The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development.

Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement.

Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.

Major aims of single-cell proteomics include increasing the consistency, sensitivity and depth of protein quantification, especially for proteins and modifications of biological interest. Here, to simultaneously advance all these aims, we developed prioritized Single-Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands of prioritized peptides across all single cells (thus increasing data completeness) while maximizing instrument time spent analyzing identifiable peptides, thus increasing proteome depth. These strategies increased the sensitivity, data completeness and proteome coverage over twofold. The gains enabled quantifying protein variation in untreated and lipopolysaccharide-treated primary macrophages. Within each condition, proteins covaried within functional sets, including phagosome maturation and proton transport, similarly across both treatment conditions. This covariation is coupled to phenotypic variability in endocytic activity. pSCoPE also enabled quantifying proteolytic products, suggesting a gradient of cathepsin activities within a treatment condition. pSCoPE is freely available and widely applicable, especially for analyzing proteins of interest without sacrificing proteome coverage. Support for pSCoPE is available at http://scp.slavovlab.net/pSCoPE .

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments.

Analyzing proteins from single cells by tandem mass spectrometry (MS) has recently become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and reproducibility of the results may be undermined by numerous factors affecting experimental design, sample preparation, data acquisition and data analysis. We expect that broadly accepted community guidelines and standardized metrics will enhance rigor, data quality and alignment between laboratories. Here we propose best practices, quality controls and data-reporting recommendations to assist in the broad adoption of reliable quantitative workflows for single-cell proteomics. Resources and discussion forums are available at https://single-cell.net/guidelines .

Detection of cell-cell interactions via photocatalytic cell tagging.

The growing appreciation of immune cell-cell interactions within disease environments has led to extensive efforts to develop immunotherapies. However, characterizing complex cell-cell interfaces in high resolution remains challenging. Thus, technologies leveraging therapeutic-based modalities to profile intercellular environments offer opportunities to study cell-cell interactions with molecular-level insight. We introduce photocatalytic cell tagging (PhoTag) for interrogating cell-cell interactions using single-domain antibodies (VHHs) conjugated to photoactivatable flavin-based cofactors. Following irradiation with visible light, the flavin photocatalyst generates phenoxy radical tags for targeted labeling. Using this technology, we demonstrate selective synaptic labeling across the PD-1/PD-L1 axis in antigen-presenting cell-T cell systems. In combination with multiomics single-cell sequencing, we monitored interactions between peripheral blood mononuclear cells and Raji PD-L1 B cells, revealing differences in transient interactions with specific T cell subtypes. The utility of PhoTag in capturing cell-cell interactions will enable detailed profiling of intercellular communication across different biological systems.

The urgent need to implement point-of-care RNA testing for hepatitis C virus to support elimination.

Hepatitis C virus (HCV) elimination is an important global public health goal. However, the United States (US) is not on track to meet the World Health Organization's 2030 targets for HCV elimination. Recently, the White House proposed an HCV elimination plan that includes point-of-care (POC) HCV RNA testing, which is currently in use in many countries, but is not approved in the US. POC HCV RNA testing is crucial for implementing community-based testing, and for enabling test-and-treat programs, assessing cure, and monitoring for reinfection.. In this commentary, we review the status of POC HCV RNA testing in the US, discuss factors that are needed for successful implementation, and issue specific public health and policy recommendations that would allow for the use of POC HCV RNA testing to support HCV elimination.

Upgrading on Per Protocol versus For Cause surveillance prostate biopsies: An opportunity to decreasing the burden of active surveillance.

BACKGROUND: Most prostate cancer (PC) active surveillance (AS) protocols recommend "Per Protocol" surveillance biopsy (PPSBx) every 1-3 years, even if clinical and imaging parameters remained stable. Herein, we compared the incidence of upgrading on biopsies that met criteria for "For Cause" surveillance biopsy (FCSBx) versus PPSBx. METHODS: We retrospectively reviewed men with GG1 PC on AS in the Michigan Urological Surgery Improvement Collaborative (MUSIC) registry. Surveillance prostate biopsies obtained 1 year after diagnosis were classified as either PPSBx or FCSBx. Biopsies were retrospectively deemed FCSBx if any of these criteria were met: PSA velocity > 0.75 ng/mL/year; rise in PSA > 3 ng from baseline; surveillance magnetic resonance imaging (MRI) (sMRI) with a PIRADS ≥ 4; change in DRE. Biopsies were classified PPSBx if none of these criteria were met. The primary outcome was upgrading to ≥GG2 or ≥GG3 on surveillance biopsy. The secondary objective was to assess for the association of reassuring (PIRADS ≤ 3) confirmatory or surveillance MRI findings and upgrading for patients undergoing PPSBx. Proportions were compared with the chi-squared test. RESULTS: We identified 1773 men with GG1 PC in MUSIC who underwent a surveillance biopsy. Men meeting criteria for FCSBx had more upgrading to ≥GG2 (45%) and ≥GG3 (12%) compared with those meeting criteria for PPSBx (26% and 4.9%, respectively, p < 0.001 and p < 0.001). Men with a reassuring confirmatory or surveillance MRI undergoing PPSBx had less upgrading to ≥GG2 (17% and 17%, respectively) and ≥GG3 (2.9% and 1.8%, respectively) disease compared with men without an MRI (31% and 7.4%, respectively). CONCLUSIONS: Patients undergoing PPSBx had significantly less upgrading compared with men undergoing FCSBx. Confirmatory and surveillance MRI seem to be valuable tools to stratify the intensity of surveillance biopsies for men on AS. These data may help inform the development of a risk-stratified, data driven AS protocol.

Characterization and Application of Precore/Core-Related Antigens in Animal Models of Hepatitis B Virus Infection.

BACKGROUND AND AIMS: The hepatitis B core-related antigen (HBcrAg), a composite antigen of precore/core gene including classical hepatitis B core protein (HBc) and HBeAg and, additionally, the precore-related antigen PreC, retaining the N-terminal signal peptide, has emerged as a surrogate marker to monitor the intrahepatic HBV covalently closed circular DNA (cccDNA) and to define meaningful treatment endpoints. APPROACH AND RESULTS: Here, we found that the woodchuck hepatitis virus (WHV) precore/core gene products (i.e., WHV core-related antigen [WHcrAg]) include the WHV core protein and WHV e antigen (WHeAg) as well as the WHV PreC protein (WPreC) in infected woodchucks. Unlike in HBV infection, WHeAg and WPreC proteins were N-glycosylated, and no significant amounts of WHV empty virions were detected in WHV-infected woodchuck serum. WHeAg was the predominant form of WHcrAg, and a positive correlation was found between the serum WHeAg and intrahepatic cccDNA. Both WHeAg and WPreC antigens displayed heterogeneous proteolytic processing at their C-termini, resulting in multiple species. Analysis of the kinetics of each component of the precore/core-related antigen, along with serum viral DNA and surface antigens, in HBV-infected chimpanzees and WHV-infected woodchucks revealed multiple distinct phases of viral decline during natural resolution and in response to antiviral treatments. A positive correlation was found between HBc and intrahepatic cccDNA but not between HBeAg or HBcrAg and cccDNA in HBV-infected chimpanzees, suggesting that HBc can be a better marker for intrahepatic cccDNA. CONCLUSIONS: In conclusion, careful monitoring of each component of HBcrAg along with other classical markers will help understand intrahepatic viral activities to elucidate natural resolution mechanisms as well as guide antiviral development.

Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity.

Ras-driven cancer cells upregulate basal autophagy that degrades and recycles intracellular proteins and organelles. Autophagy-mediated proteome degradation provides free amino acids to support metabolism and macromolecular synthesis, which confers a survival advantage in starvation and promotes tumorigenesis. While the degradation of isolated protein substrates by autophagy has been implicated in controlling cellular function, the extent and specificity by which autophagy remodels the cellular proteome and the underlying functional consequences were unknown. Here we compared the global proteome of autophagy-functional and -deficient Ras-driven cancer cells, finding that autophagy affects the majority of the proteome yet is highly selective. While levels of vesicle trafficking proteins important for autophagy are preserved during starvation-induced autophagy, deleterious inflammatory response pathway components are eliminated even under basal conditions, preventing cytokine-induced paracrine cell death. This reveals the global, functional impact of autophagy-mediated proteome remodeling on cell survival and identifies critical autophagy substrates that mediate this process.

Responding to a surge in overdose deaths: perspectives from US syringe services programs.

BACKGROUND: US overdose deaths have reached a record high. Syringe services programs (SSPs) play a critical role in addressing this crisis by providing multiple services to people who use drugs (PWUD) that help prevent overdose death. This study examined the perspectives of leadership and staff from a geographically diverse sample of US SSPs on factors contributing to the overdose surge, their organization's response, and ongoing barriers to preventing overdose death. METHODS: From 2/11/2021 to 4/23/2021, we conducted semi-structured interviews with leadership and staff from 27 SSPs sampled from the North American Syringe Exchange Network directory. Interviews were transcribed and qualitatively analyzed using a Rapid Assessment Process. RESULTS: Respondents reported that increased intentional and unintentional fentanyl use (both alone and combined with other substances) was a major driver of the overdose surge. They also described how the COVID-19 pandemic increased solitary drug use and led to abrupt increases in use due to life disruptions and worsened mental health among PWUD. In response to this surge, SSPs have increased naloxone distribution, including providing more doses per person and expanding distribution to people using non-opioid drugs. They are also adapting overdose prevention education to increase awareness of fentanyl risks, including for people using non-opioid drugs. Some are distributing fentanyl test strips, though a few respondents expressed doubts about strips' effectiveness in reducing overdose harms. Some SSPs are expanding education and naloxone training/distribution in the broader community, beyond PWUD and their friends/family. Respondents described several ongoing barriers to preventing overdose death, including not reaching certain groups at risk of overdose (PWUD who do not inject, PWUD experiencing homelessness, and PWUD of color), an inconsistent naloxone supply and lack of access to intranasal naloxone in particular, inadequate funding, underestimates of overdoses, legal/policy barriers, and community stigma. CONCLUSIONS: SSPs remain essential in preventing overdose deaths amid record numbers likely driven by increased fentanyl use and COVID-19-related impacts. These findings can inform efforts to support SSPs in this work. In the face of ongoing barriers, support for SSPs-including increased resources, political support, and community partnership-is urgently needed to address the worsening overdose crisis.

Lessons from the First Wave of COVID-19 for Improved Medications for Opioid Use Disorder (MOUD) Treatment: Benefits of Easier Access, Extended Take Homes, and New Delivery Modalities.

Background Medications for Opioid Use Disorder (MOUD) are associated with important public health benefits. Program changes implemented in response to COVID-19 hold promise as ongoing strategies to improve MOUD treatment. Methods: MOUD patients on buprenorphine or methadone, providers, government regulators, and persons who use drugs not in MOUD were recruited in the Northeast region of the United States between June and October of 2020 via advertisements, fliers, and word of mouth. Semi-structured qualitative interviews were conducted. Interviews were professionally transcribed and thematically coded by two independent coders. Results: We conducted interviews with 13 people currently on buprenorphine, 11 currently on methadone, 3 previously on buprenorphine, 4 previously on methadone, and 6 who used drugs but had never been on MOUD. In addition, we interviewed MOUD providers, clinic staff, and government officials at agencies that regulate MOUD. Most participants found increased take-home doses, home medication delivery, and telehealth implemented during COVID-19 to be favorable, reporting that these program changes reduced travel time to clinics, facilitated retention in care, and reduced stigma associated with clinic attendance. However, some participants reported negative consequences of COVID-19, most notably, decreased access to basic resources, such as food, clothing, and harm reduction materials that had previously been distributed at some MOUD clinics. Conclusion: Access to and retention in MOUD can be lifesaving for persons using drugs. COVID-19-impelled program changes, including increased take-home doses, home medication delivery, and telehealth generally improved participants' experiences with MOUD. Making these permanent could improve retention in care.

Reconsidering Assumptions of Adolescent and Young Adult Severe Acute Respiratory Syndrome Coronavirus 2 Transmission Dynamics.

Evidence regarding the important role of adolescents and young adults (AYA) in accelerating and sustaining coronavirus disease 2019 (COVID-19) outbreaks is growing. Furthermore, data suggest that 2 known factors that contribute to high severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmissibility-presymptomatic transmission and asymptomatic case presentations-may be amplified in AYA. However, AYA have not been prioritized as a key population in the public health response to the COVID-19 pandemic. Policy decisions that limit public health attention to AYA and are driven by the assumption of insignificant forward transmission from AYA pose a risk of inadvertent reinvigoration of local transmission dynamics. In this viewpoint, we highlight evidence regarding the increased potential of AYA to transmit SARS-CoV-2 that, to date, has received little attention, discuss adolescent and young adult-specific considerations for future COVID-19 control measures, and provide applied programmatic suggestions.

"It's like 'liquid handcuffs": The effects of take-home dosing policies on Methadone Maintenance Treatment (MMT) patients' lives.

BACKGROUND: Methadone Maintenance Treatment (MMT) is widely recognized as one of the most effective ways of reducing risk of overdose, arrest, and transmission of blood-borne viruses like HIV and HCV among people that use opioids. Yet, MMT's use of restrictive take-home dose policies that force most patients to attend their clinic on a daily, or near-daily, basis may be unpopular with many patients and lead to low rates of treatment uptake and retention. In response, this article examines how clinics' take-home dosing policies have affected patients' experiences of treatment and lives in general. METHODS: This article is based on semi-structured, qualitative interviews with a variety of stakeholders in MMT. Interviews explored: reasons for engaging with, or not engaging with MMT; how MMT is conceptualized by patients and treatment providers (e.g., as harm reduction or route to abstinence and/or recovery); experiences with MMT; perception of barriers to MMT (e.g., organizational/regulatory, social) and how MMT might be improved to support peoples' substance use treatment needs and goals. RESULTS: Nearly all of the patients with past or present MMT use were highly critical of the limited access to take-home doses and consequent need for daily or near daily clinic attendance. Participants described how the use of restrictive take-home dose policies negatively impacted their ability to meet day-to-day responsibilities and also cited the need for daily attendance as a reason for quitting or avoiding OAT. Responses also demonstrate how such policies contribute to an environment of cruelty and stigma within many clinics that exposes this already-stigmatized population to additional trauma. CONCLUSIONS: Take-home dose policies in MMT are not working for a substantial number of patients and are reasonably seen by participants as degrading and dehumanizing. Revision of MMT regulations and policies regarding take home doses are essential to improve patient satisfaction and the quality and effectiveness of MMT as a key evidence-based treatment and harm reduction strategy.

Acceptability and Effectiveness of Hepatitis C Care at Syringe Service Programs for People Who Inject Drugs in New York City.

Introduction/Objectives: The incidence of hepatitis C (HCV) infection is rising among people who inject drugs (PWID). Even in the context of known HCV prevention and treatment strategies, some PWID remain unengaged in HCV care. This study aimed to identify and characterize experiences and perceptions of PWID regarding the acceptability and effectiveness of HCV testing and treatment at a local syringe service program (SSP). Methods: A total of 36 PWID participated in semi-structured interviews at an SSP in New York City. Interviews were audio-recorded, transcribed, and coded by three coders, following a constructivist grounded theory approach. Relevant themes were identified as they emerged from the data. Results: Interviews with PWID revealed three themes related to the impact of SSPs on HCV care: (1) non-stigmatizing SSP environments, (2) the role of SSPs in improving HCV knowledge, and (3) acceptability of SSPs as sites for HCV care among PWID. Discussion: This paper contributes to the ongoing understanding that SSPs provide a well-accepted source of HCV services for PWID. Participants believed that SSPs are accessible and effective sites for HCV care, and suggested that stigma among PWID continues to affect receipt of HCV care in traditional settings. Conclusions: Understanding attitudes and beliefs of PWID regarding the effectiveness of SSPs as sites for HCV care is crucial for the development of focused strategies to reduce HCV transmission, and to ultimately achieve HCV elimination. Given this, further research is warranted investigating how best to improve HCV care at harm reduction sites such as SSPs.

Hepatitis C Virus (HCV) Care Continuum Outcomes and HCV Community Viral Loads Among Patients in an Opioid Treatment Program.

BACKGROUND: Hepatitis C virus (HCV) remains endemic among people who use drugs (PWUD). Measures of HCV community viral load (CVL) and HCV care continuum outcomes may be valuable for ascertaining unmet treatment need and for HCV surveillance and control. METHODS: Data from patients in an opioid treatment program during 2013-2016 were used to (1) identify proportions of antibody and viral load (VL) tested, linked-to-care, and treated, in 2013-2014 and 2015-2016, and pre- and postimplementation of qualitative reflex VL testing; (2) calculate engaged-in-care HCV CVL and "documented" and "estimated" unmet treatment need; and (3) examine factors associated with linkage-to-HCV-care. RESULTS: Among 11 267 patients, proportions of HCV antibody tested (52.5% in 2013-2014 vs 73.3% in 2015-2016), linked-to-HCV-care (15.7% vs 51.8%), and treated (12.0% vs 44.7%) all increased significantly. Hispanic ethnicity was associated with less linkage-to-care, and Manhattan residence was associated with improved linkage-to-care. The overall engaged-in-care HCV CVL was 4 351 079 copies/mL (standard deviation = 7 149 888); local HCV CVLs varied by subgroup and geography. Documented and estimated unmet treatment need decreased but remained high. CONCLUSIONS: After qualitative reflex VL testing was implemented, care continuum outcomes improved, but gaps remained. High rates of unmet treatment need suggest that control of the HCV epidemic among PWUD will require expansion of HCV treatment coverage.

Hepatitis C Virus Incidence in a Cohort in Medication-Assisted Treatment for Opioid Use Disorder in New York City.

BACKGROUND: Hepatitis C virus (HCV) incidence has increased in the worsening opioid epidemic. We examined the HCV preventive efficacy of medication-assisted treatment (MAT), and geographic variation in HCV community viral load (CVL) and its association with HCV incidence. METHODS: HCV incidence was directly measured in an open cohort of patients in a MAT program in New York City between 1 January 2013 and 31 December 2016. Area-level HCV CVL was calculated. Associations of individual-level factors, and of HCV CVL, with HCV incidence were examined in separate analyses. RESULTS: Among 8352 patients, HCV prevalence was 48.7%. Among 2535 patients seronegative at first antibody test, HCV incidence was 2.25/100 person-years of observation (PYO). Incidence was 6.70/100 PYO among those reporting main drug use by injection. Female gender, drug injection, and lower MAT retention were significantly associated with higher incidence rate ratios. Female gender, drug injection, and methadone doses <60 mg were independently associated with shorter time to HCV seroconversion. HCV CVLs varied significantly by geographic area. CONCLUSIONS: HCV incidence was higher among those with lower MAT retention and was lower among those receiving higher methadone doses, suggesting the need to ensure high MAT retention, adequate doses, and increased HCV prevention and treatment engagement. HCV CVLs vary geographically and merit further study as predictors of HCV incidence.

Application of Proteomics in Sarcoidosis.

Sarcoidosis is a multisystem disease with heterogeneity in manifestations and outcomes. System-level studies leveraging "omics" technologies are expected to define mechanisms contributing to sarcoidosis heterogeneous manifestations and course. With improvements in mass spectrometry (MS) and bioinformatics, it is possible to study protein abundance for a large number of proteins simultaneously. Contemporary fast-scanning MS enables the acquisition of spectral data for deep coverage of the proteins with data-dependent or data-independent acquisition MS modes. Studies leveraging MS-based proteomics in sarcoidosis have characterized BAL fluid (BALF), alveolar macrophages, plasma, and exosomes. These studies identified several differentially expressed proteins, including protocadherin-2 precursor, annexin A2, pulmonary surfactant A2, complement factors C3, vitamin-D-binding protein, cystatin B, and amyloid P, comparing subjects with sarcoidosis with control subjects. Other studies identified ceruloplasmin, complement factors B, C3, and 1, and others with differential abundance in sarcoidosis compared with other interstitial lung diseases. Using quantitative proteomics, most recent studies found differences in PI3K/Akt/mTOR, MAP kinase, pluripotency-associated transcriptional factor, and hypoxia response pathways. Other studies identified increased clathrin-mediated endocytosis and Fcγ receptor-mediated phagocytosis pathways in sarcoidosis alveolar macrophages. Although studies in mixed BAL and blood cells or plasma are limited, some of the changes in lung compartment are detected in the blood cells and plasma. We review proteomics for sarcoidosis with a focus on the existing MS data acquisition strategies, bioinformatics for spectral data analysis to infer protein identity and quantity, unique aspects about biospecimen collection and processing for lung-related proteomics, and proteomics studies conducted to date in sarcoidosis.

Bundling Rapid Human Immunodeficiency Virus and Hepatitis C Virus Testing to Increase Receipt of Test Results: A Randomized Trial.

BACKGROUND: The overlapping human immunodeficiency virus (HIV) and hepatitis C virus (HCV) epidemics disproportionately affect people with substance use disorders. However, many people who use substances remain unaware of their infection(s). OBJECTIVE: The objective of this study was to examine the efficacy of an on-site bundled rapid HIV and HCV testing strategy in increasing receipt of both HIV and HCV test results. RESEARCH DESIGN: Two-armed randomized controlled trial in substance use disorder treatment programs (SUDTP) in New York City. Participants in the treatment arm were offered bundled rapid HIV and HCV tests with immediate results on-site. Participants in the control arm were offered the standard of care, that is, referrals to on-site or off-site laboratory-based HIV and HCV testing with delayed results. PARTICIPANTS: A total of 162 clients with unknown or negative HIV and HCV status. MEASURES: The primary outcome was the percentage of participants with self-reported receipt of HIV and HCV test results at 1-month postrandomization. RESULTS: Over half of participants were Hispanic (51.2%), with 25.3% being non-Hispanic black and 17.9% non-Hispanic white. Two thirds were male, and 54.9% reported injection as method of drug use. One hundred thirty-four participants (82.7%) completed the 1-month assessment. Participants in the treatment arm were more likely to report having received both test results than those in the control arm (69% vs. 19%, P<0.001). Seven participants in the treatment arm received a preliminary new HCV diagnosis, versus 1 in the control arm (P=0.029). CONCLUSION: Offering bundled rapid HIV and HCV testing with immediate results on-site in SUDTPs may increase awareness of HIV and HCV infection among people with substance use disorders.

Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation.

Allostery and covalent modification are major means of fast-acting metabolic regulation. Their relative roles in responding to environmental changes remain, however, unclear. Here we examine this issue, using as a case study the rapid decrease in pyruvate kinase flux in yeast upon glucose removal. The main pyruvate kinase isozyme (Cdc19) is phosphorylated in response to environmental cues. It also exhibits positively cooperative (ultrasensitive) allosteric activation by fructose-1,6-bisphosphate (FBP). Glucose removal causes accumulation of Cdc19's substrate, phosphoenolpyruvate. This response is retained in strains with altered protein-kinase-A or AMP-activated-protein-kinase activity or with CDC19 carrying mutated phosphorylation sites. In contrast, yeast engineered with a CDC19 point mutation that ablates FBP-based regulation fail to accumulate phosphoenolpyruvate. They also fail to grow on ethanol and slowly resume growth upon glucose upshift. Thus, while yeast pyruvate kinase is covalently modified in response to glucose availability, its activity is controlled almost exclusively by ultrasensitive allostery.

Putative invasive pulmonary aspergillosis in critically ill patients with COVID-19: An observational study from New York City.

BACKGROUND: Critically ill patients with coronavirus disease-2019 (COVID-19) are at the theoretical risk of invasive pulmonary aspergillosis (IPA) due to known risk factors. PATIENTS/METHODS: We aimed to describe the clinical features of COVID-19-associated pulmonary aspergillosis at a single centre in New York City. We performed a retrospective chart review of all patients with COVID-19 with Aspergillus isolated from respiratory cultures. RESULTS: A total of seven patients with COVID-19 who had one or more positive respiratory cultures for Aspergillus fumigatus were identified, all of whom were mechanically ventilated in the ICU. Four patients were classified as putative IPA. The median age was 79 years, and all patients were male. The patients had been mechanically ventilated for a mean of 6.8 days (range: 1-14 days) before Aspergillus isolation. Serum galactomannan level was positive for only one patient. The majority of our cases received much higher doses of glucocorticoids than the dosage with a proven mortality benefit. All four patients died. CONCLUSIONS: Vigilance for secondary fungal infections will be needed to reduce adverse outcomes in critically ill patients with COVID-19.

Clinical characteristics and organ system involvement in sarcoidosis: comparison of the University of Minnesota Cohort with other cohorts.

BACKGROUND: Sarcoidosis is a systemic granulomatous disease of unknown etiology. Clinical cohort studies of different populations are important to understand the high variability in clinical presentation and disease course of sarcoidosis. The aim of the study is to evaluate clinical characteristics, including organ involvement, pulmonary function tests, and laboratory parameters, in a sarcoidosis cohort at the University of Minnesota. We compare the organ system involvement of this cohort with other available cohorts. METHODS: We conducted a retrospective data collection and analysis of 187 subjects with biopsy-proven sarcoidosis seen at a tertiary center. Organ system involvement was determined using the WASOG sarcoidosis organ assessment instrument. Clinical phenotype groups were classified using the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis criteria. RESULTS: Mean subject age at diagnosis was 45.8 ± 12.4, with a higher proportion of males (55.1%), and a higher proportion of blacks (17.1%) compared to the racial distribution of Minnesota residents (5.95%). The majority (71.1%) of subjects required anti-inflammatory therapy for at least 1 month. Compared to the A Case Control Etiologic Study of Sarcoidosis cohort, there was a higher frequency of extra-thoracic lymph node (34.2% vs. 15.2%), eye (20.9% vs. 11.8%), liver (17.6% vs. 11.5%), spleen (20.9% vs. 6.7%), musculoskeletal (9.6% vs. 0.5%), and cardiac (10.7% vs. 2.3%) involvement in our cohort. A multisystem disease with at least five different organs involved was identified in 13.4% of subjects. A restrictive physiological pattern was observed in 21.6% of subjects, followed by an obstructive pattern in 17.3% and mixed obstructive and restrictive pattern in 2.2%. Almost half (49.2%) were Scadding stages II/III. Commonly employed disease activity markers, including soluble interleukin-2 receptor and angiotensin-converting enzyme, did not differ between treated and untreated groups. CONCLUSIONS: This cohort features a relatively high frequency of high-risk sarcoidosis phenotypes including cardiac and multiorgan disease. Commonly-utilized serum biomarkers do not identify subpopulations that require or do better with treatment. Findings from this study further highlight the high-variability nature of sarcoidosis and the need for a more reliable biomarker to predict and measure disease severity and outcomes for better clinical management of sarcoidosis patients.