Prospective de novo drug design with deep interactome learning.

De novo drug design aims to generate molecules from scratch that possess specific chemical and pharmacological properties. We present a computational approach utilizing interactome-based deep learning for ligand- and structure-based generation of drug-like molecules. This method capitalizes on the unique strengths of both graph neural networks and chemical language models, offering an alternative to the need for application-specific reinforcement, transfer, or few-shot learning. It enables the "zero-shot" construction of compound libraries tailored to possess specific bioactivity, synthesizability, and structural novelty. In order to proactively evaluate the deep interactome learning framework for protein structure-based drug design, potential new ligands targeting the binding site of the human peroxisome proliferator-activated receptor (PPAR) subtype gamma are generated. The top-ranking designs are chemically synthesized and computationally, biophysically, and biochemically characterized. Potent PPAR partial agonists are identified, demonstrating favorable activity and the desired selectivity profiles for both nuclear receptors and off-target interactions. Crystal structure determination of the ligand-receptor complex confirms the anticipated binding mode. This successful outcome positively advocates interactome-based de novo design for application in bioorganic and medicinal chemistry, enabling the creation of innovative bioactive molecules.

Constitutive IL-1RA production by modified immune cells protects against IL-1-mediated inflammatory disorders.

Dysregulation of the interleukin-1 (IL-1) pathway leads to immune diseases that can result in chronic tissue and organ inflammation. Although IL-1 blockade has shown promise in ameliorating these symptoms and improving patients' quality of life, there is an urgent need for more effective, long-lasting treatments. We developed a lentivirus (LV)-mediated gene transfer strategy using transplanted autologous hematopoietic stem/progenitor cells (HSPCs) as a source of IL-1 receptor antagonist (IL-1RA) for systemic delivery to tissues and organs. Transplantation of mouse and human HSPCs transduced with an IL-1RA-encoding LV ensured stable IL-1RA production while maintaining the clonogenic and differentiation capacities of HSPCs in vivo. We examined the efficacy of cell-mediated IL-1RA delivery in three models of IL-1-dependent inflammation, for which treatment hindered neutrophil recruitment in an inducible model of gout, prevented systemic and multi-tissue inflammation in a genetic model of cryopyrin-associated periodic syndromes, and reduced disease severity in an experimental autoimmune encephalomyelitis model of multiple sclerosis. Our findings demonstrate HSPC-mediated IL-1RA delivery as a potential therapeutic modality that can be exploited to suppress tissue and organ inflammation in diverse immune-related diseases involving IL-1-driven inflammation.

Short- and long-term outcomes in ypT2 rectal cancer patients after neoadjuvant therapy and local excision: a multicentre observational study.

BACKGROUND: Although local excision (LE) after neoadjuvant treatment (NT) has achieved encouraging oncological outcomes in selected patients, radical surgery still remains the rule when unfavorable pathology occurs. However, there is a risk of undertreating patients not eligible for radical surgery. The aim of this study was to evaluate the outcomes of patients with pathological incomplete response (ypT2) in a multicentre cohort of patients undergoing LE after NT and to compare them with ypT0-is-1 rectal cancers. METHODS: From 2010 to 2019, all patients who underwent LE after NT for rectal cancer were identified from five institutional retrospective databases. After excluding 12 patients with ypT3 tumors, patients with ypT2 tumors were compared to patients with ypT0-is-1 tumors). The endpoints of the study were early postoperative and long-term oncological outcomes. RESULTS: A total of 177 patients (132 males, 45 females, median age 70 [IQR 16] years) underwent LE following NT. There were 46 ypT2 patients (39 males, 7 females, median age 72 [IQR 18.25] years) and 119 ypT0-is-1 patients (83 males, 36 females, median age 69 [IQR 15] years). Patients with pathological incomplete response (ypT2) were frailer than the ypT0-is-1 patients (mean Charlson Comorbidity Index 6.15 ± 2.43 vs. 5.29 ± 1.99; p = 0.02) and there was a significant difference in the type of NT used for the two groups (long- course radiotherapy: 100 (84%) vs. 23 (63%), p = 0.006; short-course radiotherapy: 19 (16%) vs. 17 (37%), p = 0.006). The postoperative rectal bleeding rate (13% vs. 1.7%; p = 0.008), readmission rate (10.9% vs. 0.8%; p = 0.008) and R1 resection rate (8.7% vs. 0; p = 0.008) was significantly higher in the ypT2 group. Recurrence rates were comparable between groups (5% vs. 13%; p = 0.15). Five-year overall survival was 91.3% and 94.9% in the ypT2 and ypT0-is-1 groups, respectively (p = 0.39), while 5-year cancer specific survival was 93.4% in the ypT2 group and 94.9% in the ypT0-is-1 group (p = 0.70). No difference was found in terms of 5-year local recurrence free-survival (p = 0.18) and 5-year distant recurrence free-survival (p = 0.37). CONCLUSIONS: Patients with ypT2 tumors after NT and LE have a higher risk of late-onset rectal bleeding and positive resection margins than patients with complete or near complete response. However, long-term recurrence rates and survival seem comparable.

Dual Functionalized Liposomes for Selective Delivery of Poorly Soluble Drugs to Inflamed Brain Regions.

Dual functionalized liposomes were developed to cross the blood−brain barrier (BBB) and to release their cargo in a pathological matrix metalloproteinase (MMP)-rich microenvironment. Liposomes were surface-functionalized with a modified peptide deriving from the receptor-binding domain of apolipoprotein E (mApoE), known to promote cargo delivery to the brain across the BBB in vitro and in vivo; and with an MMP-sensitive moiety for an MMP-triggered drug release. Different MMP-sensitive peptides were functionalized at both ends with hydrophobic stearate tails to yield MMP-sensitive lipopeptides (MSLPs), which were assembled into mApoE liposomes. The resulting bi-functional liposomes (i) displayed a < 180 nm diameter with a negative ζ-potential; (ii) were able to cross an in vitro BBB model with an endothelial permeability of 3 ± 1 × 10−5 cm/min; (iii) when exposed to functional MMP2 or 9, efficiently released an encapsulated fluorescein dye; (iv) showed high biocompatibility when tested in neuronal cultures; and (v) when loaded with glibenclamide, a drug candidate with poor aqueous solubility, reduced the release of proinflammatory cytokines from activated microglial cells.

Netupitant/palonosetron without dexamethasone for preventing nausea and vomiting in patients with multiple myeloma receiving high-dose melphalan for autologous stem cell transplantation: a single-center experience.

Chemotherapy-induced nausea and vomiting (CINV) is one of the most frequent adverse events compromising quality of life (QoL) in patients undergoing autologous stem cell transplantation (ASCT). However, CINV prophylaxis is still lacking uniformity for high-dose melphalan (HDM), which is used to condition patients with multiple myeloma (MM). Netupitant/palonosetron (NEPA) is administered with dexamethasone (DEXA) for CINV prevention in several chemotherapy regimens. Our study aims to assess the efficacy of NEPA, without DEXA, in preventing CINV in 106 adult patients with MM receiving HDM and ASCT. All patients had antiemetic prophylaxis with multiple doses of NEPA 1 h before the start of conditioning and after 72 h and 120 h. A complete response (CR) was observed in 99 (93%) patients at 120 h (overall phase). The percentage of patients with complete control was 93%. The CR rate during the acute phase was 94% (n = 100). During the delayed phase, the CR rate was 95% (n = 101). Grade 1 nausea and vomiting were experienced by 82% and 12% of the patients, respectively. Grade 2 nausea was reported in 18% and vomiting in 10% of patients. Our results showed, for the first time, that NEPA, without DEXA, was a well-tolerated and effective antiemetic option for MM patients receiving HDM followed by ASCT.

The Burden in Caregivers of Multiple Myeloma Patients Undergoing Outpatient Autologous Stem-Cell Transplantation Compared to Inpatient Transplantation.

BACKGROUND: The application of different models of autologous stem-cell transplantation (ASCT) in multiple myeloma has demonstrated the feasibility and safety of outpatient-based programs of care. Although several systematic reviews have evaluated the burden of caregivers, only a few studies have included outpatient ASCT. PATIENTS AND METHODS: The feelings of lack of family support, daily activities, and general health were compared between caregivers of 2 groups of patients with multiple myeloma who underwent inpatient (n = 71) or outpatient (n = 25) ASCT. RESULTS: The 3 features did not significantly differ between the 2 study groups at baseline, before, and 3 months after ASCT. Multivariate modeling showed that the baseline values were significantly related to the changes in study outcomes independent of patient and caregiver characteristics. Other correlates were caregivers' work and patient age for impact on daily activities and disease burden across time for impact on general health (all P < .05). CONCLUSION: The outpatient model neither improves nor impairs global caregivers' burden compared to standard ASCT care. Further research is needed to confirm this observation and to better assess the burden and quality of life of caregivers and their influence on patient outcomes and quality of life.

High-Resolution Mass Spectrometry-Based Approaches for the Detection and Quantification of Peptidase Activity in Plasma.

Proteomic technologies have identified 234 peptidases in plasma but little quantitative information about the proteolytic activity has been uncovered. In this study, the substrate profile of plasma proteases was evaluated using two nano-LC-ESI-MS/MS methods. Multiplex substrate profiling by mass spectrometry (MSP-MS) quantifies plasma protease activity in vitro using a global and unbiased library of synthetic peptide reporter substrates, and shotgun peptidomics quantifies protein degradation products that have been generated in vivo by proteases. The two approaches gave complementary results since they both highlight key peptidase activities in plasma including amino- and carboxypeptidases with different substrate specificity profiles. These assays provide a significant advantage over traditional approaches, such as fluorogenic peptide reporter substrates, because they can detect active plasma proteases in a global and unbiased manner, in comparison to detecting select proteases using specific reporter substrates. We discovered that plasma proteins are cleaved by endoproteases and these peptide products are subsequently degraded by amino- and carboxypeptidases. The exopeptidases are more active and stable in plasma and therefore were found to be the most active proteases in the in vitro assay. The protocols presented here set the groundwork for studies to evaluate changes in plasma proteolytic activity in shock.

Minimally invasive management of rare giant Bochdalek hernia in adults.

Bochdaleck hernia (BH) is a congenital diaphragmatic hernia that presents after birth with respiratory symptoms and needs surgical treatment in the neonatal period. However, there are some rare cases of adult presentation, which require surgery to avoid complications. BHs can be treated through several approaches, including laparoscopy. Laparoscopic treatment of a giant BH was successfully attempted on a woman affected by multiple myeloma, with severe dyspnoea and dysphagia. Preoperative work-up included chest X ray, CT-scan and MRI. The whole stomach, duodenum, the small bowel, the right and transverse colon, most descending colon and the pancreas were herniated into the thorax. The herniated viscera were totally reduced into the abdominal cavity and the large defect of the left diaphragm repaired with a biosynthetic web scaffold especially designed for diaphragmatic reconstruction. Finally, to avoid a compartment syndrome in an abdomen with not enough room for the reduced viscera, an extended right colectomy with extracorporeal anastomosis was carried out through a mini-laparotomy. At seven-month follow-up, the patient is symptomless and control CT scan showed no hernia recurrence. Laparoscopic repair of large symptomatic adult BHs can be performed successfully with significant clinical improvement, even in difficult cases and fragile patients.

Magnesium and the blood-brain barrier in vitro: effects on permeability and magnesium transport.

The blood-brain barrier (BBB) tightly regulates the homeostasis of the central nervous system, and its dysfunction has been described in several neurological disorders. Since magnesium exerts a protective effect in the brain, we assessed whether supraphysiological concentrations of different magnesium salts modulate the permeability and magnesium transport in in vitro models of rat and human BBB. Among various formulations tested, magnesium pidolate was the most efficient in reducing the permeability and in enhancing magnesium transport through the barrier. We then compared magnesium pidolate and magnesium sulfate, a widely used salt in experimental models and in clinical practice. Magnesium pidolate performs better than sulfate also in preventing lipopolysaccharide-induced damage to in vitro generated BBB. We conclude that magnesium pidolate emerges as an interesting alternative to sulfate to protect BBB and maintain correct intracerebral concentrations of magnesium.

Effects of PI3K Inhibition on Afucosylated Antibody-Driven FcγRIIIa Events and Phospho-S6 Activity in NK Cells.

PI3K is one of the most frequently mutated genes in cancers and has been the target of numerous anticancer therapies. With the additional development of therapeutics that mobilize the immune system, such as Abs with effector functions, bispecific Abs, and checkpoint inhibitors, many small molecule inhibitors that target PI3K are being combined with these immunomodulatory treatments. However, the PI3K pathway is also essential for lymphocyte function, and the presence of the PI3K inhibitor may render the immunomodulatory therapeutic ineffective in these combinatorial treatments. Therefore, therapeutics with enhanced activity, such as afucosylated Abs, which promote signaling and function, may be ideal in these types of treatments to offset the negative effect of PI3K inhibitors on immune cell function. Indeed, we show that afucosylated Abs can counterbalance these inhibitory effects on FcγRIIIa-driven signaling in human NK cells to produce signals similar to cells treated only with fucosylated Ab. Furthermore, NK cell activation, degranulation, chemokine/cytokine production, and Ab-dependent cellular cytotoxicity were similar between inhibitor-treated, afucosylated Ab-stimulated NK cells and cells activated only with its fucosylated counterpart. To our knowledge, these studies also identified a previously undefined role for phospho-S6 in human NK cells. In this study, a kinetic delay in PI3K-driven phosphorylation of S6 was observed to control transcription of the temporally regulated production of IFN-γ and TNF-α but not MIP-1α, MIP-1ß, and RANTES. Together, these studies demonstrate the importance of the PI3K pathway for S6 phosphorylation in human NK cells and the need to combine PI3K inhibitors with therapeutic molecules that enhance immunomodulatory function for anticancer therapies.

The simultaneous downregulation of TRPM7 and MagT1 in human mesenchymal stem cells in vitro: Effects on growth and osteogenic differentiation.

The magnesium transporters TRPM7 and MagT1 are overexpressed in osteoblastogenesis. We have shown that silencing either TRPM7 or MagT1 accelerates the osteogenic differentiation of human bone mesenchymal stem cells. Here we demonstrate that the simultaneous downregulation of TRPM7 and MagT1 inhibits cell growth and activates autophagy, which is required in the early phases of osteoblastogenesis. In TRPM7/MagT1 downregulating cells the expression of two transcription factors required for activating osteogenesis, i.e. RUNX2 and OSTERIX, is induced more than in the controls both in the presence and in the absence of osteogenic stimuli, while COL1A1 is upregulated in co-silencing cells as much as in the controls. This explains why we found no differences in calcium deposition. We conclude that one of the two transporters should be expressed to accelerate osteogenic differentiation.

TRPM7 and MagT1 in the osteogenic differentiation of human mesenchymal stem cells in vitro.

Mesenchymal stem cells are fundamental for bone formation and repair since they respond to microenvironmental stimuli by undergoing osteogenic differentiation. We show that the kinase and cation channel TRPM7 and the magnesium transporter MagT1 have a role in harmonizing the osteogenic differentiation of human mesenchymal stem cells. TRPM7 and MagT1 are upregulated in osteogenic differentiation and silencing either one accelerates osteogenic differentiation, partly through the activation of autophagy. Intriguingly, similar results were obtained when the cells were cultured under magnesium deficient conditions. These results underpin the contribution of magnesium, TRPM7 and MagT1 to autophagy and osteoblastogenesis.

N6-isopentenyladenosine a new potential anti-angiogenic compound that targets human microvascular endothelial cells in vitro.

N6-isopentenyladenosine is an anti-proliferative and pro-apoptotic atypical nucleoside for normal and tumor cells. Considering the role of angiogenesis in various diseases, we investigated the cytotoxic effect of N6-isopentenyladenosine on human microvascular endothelial cells, protagonists in angiogenesis. Our results show that N6-isopentenyladenosine induced a significant reduction of cell viability, upregulated p21 and promoted caspase-3 cleavage in a dose dependent manner leading to apoptotic cell death as detected by FACS analysis. To understand structure-function relationship of N6-isopentenyladenosine, we investigated the effect of some N6-isopentenyladenosine analogs. Our results suggest that N6-isopentenyladenosine and some of its derivatives are potentially novel angiostatic agents and might be associated with other anti-angiogenic compounds for a better outcome.

A method for manual and automated multiplex RNAscope in situ hybridization and immunocytochemistry on cytospin samples.

In situ analysis of biomarkers is essential for clinical diagnosis and research purposes. The increasing need to understand the molecular signature of pathologies has led to the blooming of ultrasensitive and multiplexable techniques that combine in situ hybridization (ISH) and immunohistochemistry or immunocytochemistry (IHC or ICC). Most protocols are tailored to formalin-fixed paraffin embedded (FFPE) tissue sections. However, methods to perform such assays on non-adherent cell samples, such as patient blood-derived PBMCs, rare tumor samples, effusions or other body fluids, dissociated or sorted cells, are limited. Typically, a laboratory would need to invest a significant amount of time and resources to establish one such assay. Here, we describe a method that combines ultrasensitive RNAscope-ISH with ICC on cytospin cell preparations. This method allows automated, sensitive, multiplex ISH-ICC on small numbers of non-adherent cells. We provide guidelines for both chromogenic and fluorescent ISH/ICC combinations that can be performed either in fully automated or in manual settings. By using a CD8+ T cells in vitro stimulation paradigm, we demonstrate that this protocol is sensitive enough to detect subtle differences in gene expression and compares well to commonly used methods such as RT-qPCR and flow cytometry with the added benefit of visualization at the cellular level.

Technologies, technical steps, and early postoperative results of transanal TME.

INTRODUCTION: First described in 1982, TME overcomes most of the concerns regarding adequate local control after anterior rectal resection. TME requires close sharp dissection along the so-called Heald's plane down to the levators, with distal dissection often cumbersome. In recent years, Transanal TME was introduced with the aim to improve distal rectal dissection and quality of mesorectal excision. MATERIAL AND METHODS: A prospective, non-randomized study, started in 2013, is currently ongoing in two Italian Centers. Study objectives were assessing the safety of TaTME and TME quality. TaTME technique and technologies as performed in these centers and cumulative results at ≤30 postoperative days of the first 102 patients are reported. RESULTS: Early postoperative morbidity and mortality rates were 33.3% (34 pts, 16 Clavien-Dindo I + II and 18 Clavien-Dindo III + IV + V), and 1.96% (two deaths), respectively. The quality of mesorectal excision according to Quirke was: complete in 97.1% and nearly complete in 2.9% of the cases. CONCLUSIONS: The results confirm the effectiveness of TaTME, especially regarding the quality of the mesorectal dissection. Open questions regarding standardization, anatomical landmarks, indications, morbidity (with special regard to local infection and sepsis), learning curve and oncological outcomes require further answers from larger studies and RCTs before definitive validation of this procedure. .

Cycling in the nucleus: regulation of RNA 3' processing and nuclear organization of replication-dependent histone genes.

The histones which pack new DNA during the S phase of animal cells are made from mRNAs that are cleaved at their 3' end but not polyadenylated. Some of the factors used in this reaction are unique to it while others are shared with the polyadenylation process that generates all other mRNAs. Recent work has begun to shed light on how the cell manages the assignment of these common components to the two 3' processing systems, and how it achieves their cell cycle-regulation and recruitment to the histone pre-mRNA. Moreover, recent and older findings reveal multiple connections between the nuclear organization of histone genes, their transcription and 3' end processing as well as the control of cell proliferation.

Minimizing the Access Trauma of Laparoscopic Sleeve Gastrectomy: the Transoral Specimen Extraction Technique.

BACKGROUND: Laparoscopic sleeve gastrectomy has become a popular stand-alone procedure among bariatric surgeons. Recently, Natural Orifice Specimen Extraction laparoscopic surgery has been introduced to avoid minilaparotomy, possibly reducing postoperative pain, hospital stay, and improving QoL and cosmetics. Operative steps and preliminary results of NOSE sleeve gastrectomy are described and reported. METHODS: Five patients underwent NOSE LSG from November 2014 to March 2015. Selection criteria were as follows: age <60 years, ASA score ≤III, BMI <50. Operative steps are the same of standard LSG, but the stomach transection that starts higher on the greater curvature. A 2­3 cm width opening is created on the exceeding antrum and the resected stomach sutured to the calibration probe tip, which is pull back allowing transoral specimen extraction. The exceeding antrum is stapler-trimmed, allowing breach closure and completion of tubulization. RESULTS: Mean age was 41.6 years (median 43), average weight was 123.6 Kg (median 114), mean BMI 43.6 Kg/m2 (median 44). Mean operation time was 72 min (median 75). Mean and median postoperative stay were 4.6 and 5. No intraoperative nor postoperative complications occurred. Postoperative day 1 mean and median VAS pain score at were 1.4 and 1, respectively. Follow-up ranged 1­5 months (mean and median 3), average weight loss was 19.8 Kg (median 19), and excess weight loss 36.2 % (median 32 %). CONCLUSIONS: NOSE LSG potential advantages are as follows: improved cosmetics, decreased postoperative pain, possible incisional hernia rate reduction. No objective data are available to confirm these theoretical benefits; larger observational studies and RCTs are mandatory before clinical validation.

FUS/TLS contributes to replication-dependent histone gene expression by interaction with U7 snRNPs and histone-specific transcription factors.

Replication-dependent histone genes are up-regulated during the G1/S phase transition to meet the requirement for histones to package the newly synthesized DNA. In mammalian cells, this increment is achieved by enhanced transcription and 3' end processing. The non-polyadenylated histone mRNA 3' ends are generated by a unique mechanism involving the U7 small ribonucleoprotein (U7 snRNP). By using affinity purification methods to enrich U7 snRNA, we identified FUS/TLS as a novel U7 snRNP interacting protein. Both U7 snRNA and histone transcripts can be precipitated by FUS antibodies predominantly in the S phase of the cell cycle. Moreover, FUS depletion leads to decreased levels of correctly processed histone mRNAs and increased levels of extended transcripts. Interestingly, FUS antibodies also co-immunoprecipitate histone transcriptional activator NPAT and transcriptional repressor hnRNP UL1 in different phases of the cell cycle. We further show that FUS binds to histone genes in S phase, promotes the recruitment of RNA polymerase II and is important for the activity of histone gene promoters. Thus, FUS may serve as a linking factor that positively regulates histone gene transcription and 3' end processing by interacting with the U7 snRNP and other factors involved in replication-dependent histone gene expression.

CstF64: cell cycle regulation and functional role in 3' end processing of replication-dependent histone mRNAs.

The 3' end processing of animal replication-dependent histone mRNAs is activated during G1/S-phase transition. The processing site is recognized by stem-loop binding protein and the U7 snRNP, but cleavage additionally requires a heat-labile factor (HLF), composed of cleavage/polyadenylation specificity factor, symplekin, and cleavage stimulation factor 64 (CstF64). Although HLF has been shown to be cell cycle regulated, the mechanism of this regulation is unknown. Here we show that levels of CstF64 increase toward the S phase and its depletion affects histone RNA processing, S-phase progression, and cell proliferation. Moreover, analyses of the interactions between CstF64, symplekin, and the U7 snRNP-associated proteins FLASH and Lsm11 indicate that CstF64 is important for recruiting HLF to histone precursor mRNA (pre-mRNA)-resident proteins. Thus, CstF64 is central to the function of HLF and appears to be at least partly responsible for its cell cycle regulation. Additionally, we show that misprocessed histone transcripts generated upon CstF64 depletion mainly accumulate in the nucleus, where they are targets of the exosome machinery, while a small cytoplasmic fraction is partly associated with polysomes.

Graphite nanoplatelet chemical cross-linking by elemental sulfur.

Graphite nanoplatelets (GNPs) react with elemental sulfur to provide a mechanically stable, spongy material characterized by good electrical conductivity and high surface development; such unique property combination makes these novel nanostructured materials very useful for applications in different technological fields. The carbon-sulfur reaction can be accurately investigated by thermal analysis (differential scanning calorimetry and thermogravimetric analysis) and energy-dispersive X-ray spectroscopy combined with scanning electron microscopy. The thermal treatment required for the formation of electrically conductive monosulfur connections among the GNP unities has been investigated. PACS: 81.05.Ue, 81.05.Rm, 81.16.Be.