optimized-workflow-for-iterative-bleaching-extends-multiplexity

Optimized Workflow for Iterative Bleaching Extends Multiplexity Imaging of Highly Autofluorescent Clinical Samples

The prevalence of pulmonary disease due to nontuberculous mycobacteria (NTM) has been increasing globally. Though NTM-induced pulmonary disease often ...

National Institutes of Health

Pulmonary Rehabilitation for Post-Tuberculosis Lung Disease.

Standard treatment of nontuberculous mycobacterial pulmonary disease (NTM-PD) infection involves a multi-drug antimicrobial regimen for at least 12 months. The length, complexity, and side effect profile of antibiotic therapy for NTM-PD pose significant difficulties for maintaining patient adherence. Furthermore, physician adherence to NTM guidelines suffers for similar reasons to the extent that a study evaluating treatment approaches across multiple specialties found that only 13% of antibiotic regimens met ATS/IDSA guidelines. For this reason, a great need exists for therapy that augments the current armamentarium of antimicrobial chemotherapeutics or provides an alternative approach for decreasing host mycobacterial burden. As our knowledge of the mechanisms driving protective responses to NTM-PD infections by mammalian hosts expand, these processes provide novel therapeutic targets. These agents, which are commonly referred to as host-directed therapies (HDTs) have the potential of providing the much-needed boost to the nontuberculous mycobacterial therapeutic pipeline. In this review, we will focus on translational research and clinical trial data that detail the creation of therapeutic modalities developed to improve host mechanical protection and immunologic responses to PNTM infection.

Host-Directed Therapy in Nontuberculous Mycobacterial Pulmonary Disease: Preclinical and Clinical Data Review.

Blockade of the co-inhibitory receptor PD-1 enhances antitumor responses by boosting the function of antigen-specific T cells. Although rare, PD-1 blockade in patients with cancer can lead to exacerbation of infection-associated pathology. Here, we detail the case of a 38-year-old man who was enrolled in a clinical trial for assessment of the safety and activity of anti-PD-1 therapy for Kaposi sarcoma in people with HIV well-controlled on antiretroviral therapy. Less than a week after receiving the first dose of anti-PD-1 antibody (pembrolizumab), he presented with severe abdominal pain associated with sudden exacerbations of preexisting cytomegalovirus (CMV) enteritis and nontuberculous mycobacterial mesenteric lymphadenitis. Plasma biomarkers of gastrointestinal tract damage were highly elevated compared with healthy controls, consistent with HIV-associated loss of gut epithelial barrier integrity. Moreover, CMV-specific CD8 T cells expressed high levels of PD-1, and 7 days following PD-1 blockade, there was an increase in the frequency of activated CD38 Ki67 CMV-specific CD8 T cells. This case highlights the potential for PD-1 blockade to drive rapid exacerbations of inflammatory symptoms when administered to individuals harboring multiple unresolved infections.

Exacerbation of CMV and Nontuberculous Mycobacterial Infections Following PD-1 Blockade for HIV-Associated Kaposi Sarcoma.

We present a patient with a post-pneumonectomy empyema refractory to surgical debridement and systemic antibiotics. The patient initially presented with a bronchopleural fistula and pneumothorax secondary to tuberculosis (TB) destroyed lung, which required a pneumonectomy with Eloesser flap. Ongoing pleural infection delayed the closure of the Eloesser flap, and thoracoscopic inspection of his chest cavity revealed a green, mucous biofilm-like structure lining the postpneumonectomy pleural cavity. Cultures identified pan-susceptible  Despite debriding this biofilm-like structure and administering systemic antibiotics, the patient continued to show persistent signs of infection and regrowth of the film. We employed a novel approach to dissolve the biofilm-like structure using intrapleural dornase alfa followed by intrapleural antibiotic washes. After 3 weeks of daily washes, repeat inspection demonstrated the biofilm-like structure had completely resolved. Resolving the pseudomonas biofilm-like structure allowed permanent closure of his chest without further need for systemic antibiotics. At follow up 3 months later, he showed no sequalae. This treatment option can be an important adjunct to improve likelihood of chest closure in patients with post-pneumonectomy empyema that resists standard treatment options due to biofilm formation.

Novel management of pseudomonas biofilm-like structure in a post-pneumonectomy empyema.

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, e.g., primary and secondary antibodies. In addition to reporting negative data, the Knowledge-Base empowers method adoption and evolution by providing a venue for sharing protocols, videos, datasets, software, and publications. A dedicated discussion forum fosters a sense of community among researchers while addressing questions not covered in published manuscripts. Together, scientists from around the world are advancing scientific discovery at a faster pace, reducing wasted time and effort, and instilling greater confidence in the resulting data.

The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods.

Multiplexed imaging is a powerful approach in spatial biology, although it is complex, expensive and labor-intensive. Here, we present the IBEX Knowledge-Base, a central resource for reagents, protocols and more, to enhance knowledge sharing, optimization and innovation of spatial proteomics techniques.

Article	Year
Pulmonary Rehabilitation for Post-Tuberculosis Lung Disease. American journal of respiratory and critical care medicine\| PubMed ID: 37797326	2023
Host-Directed Therapy in Nontuberculous Mycobacterial Pulmonary Disease: Preclinical and Clinical Data Review. Clinics in chest medicine\| PubMed ID: 37890920	2023
Exacerbation of CMV and Nontuberculous Mycobacterial Infections Following PD-1 Blockade for HIV-Associated Kaposi Sarcoma. Open forum infectious diseases\| PubMed ID: 38680611	2024
Novel management of pseudomonas biofilm-like structure in a post-pneumonectomy empyema. Frontiers in cellular and infection microbiology\| PubMed ID: 39483118	2024
The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods. ArXiv\| PubMed ID: 39764400	2024
The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques. PLoS biology\| PubMed ID: 40106489	2025

Ifeanyichukwu U. Anidi

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