Mayte Suarez-Farinas

Icahn School of Medicine at Mount Sinai | MSSM · Dept. of Population Health Science and Policy/ Genetics and Genomics

Systems vaccinology has defined molecular signatures and mechanisms of immunity to vaccination. However, comparative analysis of immunity to different vaccines is lacking. We integrated transcriptional data of over 3,000 samples, from 820 adults across 28 studies of 13 vaccines and analyzed vaccination-induced signatures of antibody responses. Most...

Vaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding the mechanisms by which vaccines protect. Systems immunology combines traditional immunology with modern ‘omic profiling techniques and computational modeling to promote rapid and...

Several studies have shown that the pre-vaccination immune state is associated with the antibody response to vaccination. However, the generalizability and mechanisms that underlie this association remain poorly defined. Here, we sought to identify a common pre-vaccination signature and mechanisms that could predict the immune response across 13 di...

Objective IBD therapies and treatments are evolving to deeper levels of remission. Molecular measures of disease may augment current endpoints including the potential for less invasive assessments. Design Transcriptome analysis on 712 endoscopically defined inflamed (Inf) and 1778 non-inflamed (Non-Inf) intestinal biopsies (n=498 Crohn’s disease,...

Objective To determine whether a machine learning model can detect SARS-CoV-2 infection from physiological metrics collected from wearable devices. Materials and Methods Health care workers from 7 hospitals were enrolled and prospectively followed in a multicenter observational study. Subjects downloaded a custom smart phone app and wore Apple Wat...

Understanding the immune response to dengue virus (DENV) is essential for developing a dengue vaccine that is protective against all four DENV serotypes. We evaluated the immune response post-vaccination (live attenuated tetravalent dengue vaccine TV005 or trivalent admixture) and post-challenge with DEN2Δ30 (Tonga/74) to better understand the impo...

There is a need for better classification and understanding of tumor-infiltrating lymphocytes (TILs). Here, we applied advanced functional genomics to interrogate 9,000 human tumors and multiple single-cell sequencing sets using benchmarked T cell states, comprehensive T cell differentiation trajectories, human and mouse vaccine responses, and othe...

Systems biology approaches have been used to define molecular signatures and mechanisms of immunity to vaccination. However, most such studies have been done with single vaccines, and comparative analysis of the response to different vaccines is lacking. We integrated temporal transcriptional data of over 3,000 samples, obtained from 820 healthy ad...

B cells, which are critical for intestinal homeostasis, remain understudied in ulcerative colitis (UC). In this study, we recruited three cohorts of patients with UC (primary cohort, n = 145; validation cohort 1, n = 664; and validation cohort 2, n = 143) to comprehensively define the landscape of B cells during UC-associated intestinal inflammatio...

Background Wearable devices enable monitoring and measurement of physiological parameters over a 24-h period, and some of which exhibit circadian rhythm characteristics. However, the currently available R package cosinor could only analyze daily cross-sectional data and compare the parameters between groups with two levels. To evaluate longitudinal...

Vaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding the mechanisms by which vaccines protect. Systems immunology combines traditional immunology with modern 'omic profiling techniques and computational modeling to promote rapid and...

Importance: Passive and non-invasive identification of SARS-CoV-2 infection remains a challenge. Widespread use of wearable devices represents an opportunity to leverage physiological metrics and fill this knowledge gap. Objective: To determine whether a machine learning model can detect SARS-CoV-2 infection from physiological metrics collected fro...

Background Polygenic and environmental factors are underlying causes of inflammatory bowel disease (IBD). We hypothesized that integration of the genetic loci controlling a metabolite’s abundance, with known IBD genetic susceptibility loci, may help resolve metabolic drivers of IBD. Methods We measured the levels of 1300 metabolites in the serum o...

Many factors determine whether an individual responding to vaccination will generate an immune response that can lead to protection. Several studies have shown that the pre-vaccination immune state associate with the antibody response to vaccines. However, the generalizability and mechanisms that underlie this association remain poorly defined. Her...

Background Disease extent varies in ulcerative colitis (UC) from proctitis to left-sided colitis to pancolitis and is a major prognostic factor. When the extent of UC is limited there is often a sharp demarcation between macroscopically involved and uninvolved areas and what defines this or subsequent extension, is unknown. We characterized the dem...

An important goal of clinical genomics is to be able to estimate the risk of adverse disease outcomes. Between 5% and 10% of individuals with ulcerative colitis (UC) require colectomy within 5 years of diagnosis, but polygenic risk scores (PRSs) utilizing findings from genome-wide association studies (GWASs) are unable to provide meaningful predict...

Respiratory failure is the leading cause of death in patients with severe SARS-CoV-2 infection1,2, yet the host response at the lung tissue-level is poorly understood. Here, we performed single-nucleus RNA-sequencing of ~116,000 nuclei of lungs from 19 COVID-19 decedents who underwent rapid autopsy and 7 control lungs. Integrated analyses revealed...

Background: The Coronavirus Disease 2019 (COVID-19) pandemic has resulted in a high degree of psychological distress in health care workers (HCWs). There is a need to characterize which HCWs are at an increased risk of developing psychological effects from the pandemic. Given differences in the response of individuals to stress, evaluation of both...

BACKGROUND The COVID-19 pandemic has resulted in a high degree of psychological distress among health care workers (HCWs). There is a need to characterize which HCWs are at an increased risk of developing psychological effects from the pandemic. Given the differences in the response of individuals to stress, an analysis of both the perceived and ph...

Patients with a disorder of mitochondrial long-chain fatty acid β-oxidation (FAO) have reduced fasting tolerance and may present with hypoketotic hypoglycemia, hepatomegaly, (cardio)myopathy and rhabdomyolysis. Patients should avoid a catabolic state because it increases reliance on FAO as energy source. It is currently unclear whether weight loss...

Background Accurate diagnosis of peanut allergy is a significant clinical challenge. Here, a novel diagnostic blood test using the peanut Bead‐Based Epitope Assay (“peanut BBEA”) was developed utilizing the LEAP cohort and then validated using two independent cohorts. Methods The development of the peanut BBEA diagnostic test followed the National...

With the fast evolution of high-throughput technology, longitudinal gene expression experiments have become affordable and increasingly common in biomedical fields. Generalized estimating equation (GEE) approach is a widely used statistical method for the analysis of longitudinal data. Feature selection is imperative in longitudinal omics data anal...

An important goal of clinical genomics is to be able to estimate the risk of adverse disease outcomes. Between 5% and 10% of ulcerative colitis (UC) patients require colectomy within five years of diagnosis, but polygenic risk scores (PRS) utilizing findings from GWAS are unable to provide meaningful prediction of this adverse status. By contrast,...

Background Inflammatory bowel disease (IBD) is a complex disease with variable presentation, progression and response to therapies. Current disease classification is based on subjective clinical phenotypes. The peripheral blood immunophenome can reflect local inflammation, thus we measured 39 circulating immune cell types in a large cohort of IBD a...

The cover image is based on the Original Article The erythema Q‐score, an imaging biomarker for redness in skin inflammation by John Frew et al., https://doi.org/10.1111/exd.14224.

Background In the Learning Early About Peanut Allergy (LEAP) trial, early consumption of peanut in high-risk infants was found to decrease the rate of peanut allergy at 5 years of age. Sequential epitope-specific (ses-)IgE is a promising biomarker of clinical peanut reactivity. Objective To compare the evolution of ses-IgE and ses-IgG4 in children...

Analysis of epitope-specific antibody repertoires has provided novel insights into the pathogenesis of inflammatory disorders, especially allergies. A novel multiplex immunoassay, termed Bead-Based Epitope Assay (BBEA), was developed to quantify levels of epitope-specific immunoglobulins, including IgE, IgG, IgA and IgD isotypes. bbeaR is an open-s...

Patients with a disorder of mitochondrial long-chain fatty acid β-oxidation (FAO) have reduced fasting tolerance and may present with hypoketotic hypoglycemia, hepatomegaly, (cardio)myopathy and rhabdomyolysis. Patients should avoid a catabolic state because it increases reliance on FAO as energy source. It is currently unclear whether weight loss...

Significance: Melanoma is a deadly cancer that physicians struggle to diagnose early because they lack the knowledge to differentiate benign from malignant lesions. Deep machine learning approaches to image analysis offer promise but lack the transparency to be widely adopted as stand-alone diagnostics. Aim: We aimed to create a transparent machine...

Significance: Melanoma is a deadly cancer that physicians struggle to diagnose early because they lack the knowledge to differentiate benign from malignant lesions. Deep machine learning approaches to image analysis offer promise but lack the transparency to be widely adopted as stand-alone diagnostics. Aim: We aimed to create a transparent mach...

Background: Changes in autonomic nervous system function, characterized by heart rate variability (HRV), have been associated with and observed prior to the clinical identification of infection. Objective: We performed an evaluation of HRV collected by a wearable device to identify and predict Coronavirus disease 2019 (COVID-19) and its related...

BACKGROUND Changes in autonomic nervous system function, characterized by heart rate variability (HRV), have been associated with infection and observed prior to its clinical identification. OBJECTIVE We performed an evaluation of HRV collected by a wearable device to identify and predict COVID-19 and its related symptoms. METHODS Health care wor...

Background Changes in autonomic nervous system function, characterized by heart rate variability (HRV), have been associated with and observed prior to the clinical identification of infection. We performed an evaluation of this metric collected by wearable devices, to identify and predict Coronavirus disease 2019 (COVID-19) and its related symptom...

Background Physician rating of cutaneous erythema is central to clinical dermatological assessment as well as quantification of outcome measures in clinical trials in a number of dermatologic conditions. However, issues with interrater reliability and variability in the setting of higher Fitzpatrick skin types makes visual erythema assessment unrel...

Background and aims: The presence of gastrointestinal symptoms and high levels of viral RNA in the stool suggest active Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) replication within enterocytes. Methods: Here, in multiple, large cohorts of patients with inflammatory bowel disease (IBD), we have studied the intersections between...

With the fast evolution of high-throughput technology, longitudinal gene expression experiments have become affordable and increasingly common in biomedical fields. Generalized estimating equation (GEE) approach is a widely used statistical method for the analysis of longitudinal data. Feature selection is imperative in longitudinal omics data anal...

Background Peanut allergy is characterized by the development of IgE against peanut antigen. Bjective Evaluate the evolution of epitope-specific (es)IgE and esIgG4 in a prospective cohort of high-risk infants to determine if antibody profiles can predict peanut allergy after 4 years of age. Methods The endpoint was allergy status at 4⁺ years; sam...

Background: Misdiagnosis of peanut allergy is a significant clinical challenge. Here, a novel diagnostic blood-based test using a Bead-Based Epitope Assay (peanut BBEA) has been developed on the LEAP cohort and then independently validated on the CoFAR2 and POISED cohorts. Methods: Development of the peanut BBEA followed the National Academy of Med...

Background & Aims It is not clear whether concomitant therapy with corticosteroids and anti-tumor necrosis factor (TNF) agents is more effective at inducing remission in patients with Crohn’s disease (CD) than anti-TNF monotherapy. We aimed to determine whether patients with active CD receiving corticosteroids during induction therapy with anti-TNF...

Immune dysregulation and cytokine release syndrome have emerged as pathological hallmarks of severe Coronavirus Disease 2019 (COVID-19), leading to the evaluation of cytokine antagonists as therapeutic agents. A number of immune-directed therapies being considered for COVID-19 patients are already in clinical use in chronic inflammatory conditions...

Background Egg‐white ovomucoid, i.e. Gal d 1, is associated with IgE‐mediated allergic reactions in most egg allergic children. Epitope‐specific IgE levels have been correlated with the severity of egg allergy, while emerging evidence suggests that other antibodies, i.e. IgG1, IgG4, IgA1 and IgD, may have a protective function; yet, their epitope‐s...

Zika virus (ZIKV) is an emerging, mosquito-borne flavivirus responsible for recent epidemics across the Americas, and it is closely related to dengue virus (DENV). Here, we study samples from 46 DENV-naive and 43 DENV-immune patients with RT-PCR-confirmed ZIKV infection at early-acute, late-acute, and convalescent time points from our pediatric coh...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Peanut epitope-specific IgE antibodies (esIgE) have been associated with the severity of peanut allergy; whereas concomitant increases in epitope-specific IgG1, IgG4, IgA and IgD might ameliorate allergic symptoms by “blocking” IgE-mediated reactions. In this study, we analyzed antibody repertoires in a CoFAR2 cohort of high-risk children to elucid...

The interleukin (IL)-23/T-helper type 17 cell axis is a target for psoriasis. The tyrosine kinase 2 (TYK2)/Janus kinase 1 (JAK1) inhibitor, PF-06700841, will directly suppress TYK2-dependent IL-12 and IL-23 signaling and JAK1-dependent signaling in cells expressing these signaling molecules, including T cells and keratinocytes. This clinical study...

Background Among the adaptive immune cells, B cells, dominated by IgA producing plasma cells (PC), are critical for intestinal homeostasis. However, the B-cell response remains under studied in ulcerative colitis (UC). Methods Using single-cell RNA sequencing (scRNA seq), single-cell IgH sequencing (sc IgH seq), multiparameter flow cytometry (FC),...

Identification of allergenic IgE epitopes is instrumental for the development of novel diagnostic and prognostic methods in food allergy. In this work, we present the quantification and validation of a Bead-Based Epitope Assay (BBEA) that through multiplexing of epitopes and multiple sample processing enables completion of large experiments in a sh...

Background: IL-17 antagonists induce impressive clinical benefit in psoriasis, but it is unknown to what extent cellular and molecular psoriasis characteristics are suppressed by a clinically relevant dose/schedule of any IL-17-receptor antagonist. Objective: Examine the effects of the IL-17-receptor-A antagonist brodalumab, on clinical and mole...

The application of machine-learning to longitudinal gene-expression profiles has demonstrated potential to decrease the "assessment gap", between biochemical determination and clinical manifestation, of a patient's response to treatment. Although Psoriasis is a proven testing ground for treatment-response prediction using transcriptomic data from c...

An excess incidence of prostate cancer has been identified among World Trade Center (WTC) responders. In this study, we hypothesized that WTC dust, which contained carcinogens and tumor-promoting agents, could facilitate prostate cancer development by inducing DNA damage, promoting cell proliferation, and causing chronic inflammation. We compared e...

Although hidradenitis suppurativa (HS) has a reported mean age at onset of 21.8 years,¹ we have observed initial onset of HS lesions in individuals older than 40 years more commonly than expected. In this retrospective study, we investigated age at HS onset and its distribution.

Background: Current in vitro methods for peanut allergy diagnosis have limitations in utility. Here we present a novel diagnostic blood-based test using a Bead-Based Epitope Assay (BBEA) that has been developed and then independently validated. Methods: Development of the test followed the National Academy of Medicine’s established guidelines. Dis...