Smoking history is associated with reduced efficacy of neoadjuvant therapy in pancreatic adenocarcinoma.

BACKGROUND: Differential responses to neoadjuvant therapy (NAT) exist in pancreatic ductal adenocarcinoma (PDAC); however, contributing factors are poorly understood. Tobacco smoke is a common risk factor for PDAC, with nicotine-induced chemoresistance observed in other cancers. This study aimed to explore the potential association between tobacco use and NAT efficacy in PDAC. METHODS: A single-center, retrospective analysis was conducted that included all consecutive patients with PDAC who underwent surgical resection after NAT with a documented smoking history (N = 208). NAT response was measured as percentage fibrosis in the surgical specimen. Multivariable models controlled for covariates and survival were modeled using the Kaplan-Meier method. RESULTS: Postoperatively, major responses to NAT (>95% fibrosis) were less frequently observed in smokers than in nonsmokers (13.7% vs 30.4%, respectively; P = .021). Pathologic complete responses were similarly less frequent in smokers than in nonsmokers (2.1% vs 9.9%, respectively; P = .023). On multivariate analysis controlling for covariates, smoking history remained independently associated with lower odds of major fibrosis (odds ratio [OR], 0.25; 95% CI, 0.10-0.59; P = .002) and pathologic complete response (OR, 0.21; 95% CI, 0.03-0.84; P = .05). The median overall survival was significantly longer in nonsmokers than in smokers (39.1 vs 26.6 months, respectively; P = .05). CONCLUSION: Tobacco use was associated with diminished pathologic responses to NAT. Future research to understand the biology underlying this observation is warranted and may inform differential NAT approaches or counseling among these populations.

Capsule endoscopy for obscure gastrointestinal bleed in the tropics: A single-center experience on 350 patients.

BACKGROUND: Obscure gastrointestinal bleed (OGIB), now called small bowel bleed (SBB), comprises 5% to 10% of all gastrointestinal (GI) bleed episodes and capsule endoscopy (CE) is a tool for its evaluation. Studies on CE in a large sample of SBB patients from the tropics are limited. METHODS: We did a retrospective analysis of a prospectively maintained database of patients with SBB undergoing CE using PillCam or MiroCam CE. RESULTS: Of 350 patients (age 52.4 ± 17.4 years; 248 [70.9%] male) undergoing CE, 243 (69.4%) and 107 (30.6%) had overt and occult SBB, respectively. CE detected lesions in 244 (69.7%) patients (single lesion in 172 [49.1%]; multiple in 72 [20.6%]). The single lesions included vascular malformations (52, 14.9%), ulcer/erosion (47, 13.4%), tumor (24, 6.9%), hookworm (19, 5.4%), stricture (15, 4.3%), hemobilia (1, 0.3%) and blood without identifiable lesion (9, 2.6%). Of 72 with multiple lesions, ulcer with stricture was the commonest finding (n = 43, 12.3%). No abnormality was detected in 106 (30.3%) patients. The frequency of lesion detection was comparable among patients with overt and occult SBB (173/243, 71.2% vs. 71/107, 66.3%, respectively; p = 0.4). Younger patients (0 to 39 years) more often had multiple lesions on CE than the older (≥ 40 years) ones (26/76, 34.2% vs. 46/228, 20.2%, respectively; p = 0.001). CONCLUSION: CE has a high diagnostic yield in SBB in the tropics, regardless of the type of bleed or of CE brand and the duration of recording. Multiple lesions associated with SBB are commoner among younger (< 40 years) patients.

Feud, Flower, and Fatal Electrocardiograms.

Oleander is a prevalent tropical plant used in many parts of India for deliberate self-harm. The active ingredients act in a mechanism similar to cardiac glycosides; hence, the toxicological profile is similar to digoxin toxicity. Cardiac toxicity occurs in the form of a heart block with concomitant ventricular arrhythmia. Identifying the distinct electrocardiographic pattern for early diagnosis and initiating emergency management is imperative. Here, we present two such interesting cases of oleander intoxication, one with Nerium oleander and the other with Thevetia peruviana.

The elusive extremities: a case of extramammary Paget disease.

Extramammary Paget disease is a rare dermatological condition resembling Paget disease that occurs most commonly in the anogenital area and axilla. We present the case of an elderly male who had come with complaints of an itchy, erythematous and raised lesion in the perianal region for 3 months that did not respond to antifungals. A biopsy was taken from the lesion site and the diagnosis was confirmed by histopathological examination. It is important to be aware of conditions like extramammary Paget disease when an elderly individual presents with a non-specific pruritic lesion in the perianal area that is non-responsive to treatment; the diagnosis of which can be made only by doing a biopsy from the concerned site. This highlights the importance of histopathological examination in such ambiguous cases.

Meta learning addresses noisy and under-labeled data in machine learning-guided antibody engineering.

Machine learning-guided protein engineering is rapidly progressing; however, collecting high-quality, large datasets remains a bottleneck. Directed evolution and protein engineering studies often require extensive experimental processes to eliminate noise and label protein sequence-function data. Meta learning has proven effective in other fields in learning from noisy data via bi-level optimization given the availability of a small dataset with trusted labels. Here, we leverage meta learning approaches to overcome noisy and under-labeled data and expedite workflows in antibody engineering. We generate yeast display antibody mutagenesis libraries and screen them for target antigen binding followed by deep sequencing. We then create representative learning tasks, including learning from noisy training data, positive and unlabeled learning, and learning out of distribution properties. We demonstrate that meta learning has the potential to reduce experimental screening time and improve the robustness of machine learning models by training with noisy and under-labeled training data.

Advancing Antibody Engineering through Synthetic Evolution and Machine Learning.

Abs are versatile molecules with the potential to achieve exceptional binding to target Ags, while also possessing biophysical properties suitable for therapeutic drug development. Protein display and directed evolution systems have transformed synthetic Ab discovery, engineering, and optimization, vastly expanding the number of Ab clones able to be experimentally screened for binding. Moreover, the burgeoning integration of high-throughput screening, deep sequencing, and machine learning has further augmented in vitro Ab optimization, promising to accelerate the design process and massively expand the Ab sequence space interrogated. In this Brief Review, we discuss the experimental and computational tools employed in synthetic Ab engineering and optimization. We also explore the therapeutic challenges posed by developing Abs for infectious diseases, and the prospects for leveraging machine learning-guided protein engineering to prospectively design Abs resistant to viral escape.

Self-assembled and perfusable microvasculature-on-chip for modeling leukocyte trafficking.

Leukocyte recruitment from blood to tissue is a process that occurs at the level of capillary vessels during both physiological and pathological conditions. This process is also relevant for evaluating novel adoptive cell therapies, in which the trafficking of therapeutic cells such as chimeric antigen receptor (CAR)-T cells throughout the capillaries of solid tumors is important. Local variations in blood flow, mural cell concentration, and tissue stiffness contribute to the regulation of capillary vascular permeability and leukocyte trafficking throughout the capillary microvasculature. We developed a platform to mimic a biologically functional human arteriole-venule microcirculation system consisting of pericytes (PCs) and arterial and venous primary endothelial cells (ECs) embedded within a hydrogel, which self-assembles into a perfusable, heterogeneous microvasculature. Our device shows a preferential association of PCs with arterial ECs that drives the flow-dependent formation of microvasculature networks. We show that PCs stimulate basement membrane matrix synthesis, which affects both vessel diameter and permeability in a manner correlating with the ratio of ECs to PCs. Moreover, we demonstrate that hydrogel concentration can affect capillary morphology but has no observed effect on vascular permeability. The biological function of our capillary network was demonstrated using an inflammation model, where significantly higher expression of cytokines, chemokines, and adhesion molecules was observed after tumor necrosis factor-alpha (TNF-α) treatment. Accordingly, T cell adherence and transendothelial migration were significantly increased in the immune-activated state. Taken together, our platform allows the generation of a perfusable microvasculature that recapitulates the structure and function of an in vivo capillary bed that can be used as a model for developing potential immunotherapies.

Food Desert Residence Is Not Associated With Dietary Adherence or Complication Rates in Patients With Isolated Mandibular Fractures.

BACKGROUND: Mandible fracture management requires postoperative dietary modifications to promote healing. Over 20 million Americans live in food deserts, low-income neighborhoods over one mile from a grocery store. The relationship between food desert residence (FDR) and adherence to postoperative dietary instructions remains unexplored. PURPOSE: This study's purpose is to evaluate the relationships between FDR, known risk factors, dietary adherence, and complications among patients with isolated mandible fractures. STUDY DESIGN, SETTING, SAMPLE: This retrospective cohort study was conducted at a level 1 trauma center and analyzed patients with mandible fractures between January 2015 and December 2020. Inclusion criteria included operative treatment of adult patients for mandible fractures; pregnant, incarcerated, and patients with incomplete data were excluded. PREDICTOR VARIABLE: FDR was the predictor variable of interest. FDR (coded yes or no) was generated by converting patient addresses to census tract GeoIDs and comparing them to the US Department of Agriculture Food Access Research Atlas. MAIN OUTCOME VARIABLES: The study examined two outcome variables: dietary adherence and postoperative complications. Dietary adherence was coded as adherent or nonadherent, indicating documented compliance with postoperative dietary modifications. Postoperative complications were coded as present or absent, reflecting infection, hardware failure, and mandible malunion or nonunion. COVARIATES: The covariates analyzed included age, sex, ethnicity, mechanism of injury, medical and psychiatric comorbidities (including diagnoses such as diabetes, hypertension, and schizophrenia), and tobacco use. ANALYSES: Relative risks (RRs) and multivariate logistic regression models were generated for both outcome variables. Two-tailed P values < 0.05 were considered statistically significant. RESULTS: During the study period, 143 patients had complete data allowing for FDR and dietary adherence determination, 124 of whom (86.7%) had complication data recorded. Of the cohort, 51/143 (35.7%) resided within a food desert, 30/143 (21.0%) exhibited dietary nonadherence, and 46/124 (37.1%) experienced complications. FDR was not associated with increased risk of dietary nonadherence (RR 0.92, 95% confidence interval [CI] 0.52 to 1.61, P = .76) or complications (RR 1.19, 95% CI 0.75 to 1.89; P = .46). On multivariate regression, dietary nonadherence was associated with increased complications (odds ratio 2.85, 95% CI 1.01 to 8.09, P = .049). CONCLUSION AND RELEVANCE: There was no association between FDR and dietary nonadherence or complications in mandible fracture patients. However, dietary nonadherence was associated with complications, highlighting the need for further research and intervention.

Type of neoadjuvant treatment strategy is associated with differential pathologic responses in pancreatic ductal adenocarcinoma.

BACKGROUND: Tumor fibrosis after neoadjuvant treatment (NAT) for pancreatic ductal adenocarcinoma (PDAC) correlates with treatment response. Herein we assessed how different NAT strategies influence pathologic responses and survival. METHODS: Patients with surgically resected PDAC who received NAT (1991-2020) were included. Descriptive statistics compared outcomes amongst fibrosis groups (none, minor <50 â€‹%, partial 51%-94 â€‹%, major ≥95 â€‹%) and NAT (chemotherapy alone, chemoradiation, or chemotherapy â€‹+ â€‹chemoradiation (total neoadjuvant therapy, TNT)). RESULTS: Patients with major fibrosis most often received TNT (65.8 â€‹%, p â€‹< â€‹0.001). Major fibrosis was associated with the greatest rate of downstaging (77.8 â€‹%, p â€‹< â€‹0.001), highest R0 margin rate (100 â€‹%, p â€‹< â€‹0.01), and lowest mean positive lymph node ratio (0.80, p â€‹< â€‹0.01). Amongst complete responders, 11/14 (78.6 â€‹%) received TNT. Median overall (66.3 months, p â€‹= â€‹0.003) and disease-free (54.7months, p â€‹= â€‹0.05) survival were highest with major fibrosis. CONCLUSIONS: Major fibrosis and complete pathologic responses after NAT are most frequent with a TNT strategy and are associated with improved outcomes.

Corticosteroid injection of the knee within one month prior to meniscus repair increases the risk of repair failure requiring meniscectomy.

OBJECTIVE: Meniscal tears are common knee injuries with limited endogenous healing capacity. This study aimed to investigate the association between the timing and administration of preoperative intra-articular corticosteroid injections (CSIs) and the risk of subsequent meniscectomy following meniscus repair. METHODS: Using a national insurance claims database, patients aged 18-40 years undergoing meniscus repair within six months of tear diagnosis were studied. Patients were categorized based on whether they received preoperative CSIs within three intervals prior to repair. Multivariable logistic regression was used to analyze the risk of follow-up meniscectomy while controlling for various patient-related variables. RESULTS: Among 5,390 patients meeting inclusion criteria, 201 received preoperative CSIs. The CSI group was older and had higher rates of diabetes, obesity, and knee osteoarthritis. The overall rate of follow-up meniscectomy did not differ between groups. However, CSIs performed within one month prior to repair were associated with significantly higher odds of subsequent meniscectomy compared to CSIs performed between three and six months prior. Obesity, tobacco use, and knee osteoarthritis were also independently associated with higher risk, while increasing age was associated with lower risk. CONCLUSION: The study highlights an increased risk of repair failure requiring follow-up meniscectomy for patients receiving intra-articular CSIs within one month prior to meniscus repair. These findings suggest caution when considering CSIs as a treatment option for patients scheduled for meniscus repair. Further research is needed to establish optimal timing guidelines for CSIs in relation to meniscus repair and to understand the underlying mechanisms.

The Unexpected Benefit of TCR Cross-Reactivity in Cancer Immunotherapy.

The ability of T-cell receptors (TCR) to recognize tumor-associated antigens (TAA) is a key driver of adoptive transfer of tumor-infiltrating lymphocyte (TIL) T cells, which can be a highly effective cancer immunotherapy. While it is common knowledge that TCRs are cross-reactive and can bind multiple different peptide antigens, this is typically considered an unattractive feature and limitation for TCR-based therapies. In a recent publication in Cell, Dolton and colleagues discover that certain TCRs, isolated from TILs used for successful treatment of melanoma, possess beneficial cross-reactivity by recognizing multiple TAA. Moreover, they elucidate the cumulative value of TCR cross-reactivity on cancer cell eradication and its prospective advantages for targeted cancer immunotherapies.

ePlatypus: an ecosystem for computational analysis of immunogenomics data.

MOTIVATION: The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner. RESULTS: Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is an open-source web-based platform and provides programming tutorials and an integrative database that helps elucidate signatures of B and T cell clonal selection. Furthermore, the ecosystem links novel and established bioinformatics pipelines relevant for single-cell immune repertoires and other aspects of computational immunology such as predicting ligand-receptor interactions, structural modeling, simulations, machine learning, graph theory, pseudotime, spatial transcriptomics, and phylogenetics. The ePlatypus ecosystem helps extract deeper insight in computational immunology and immunogenomics and promote open science. AVAILABILITY AND IMPLEMENTATION: Platypus code used in this manuscript can be found at github.com/alexyermanos/Platypus.

Magnetic Resonance Imaging Findings in a Rare Case of a Ruptured Intracranial Dermoid Cyst.

Intracranial dermoid cysts are rare, benign, congenital, and slow-growing cystic lesions. They contain mature squamous epithelium, apocrine, eccrine, sebaceous glands, and ectodermal structures. The rupture of intracranial dermoid cysts is a rare event and can cause life-threatening conditions.

Deploying synthetic coevolution and machine learning to engineer protein-protein interactions.

Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a platform for synthetic protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes drove a systems-level analysis of molecular recognition between Z domain-affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pretrained protein language models to expand, in silico, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. The integration of these approaches provides a means of simulating protein coevolution and generating protein complexes with diverse molecular recognition properties for biotechnology and synthetic biology.

A method for polyclonal antigen-specific T cell-targeted genome editing (TarGET) for adoptive cell transfer applications.

Adoptive cell therapy of donor-derived, antigen-specific T cells expressing native T cell receptors (TCRs) is a powerful strategy to fight viral infections in immunocompromised patients. Determining the fate of T cells following patient infusion hinges on the ability to track them in vivo. While this is possible by genetic labeling of parent cells, the applicability of this approach has been limited by the non-specificity of the edited T cells. Here, we devised a method for CRISPR-targeted genome integration of a barcoded gene into Epstein-Barr virus-antigen-stimulated T cells and demonstrated its use for exclusively identifying expanded virus-specific cell lineages. Our method facilitated the enrichment of antigen-specific T cells, which then mediated improved cytotoxicity against Epstein-Barr virus-transformed target cells. Single-cell and deep sequencing for lineage tracing revealed the expansion profile of specific T cell clones and their corresponding gene expression signature. This approach has the potential to enhance the traceability and the monitoring capabilities during immunotherapeutic T cell regimens.

Reversal of uniocular blindness with corticosteroids in a solid organ transplant recipient with cryptococcal meningitis and immune reconstitution syndrome (IRIS): A case report.

Cryptococcal meningitis is a life-threatening infection commonly seen in patients with advanced HIV infection and solid organ transplant recipients. We report a case of cryptococcal meningitis with immune reconstitution syndrome (IRIS) who presented to us with a headache and complete loss of vision in the left eye. He was managed with antifungals and a short course of steroids, and he regained vision completely. In the hospital, he developed complications including tacrolimus toxicity, fluconazole-induced QT prolongation, and flucytosine-induced thrombocytopenia. Our case demonstrates the importance of a multidisciplinary approach in the management of complex cases like cryptococcal meningitis in solid organ transplant recipients.

MicroRNAs as a therapeutic target in IgA nephropathy in Indian population.

Immunoglobulin A nephropathy (IgAN) is the most frequent glomerular disease with rapid development to end stage renal disease, requiring renal replacement therapy. Genome-wide studies suggest geographical variations in genetic susceptibility to IgAN and disease progression. Specific 'candidate genes' were indicated to correlate with different functions that are involved in the pathogenesis of renal conditions. MicroRNAs (miRNAs/miRs) have a major role in mRNA degradation or translation repression, thereby regulating the expression of their target proteins. Previously, a small number of miRNAs were reported to have direct associations with IgAN. In the present study, new miRNAs linked to IgAN were identified in the Indian population. The miRNA was isolated from kidney biopsies of patients with IgAN (n=6) and healthy control tissue from patients with renal cell carcinoma (n=6). The sequencing results indicated that the miRNA percentage acquired from controls and patients with IgAN was 5.61 and 4.35%, respectively. From the results, 10 upregulated and 15 downregulated miRNAs were identified. Of the 25 differentially expressed miRNAs (DEMs), miR-181a-5p, miR-28-3p, let-7g-5p, miR-92a-3p and miR-30c-5p were not reported previously. Furthermore, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses suggested that the target genes of the DEMs were mainly enriched in pathways such as cancer, ErbB signalling, proteoglycans in cancer, Hippo signalling and MAPK pathways. The newly identified miRNAs may impact the behaviour of tissues or IgA deposition by regulating signalling pathways, which forms a basis for future studies aimed at improving the diagnosis and care of patients with IgAN in the Indian community.

Generation of a single-cell B cell atlas of antibody repertoires and transcriptomes to identify signatures associated with antigen specificity.

Although new genomics-based pipelines have potential to augment antibody discovery, these methods remain in their infancy due to an incomplete understanding of the selection process that governs B cell clonal selection, expansion, and antigen specificity. Furthermore, it remains unknown how factors such as aging and reduction of tolerance influence B cell selection. Here we perform single-cell sequencing of antibody repertoires and transcriptomes of murine B cells following immunizations with a model therapeutic antigen target. We determine the relationship between antibody repertoires, gene expression signatures, and antigen specificity across 100,000 B cells. Recombinant expression and characterization of 227 monoclonal antibodies revealed the existence of clonally expanded and class-switched antigen-specific B cells that were more frequent in young mice. Although integrating multiple repertoire features such as germline gene usage and transcriptional signatures failed to distinguish antigen-specific from nonspecific B cells, other features such as immunoglobulin G (IgG) subtype and sequence composition correlated with antigen specificity.

Persistent virus-specific and clonally expanded antibody-secreting cells respond to induced self-antigen in the CNS.

B cells contribute to the pathogenesis of both cellular- and humoral-mediated central nervous system (CNS) inflammatory diseases through a variety of mechanisms. In such conditions, B cells may enter the CNS parenchyma and contribute to local tissue destruction. It remains unexplored, however, how infection and autoimmunity drive transcriptional phenotypes, repertoire features, and antibody functionality. Here, we profiled B cells from the CNS of murine models of intracranial (i.c.) viral infections and autoimmunity. We identified a population of clonally expanded, antibody-secreting cells (ASCs) that had undergone class-switch recombination and extensive somatic hypermutation following i.c. infection with attenuated lymphocytic choriomeningitis virus (rLCMV). Recombinant expression and characterisation of these antibodies revealed specificity to viral antigens (LCMV glycoprotein GP), correlating with ASC persistence in the brain weeks after resolved infection. Furthermore, these virus-specific ASCs upregulated proliferation and expansion programs in response to the conditional and transient induction of the LCMV GP as a neo-self antigen by astrocytes. This class-switched, clonally expanded, and mutated population persisted and was even more pronounced when peripheral B cells were depleted prior to autoantigen induction in the CNS. In contrast, the most expanded B cell clones in mice with persistent expression of LCMV GP in the CNS did not exhibit neo-self antigen specificity, potentially a consequence of local tolerance induction. Finally, a comparable population of clonally expanded, class-switched, and proliferating ASCs was detected in the cerebrospinal fluid of relapsing multiple sclerosis (RMS) patients. Taken together, our findings support the existence of B cells that populate the CNS and are capable of responding to locally encountered autoantigens.