLEMENTATION: NPS is available as a command line tool and as a web application at http://cab.spbu.ru/software/NPS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

5-ALA-assisted stereotactic brain tumor biopsy improve diagnostic yield.

BACKGROUND: Abnormal tissue in stereotactic brain biopsies (SBB) is traditionally identified intraoperatively via pathological frozen section (FS), a time-consuming and error-prone process. The objective of this study was to assess the efficacy of 5-aminolevulinic acid (5-ALA) administration on SBB operation time, diagnostic yield, and the associated complication rate. METHODS: We retrospectively evaluated all consecutive patients undergoing SBB with preoperative 5-ALA administration and intraoperative assessment of fluorescence (5-ALA group) between 2010 and 2017 in a single center. They were compared to all consecutive patients who underwent traditional brain biopsy with FS (control group). Demographics, clinical data, diagnostic yield of biopsies, and complication rates were documented. RESULTS: In all, 376 patients underwent SBB for suspected oncological pathology during the study period. All 34 of the 5-ALA-assisted SBB were diagnostic compared to 96.8% of the control group. The mean operative time was the same for both groups, but it was significantly shorter for the 5-ALA patients with florescent samples compared to patients with negative fluorescence (61 ±â€¯25 min vs. 136 ±â€¯54 min, P = 0.003) and compared to the control group (74 ±â€¯34 min vs. 61 ±â€¯25 min, P = 0.03). Symptomatic bleed was absent in the 5-ALA group and present in 5.4% of the controls. No adverse events were associated with preoperative 5-ALA administration. CONCLUSIONS: Preoperative administration of 5-ALA may improve the diagnostic yield of SBB and shortens operation time in cases of fluorescent pathological tissue. In addition, it may reduce the risk for associated postoperative symptomatic bleed. 5-ALA-assisted SBB is a viable alternative to traditional biopsies with FS.

Valve Failure in Ventriculoperitoneal Shunts of Neuro-Oncologic Patients: A Historical Cohort Study.

OBJECTIVE: To investigate malfunctioning of ventriculoperitoneal shunt (VPS) valves in patients with brain tumors compared with patients with VPS for nontumoral etiologies to identify risk factors for shunt malfunction. METHODS: Medical charts of all adult patients who underwent VPS surgery for hydrocephalus between 2011 and 2016 were reviewed. Incidence and risk factors for revision surgery due to valve malfunction were identified in patients with brain tumors (group A) and patients without brain tumors (group B). RESULTS: Group A comprised 89 patients, and group B comprised 164 patients. The median follow-up time was 17 months for the entire cohort (9.4 months for group A vs. 25 months for group B, P < 0.001). VPS revision was performed in 60 patients (23.7%); 11 revisions involved valve failures necessitating valve replacement. Valve failures were significantly more common in group A (10 group A patients vs. 1 group B patient, P < 0.001). The distal or proximal shunt revision rate for reasons other than the valve was similar for both groups. Group A patients had a significantly higher cerebrospinal fluid protein level (44.5 mg/dL vs. 27.79 mg/dL, P < 0.05), and patients with valve failure had a 3-fold higher cerebrospinal fluid protein level compared with group A patients who experienced any type of shunt failure (96.3 mg/dL vs. 30.6 mg/dL, P < 0.05). CONCLUSIONS: Shunt malfunction occurred mainly in patients with brain tumors and high cerebrospinal fluid protein levels. These patients are at high risk of valve failure and should be closely observed for emergent valve revision.

Novel Lymphatic Imaging and Percutaneous Treatment of Chyluria.

Chyluria is characterized by the presence of chyle in the urine and often presents clinically as urinary obstruction. Traditional treatments include dietary modifications, surgery and sclerotherapy. The recently developed intranodal lymphangiography and dynamic contrast-enhanced MR lymphangiography (DCMRL) provide better imaging of the lymphatic system. Interstitial lymphatic embolization is a new interventional technique that allows delivery of n-butyl cyanoacrylate glue into the network of the lymphatic vessels. This report describes the demonstration of lympho-urinary tract communications using DCMRL and intranodal lymphangiography in three patients who presented with chyluria, and successful treatment of chyluria in two patients using interstitial lymphatic embolization.

Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra.

Peptidic natural products (PNPs) include many antibiotics and other bioactive compounds. While the recent launch of the Global Natural Products Social (GNPS) molecular networking infrastructure is transforming PNP discovery into a high-throughput technology, PNP identification algorithms are needed to realize the potential of the GNPS project. GNPS relies on the assumption that each connected component of a molecular network (representing related metabolites) illuminates the 'dark matter of metabolomics' as long as it contains a known metabolite present in a database. We reveal a surprising diversity of PNPs produced by related bacteria and show that, contrary to the 'comparative metabolomics' assumption, two related bacteria are unlikely to produce identical PNPs (even though they are likely to produce similar PNPs). Since this observation undermines the utility of GNPS, we developed a PNP identification tool, VarQuest, that illuminates the connected components in a molecular network even if they do not contain known PNPs and only contain their variants. VarQuest reveals an order of magnitude more PNP variants than all previous PNP discovery efforts and demonstrates that GNPS already contains spectra from 41% of the currently known PNP families. The enormous diversity of PNPs suggests that biosynthetic gene clusters in various microorganisms constantly evolve to generate a unique spectrum of PNP variants that differ from PNPs in other species.

Dereplication of peptidic natural products through database search of mass spectra.

Peptidic natural products (PNPs) are widely used compounds that include many antibiotics and a variety of other bioactive peptides. Although recent breakthroughs in PNP discovery raised the challenge of developing new algorithms for their analysis, identification of PNPs via database search of tandem mass spectra remains an open problem. To address this problem, natural product researchers use dereplication strategies that identify known PNPs and lead to the discovery of new ones, even in cases when the reference spectra are not present in existing spectral libraries. DEREPLICATOR is a new dereplication algorithm that enables high-throughput PNP identification and that is compatible with large-scale mass-spectrometry-based screening platforms for natural product discovery. After searching nearly one hundred million tandem mass spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure, DEREPLICATOR identified an order of magnitude more PNPs (and their new variants) than any previous dereplication efforts.