Geometric deep learning of protein-DNA binding specificity.

Predicting protein-DNA binding specificity is a challenging yet essential task for understanding gene regulation. Protein-DNA complexes usually exhibit binding to a selected DNA target site, whereas a protein binds, with varying degrees of binding specificity, to a wide range of DNA sequences. This information is not directly accessible in a single structure. Here, to access this information, we present Deep Predictor of Binding Specificity (DeepPBS), a geometric deep-learning model designed to predict binding specificity from protein-DNA structure. DeepPBS can be applied to experimental or predicted structures. Interpretable protein heavy atom importance scores for interface residues can be extracted. When aggregated at the protein residue level, these scores are validated through mutagenesis experiments. Applied to designed proteins targeting specific DNA sequences, DeepPBS was demonstrated to predict experimentally measured binding specificity. DeepPBS offers a foundation for machine-aided studies that advance our understanding of molecular interactions and guide experimental designs and synthetic biology.

RNAscape: geometric mapping and customizable visualization of RNA structure.

Analyzing and visualizing the tertiary structure and complex interactions of RNA is essential for being able to mechanistically decipher their molecular functions in vivo. Secondary structure visualization software can portray many aspects of RNA; however, these layouts are often unable to preserve topological correspondence since they do not consider tertiary interactions between different regions of an RNA molecule. Likewise, quaternary interactions between two or more interacting RNA molecules are not considered in secondary structure visualization tools. The RNAscape webserver produces visualizations that can preserve topological correspondence while remaining both visually intuitive and structurally insightful. RNAscape achieves this by designing a mathematical structural mapping algorithm which prioritizes the helical segments, reflecting their tertiary organization. Non-helical segments are mapped in a way that minimizes structural clutter. RNAscape runs a plotting script that is designed to generate publication-quality images. RNAscape natively supports non-standard nucleotides, multiple base-pairing annotation styles and requires no programming experience. RNAscape can also be used to analyze RNA/DNA hybrid structures and DNA topologies, including G-quadruplexes. Users can upload their own three-dimensional structures or enter a Protein Data Bank (PDB) ID of an existing structure. The RNAscape webserver allows users to customize visualizations through various settings as desired. URL: https://rnascape.usc.edu/.

Using Voxel-Based Dosimetry to Evaluate Sphere Concentration and Tumor Dose in Hepatocellular Carcinoma Treated with Yttrium-90 Radiation Segmentectomy with Glass Microspheres.

PURPOSE: To utilize voxel-based dosimetry following radiation segmentectomy (RS) to understand microsphere distribution and validate current literature regarding radiologic and pathologic outcomes. MATERIALS AND METHODS: A retrospective, single-center analysis of patients with solitary hepatocellular carcinoma (N = 56) treated with yttrium-90 (90Y) RS with glass microspheres (Therasphere; Boston Scientific, Marlborough, Massachusetts) from 2020 to 2022 was performed. Posttreatment voxel-based dosimetry was evaluated using Mirada DBx Build 1.2.0 Simplicit90Y software (Boston Scientific) and utilized to calculate sphere concentration to tumor as well as D70 (minimum dose to 70% total tumor volume), D90, and D99. Time to progression (TTP), treatment response, and adverse events were studied. RESULTS: Fifty-six solitary tumors were analyzed with a median tumor diameter of 3.4 cm (range, 1.2-6.8 cm) and median tumor absorbed dose of 732 Gy (range, 252-1,776 Gy). Median sphere activity (SA) at the time of delivery was 1,446 Bq (range, 417-2,621 Bq). Median tumor sphere concentration was 12,868 spheres/mL (range, 2,655-37,183 spheres/mL). Sphere concentration into tumor and normal tissue was inversely correlated with perfused treatment volume (R2 = 0.21 and R2 = 0.39, respectively). Of the 51 tumors with posttreatment imaging, objective response was noted in 49 patients (96%) and complete response in 42 patients (82%). The median TTP was not reached with a 2-year progression rate of 11%. Fifteen patients underwent liver transplant. Median tumor necrosis was 99% (range, 80%-100%). Lower tumor volumes and higher D99 were associated with complete pathologic necrosis (P < .001 and P = .022, respectively). CONCLUSIONS: Voxel-based dosimetry following 90Y radioembolization can be utilized to account for sphere deposition and distribution into tumor. Ablative RS with high SA yields durable radiologic and pathologic outcomes.

Pediatric Patients Discharged After Transfer to a Pediatric Emergency Department: Opportunities for Telehealth?

STUDY OBJECTIVE: Interemergency department pediatric transfers can be costly, involve risk, and may be disruptive to patients and families. Telehealth could be a way to safely reduce the number of transfers. We made an estimate of the proportion of transfers of pediatric patients to our emergency department (ED) that may have been avoidable using telehealth. METHODS: This was a retrospective analysis of electronic health record data of all pediatric patients (younger than 19 years) who were transferred to a single urban, academic medical center pediatric emergency department (PED) (annual pediatric volume approximately 15,000) between June 1, 2016, and December 29, 2021. We defined transfers as potentially avoidable with telehealth (the primary outcome) when the encounter at the receiving ED resulted in ED discharge and 1) met our definition of low-resource intensity (had no laboratory tests, diagnostic imaging, procedures, or consultations) or 2) could have used initial ED resources with telehealth guidance. RESULTS: Among 4,446 PED patients received in transfer during the study period, 406 (9%) were low-resource intensity. Of the non-low-resource intensity encounters, as many as another 1,103 (24.8%) potentially could have been avoided depending on available telehealth and initial ED resources, ranging from 210 (4.7%) with only telehealth specialty consultation to 538 (7.4%) with imaging and telehealth specialty consultation, and up to 1,034 (23.3%) with laboratory, imaging, and telehealth specialty consultation. CONCLUSION: Our results suggest that depending on available telehealth and initial ED resources, between 9% and 33% of pediatric inter-ED transfers may have been avoidable. This information may guide health system design and PED operations when considering implementing pediatric telehealth.

Normothermic Machine Perfusion of Donor Livers for Transplantation in the United States: A Randomized Controlled Trial.

OBJECTIVE: To compare conventional low-temperature storage of transplant donor livers [static cold storage (SCS)] with storage of the organs at physiological body temperature [normothermic machine perfusion (NMP)]. BACKGROUND: The high success rate of liver transplantation is constrained by the shortage of transplantable organs (eg, waiting list mortality >20% in many centers). NMP maintains the liver in a functioning state to improve preservation quality and enable testing of the organ before transplantation. This is of greatest potential value with organs from brain-dead donor organs (DBD) with risk factors (age and comorbidities), and those from donors declared dead by cardiovascular criteria (donation after circulatory death). METHODS: Three hundred eighty-three donor organs were randomized by 15 US liver transplant centers to undergo NMP (n = 192) or SCS (n = 191). Two hundred sixty-six donor livers proceeded to transplantation (NMP: n = 136; SCS: n = 130). The primary endpoint of the study was "early allograft dysfunction" (EAD), a marker of early posttransplant liver injury and function. RESULTS: The difference in the incidence of EAD did not achieve significance, with 20.6% (NMP) versus 23.7% (SCS). Using exploratory, "as-treated" rather than "intent-to-treat," subgroup analyses, there was a greater effect size in donation after circulatory death donor livers (22.8% NMP vs 44.6% SCS) and in organs in the highest risk quartile by donor risk (19.2% NMP vs 33.3% SCS). The incidence of acute cardiovascular decompensation at organ reperfusion, "postreperfusion syndrome," as a secondary outcome was reduced in the NMP arm (5.9% vs 14.6%). CONCLUSIONS: NMP did not lower EAD, perhaps related to the inclusion of lower-risk liver donors, as higher-risk donor livers seemed to benefit more. The technology is safe in standard organ recovery and seems to have the greatest benefit for marginal donors.

Timing of Transport of Patients with COVID-19.

RATIONALE: The objective of this study was to evaluate the risk of mortality or ECMO cannulation for patients with confirmed or suspected COVID-19 transferred from sending hospitals to receiving tertiary care centers as a function of the duration of time at the sending hospital. OBJECTIVE: To determine outcomes of critically ill patients with COVID-19 who were transferred to tertiary or quarternary care medical centers. MATERIALS AND METHODS: Retrospective cohort study of critical care transports of patients to one of seven consortium tertiary care centers from March 1, 2020, through September 4, 2020. Age 14 years and older with confirmed or suspected COVID-19 transported from a sending hospital to a receiving tertiary care center by the critical care transport organization. RESULTS: Patients transported with confirmed or suspected COVID-19 to tertiary care centers had a mortality rate of 38.0%. Neither the number of days admitted, nor the number of days intubated at the sending hospital correlated with mortality (correlation coefficient 0.051 and -0.007, respectively). Similarly, neither the number of days admitted, nor number of days intubated at the sending hospital correlated with ECMO cannulation (correlation coefficient 0.008 and -0.036, respectively). CONCLUSION: It may be reasonable to transfer a critically ill COVID-19 patient to a tertiary care center even if they have been admitted at the sending hospital for several days.

COVID-19 and transplantation-Data censoring.

During the early wave of the COVID-19 pandemic, the Scientific Registry of Transplant Recipients (SRTR) designated a "black out" period between March 12, 2020, and June 12, 2020, for transplant outcomes reporting. We discuss the implications and potential bias it has introduced as it may selectively favor the outcomes for certain regions and harm other regions due to varied effects of different waves of COVID-19 infections across the United States.

SLAMF1 is expressed and secreted by hepatocytes and the liver in nonalcoholic fatty liver disease.

Nonalcoholic fatty liver disease (NAFLD) is one of the most prevalent forms of chronic liver disease in the United States and worldwide. Nonalcoholic steatohepatitis (NASH), the most advanced form of NAFLD, is characterized by hepatic steatosis associated with inflammation and hepatocyte death. No treatments are currently available for NASH other than lifestyle changes, and the disease lacks specific biomarkers. The signaling lymphocytic activation molecule family 1 (SLAMF1) protein is a self-ligand receptor that plays a role in orchestrating an immune response to some pathogens and cancers. We found that livers from humans and mice with NASH showed a more prominent immunohistochemistry staining for SLAMF1 than non-NASH controls. Furthermore, SLAMF1 levels are significantly increased in NASH plasma samples from mice and humans compared with their respective controls. In mice, the levels of SLAMF1 correlated significantly with the severity of the NASH phenotype. To test whether SLAMF 1 is expressed by hepatocytes, HepG2 cells and primary murine hepatocytes were treated with palmitic acid (PA) to induce a state of lipotoxicity mimicking NASH. We found that PA treatments of HepG2 cells and primary hepatocytes lead to significant increases in SLAMF1 levels. The downregulation of SLAMF1 in HepG2 cells improved the cell viability and reduced cytotoxicity. The in vivo data using mouse and human NASH samples suggests a potential role for this protein as a noninvasive biomarker for NASH. The in vitro data suggest a role for SLAMF1 as a potential therapeutic target to prevent hepatocyte death in response to lipotoxicity.NEW & NOTEWORTHY This study identified for the first time SLAMF1 as a mediator of hepatocyte death in nonalcoholic fatty liver disease (NASH) and as a marker of NASH in humans. There are no pharmacological treatments available for NASH, and diagnostic tools are limited to invasive liver biopsies. Therefore, since SLAMF1 levels correlate with disease progression and SLAMF1 mediates cytotoxic effects, this protein can be used as a therapeutic target and a clinical biomarker of NASH.

PD-1 expression in hepatocellular carcinoma predicts liver-directed therapy response and bridge-to-transplant survival.

BACKGROUND: Hepatocellular carcinoma (HCC) patients undergo liver-directed therapy (LDT) to control tumor burden while awaiting liver transplantation with response impacting waitlist survival. In this study, we investigate the link between absolute lymphocyte count (ALC) and PD-1 expression with response to LDT and bridge-to-transplant survival. METHODS: Treatment-naïve HCC patients (n = 86) undergoing LDT were enrolled at a single center from August 2016-March 2020. Response to LDT was determined using mRECIST. Blood samples were collected on the day of LDT and at follow-up. Cells were analyzed for phenotype by flow cytometry. Outcomes were liver transplantation or tumor progression. RESULTS: Incomplete response to initial LDT was associated with tumor progression precluding liver transplantation (OR: 7.6, 1.7 - 33.3, P < 0.001). Univariate analysis of baseline T cell phenotypes revealed ALC (OR: 0.44, 0.24-0.85, P = 0.009) as well as intermediate expression of PD-1 on CD4 (OR: 3.3, 1.03-10.3, P = 0.034) and CD8 T cells (OR: 3.0, 0.99-8.8 P = 0.043) associated with incomplete response to LDT. Elevations in PD-1 expression were associated with increased risk of bridge-to-transplant tumor progression (HR: 3.2, 1.2-9.4). In patients successfully bridged to liver transplantation, pre-treatment peripheral PD-1 profile was associated with advanced tumor staging (P < 0.005) with 2/4 of patients with elevations in PD-1 having T3-T4 TNM staging compared to 0 with low PD-1 expression. CONCLUSION: Low lymphocyte count or elevated expression of the PD-1 checkpoint inhibitor is associated with incomplete response to LDT and increased risk of bridge-to-transplant tumor progression. Patients with impaired T cell homeostasis may benefit from PD-1 immunotherapy to improve response to LDT and improve bridge-to-transplant outcomes.

Hepatitis C-associated focal proliferative glomerulonephritis in an aviremic recipient of a hepatitis C-positive antibody donor liver.

Shortage of organs for liver transplantation (LT) and the availability of highly efficient pan-genotypic direct-acting antivirals (DAAs) against hepatitis C virus (HCV) have allowed the use of livers from HCV-positive antibody/negative nucleic acid test donors (dHCV Ab+/NAT-) into aviremic HCV recipients over the last few years. We report the case of a patient who received an LT from an HCV Ab+/NAT- donor and, after HCV viremic conversion, developed a nephrotic syndrome due to a focal proliferative glomerulonephritis early after LT. Patient's renal function and proteinuria resolved after successful treatment with DAAs. Renal and hepatic function remain normal over 24 months of follow-up. This case restates the success of LT using livers from dHCV Ab+/NAT- in aviremic recipients in the context of DAAs while illustrating the risk for potential complications associated with the HCV transmission and reinforcing the importance of early initiation of anti-HCV therapy.