Biology subjects

Feld, J. J.

Publications and source records attributed to Feld, J. J..

3 recordsLinked to original sources

bioRxiv2024

Defining the multiplex probe panel for detecting mutating viruses with high clinical sensitivity

Nucleic acid technology has emerged as an important diagnostic for infectious diseases, cancer, cardiovascular diseases, and other diseases. However, mismatches between the probes and targets can lead to misdiagnosis. Here we determine how many mismatches between the probe and target lead to poor clinical performance and respond by developing a rationale multiplex strategy to overcome this detection problem. We found that the probe-target mismatches of greater than 20% yielded clinical sensitivity of 22% or less, rendering the diagnostic test useless. We designed probe panels to improve the clinical sensitivity. We tested our multiplex probe strategy using hepatitis C virus as the model pathogen because this virus has high mutation rates. We showed that we can improve the clinical sensitivity for detecting hepatitis C virus from 31 to 89% when we designed and applied a four-probe panel to the diagnostic test instead of a single probe system. Interestingly, increasing beyond four probes did not significantly increase the clinical sensitivity. We present a strategy to overcome the poor clinical sensitivity of nucleic acid tests for mutating genetic targets. Incorporating this panel design strategy can lead to improved diagnostic test performance, fewer false negatives and more accurate treatment planning for patients.

molecular biology↗

bioRxiv2024

Virus-associated Inflammation Imprints an Inflammatory Profile on Long-lived Monocyte-derived Macrophages in the Human Liver

Chronic liver injury triggers the activation and recruitment of immune cells, causing antigen-independent tissue damage and liver disease progression. Tissue inflammation can reshape macrophage composition through monocyte replacement. Replacement of tissue macrophages with monocytes differentiating in an inflammatory environment can potentially imprint a phenotype that switches the liver from an immunotolerant organ to one predisposed to tissue damage. We longitudinally sampled the liver of chronic hepatitis B (CHB) patients with active liver inflammation starting antiviral therapy. Antiviral therapy suppressed viral replication and liver inflammation, which coincided with decreased myeloid activation markers. Single-cell RNA sequencing mapped peripheral inflammatory markers to a monocyte-derived macrophage population, distinct from Kupffer cells, with an inflammatory transcriptional profile. The inflammatory macrophages (iMacs) differentiated from blood monocytes and established a long-lived population. The iMacs retained their core transcriptional signature, consistent with trained immunity, resulting in a population of macrophages primed for inflammation potentially driving progressive liver disease.

immunology↗

bioRxiv2023

Liver-specific Inflammatory Signatures Predict Clinically Significant Liver Damage.

Background and AimsInflammation drives progression of chronic liver disease. However, the triggers of inflammation remain undefined during chronic hepatitis B (CHB) because hepatic flares are spontaneous and difficult to capture. We used nucleoside analogue (NA) withdrawal to investigate early inflammatory events because liver damage after stopping therapy occurs in a predictable time frame. 11 CHB patients underwent 192 weeks of NA therapy before a protocol defined stop. Liver fine-needle aspirates (FNAs) were collected at baseline and 4-weeks post-withdrawal and analyzed using flow cytometry and single-cell RNA sequencing (scRNA-seq). Intrahepatic mononuclear cells (IHMCs) from uninfected livers were used to validate transcriptomic findings. At 4 weeks post NA-withdrawal, HBV DNA rebounded but alanine aminotransferase (ALT) levels remained normal, 7/11 patients developed ALT elevations (>2xULN) at later timepoints. There were no changes in cell frequencies between baseline and viral rebound. ScRNA-seq revealed upregulation of IFN stimulated genes (ISGs) and pro-inflammatory cytokine MIF upon viral rebound. In vitro experiments confirmed the type I IFN-dependent ISG profile whereas MIF was induced primarily by IL-12. MIF exposure further amplified inflammatory cytokine production by myeloid cells. Our data show that innate immune activation is detectable in the liver before clinically-significant liver damage is detectable in the serum.

immunology↗