Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq

Phage Immunoprecipitation-Sequencing (PhIP-Seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-Seq for autoantigen discovery, including our previous work (Vazquez et al. 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki Disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), and finally, mild and severe forms of COVID19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as PDYN in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in 2 patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-Seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID19, including the endosomal protein EEA1. Together, scaled PhIP-Seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.

Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19

Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we found IFN-I autoantibodies in 19% of critical, 6% of severe and none of the moderate cases. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single-cell epitope and transcriptome sequencing from 54 COVID-19 patients, 15 non-COVID-19 patients and 11 non-hospitalized healthy controls, revealed a lack of IFN-I stimulated gene (ISG-I) response in myeloid cells from critical cases, including those producing anti-IFN-I autoantibodies. Moreover, surface protein analysis showed an inverse correlation of the inhibitory receptor LAIR-1 with ISG-I expression response early in the disease course. This aberrant ISG-I response in critical patients with and without IFN-I autoantibodies, supports a unifying model for disease pathogenesis involving ISG-I suppression via convergent mechanisms.

Early Detection for Colorectal Cancer: ASCO Resource-Stratified Guideline.

PURPOSE: To provide resource-stratified, evidence-based recommendations on the early detection of colorectal cancer in four tiers to clinicians, patients, and caregivers. METHODS: American Society of Clinical Oncology convened a multidisciplinary, multinational panel of medical oncology, surgical oncology, surgery, gastroenterology, health technology assessment, cancer epidemiology, pathology, radiology, radiation oncology, and patient advocacy experts. The Expert Panel reviewed existing guidelines and conducted a modified ADAPTE process and a formal consensus-based process with additional experts (Consensus Ratings Group) for two round(s) of formal ratings. RESULTS: Existing sets of guidelines from eight guideline developers were identified and reviewed; adapted recommendations form the evidence base. These guidelines, along with cost-effectiveness analyses, provided evidence to inform the formal consensus process, which resulted in agreement of 75% or more. CONCLUSION: In nonmaximal settings, for people who are asymptomatic, are ages 50 to 75 years, have no family history of colorectal cancer, are at average risk, and are in settings with high incidences of colorectal cancer, the following screening options are recommended: guaiac fecal occult blood test and fecal immunochemical testing (basic), flexible sigmoidoscopy (add option in limited), and colonoscopy (add option in enhanced). Optimal reflex testing strategy for persons with positive screens is as follows: endoscopy; if not available, barium enema (basic or limited). Management of polyps in enhanced is as follows: colonoscopy, polypectomy; if not suitable, then surgical resection. For workup and diagnosis of people with symptoms, physical exam with digital rectal examination, double contrast barium enema (only in basic and limited); colonoscopy; flexible sigmoidoscopy with biopsy (if contraindication to latter) or computed tomography colonography if contraindications to two endoscopies (enhanced only).