All Publications

  • Automated Spatial Omics Landscape Analysis Approach Reveals Novel Tissue Architectures in Ulcerative Colitis. Research square Rogalla, S., Holman, D., Rubin, S., Ferenc, M., Holman, E., Koron, A., Daniel, R., Boland, B., Nolan, G., Chang, J. 2024


    The utility of spatial omics in leveraging cellular interactions in normal and diseased states for precision medicine is hampered by a lack of strategies for matching disease states with spatial heterogeneity-guided cellular annotations. Here we use a spatial context-dependent approach that matches spatial pattern detection to cell annotation. Using this approach in existing datasets from ulcerative colitis patient colonic biopsies, we identified architectural complexities and associated difficult-to-detect rare cell types in ulcerative colitis germinal-center B cell follicles. Our approach deepens our understanding of health and disease pathogenesis, illustrates a strategy for automating nested architecture detection for highly multiplexed spatial biology data, and informs precision diagnosis and therapeutic strategies.

    View details for DOI 10.21203/

    View details for PubMedID 38559236

    View details for PubMedCentralID PMC10980100

  • An Update on Protein Kinases as Therapeutic Targets-Part I: Protein Kinase C Activation and Its Role in Cancer and Cardiovascular Diseases. International journal of molecular sciences Silnitsky, S., Rubin, S. J., Zerihun, M., Qvit, N. 2023; 24 (24)


    Protein kinases are one of the most significant drug targets in the human proteome, historically harnessed for the treatment of cancer, cardiovascular disease, and a growing number of other conditions, including autoimmune and inflammatory processes. Since the approval of the first kinase inhibitors in the late 1990s and early 2000s, the field has grown exponentially, comprising 98 approved therapeutics to date, 37 of which were approved between 2016 and 2021. While many of these small-molecule protein kinase inhibitors that interact orthosterically with the protein kinase ATP binding pocket have been massively successful for oncological indications, their poor selectively for protein kinase isozymes have limited them due to toxicities in their application to other disease spaces. Thus, recent attention has turned to the use of alternative allosteric binding mechanisms and improved drug platforms such as modified peptides to design protein kinase modulators with enhanced selectivity and other pharmacological properties. Herein we review the role of different protein kinase C (PKC) isoforms in cancer and cardiovascular disease, with particular attention to PKC-family inhibitors. We discuss translational examples and carefully consider the advantages and limitations of each compound (Part I). We also discuss the recent advances in the field of protein kinase modulators, leverage molecular docking to model inhibitor-kinase interactions, and propose mechanisms of action that will aid in the design of next-generation protein kinase modulators (Part II).

    View details for DOI 10.3390/ijms242417600

    View details for PubMedID 38139428

  • An Update on Protein Kinases as Therapeutic Targets-Part II: Peptides as Allosteric Protein Kinase C Modulators Targeting Protein-Protein Interactions. International journal of molecular sciences Zerihun, M., Rubin, S. J., Silnitsky, S., Qvit, N. 2023; 24 (24)


    Human protein kinases are highly-sought-after drug targets, historically harnessed for treating cancer, cardiovascular disease, and an increasing number of autoimmune and inflammatory conditions. Most current treatments involve small molecule protein kinase inhibitors that interact orthosterically with the protein kinase ATP-binding pocket. As a result, these compounds are often poorly selective and highly toxic. Part I of this series reviews the role of PKC isoforms in various human diseases, featuring cancer and cardiovascular disease, as well as translational examples of PKC modulation applied to human health and disease. In the present Part II, we discuss alternative allosteric binding mechanisms for targeting PKC, as well as novel drug platforms, such as modified peptides. A major goal is to design protein kinase modulators with enhanced selectivity and improved pharmacological properties. To this end, we use molecular docking analysis to predict the mechanisms of action for inhibitor-kinase interactions that can facilitate the development of next-generation PKC modulators.

    View details for DOI 10.3390/ijms242417504

    View details for PubMedID 38139336

  • Looking to Future Applications of Large Language Models. The American journal of gastroenterology Liu, X., Rubin, S. J., Rogalla, S. 2023; 118 (12): 2305

    View details for DOI 10.14309/ajg.0000000000002401

    View details for PubMedID 38033226

  • Mass-cytometry-based quantitation of global histone post-translational modifications at single-cell resolution across peripheral immune cells in IBD. Journal of Crohn's & colitis Bai, L., Dermadi, D., Kalesinskas, L., Dvorak, M., Chang, S. E., Ganesan, A., Rubin, S. J., Kuo, A., Cheung, P., Donato, M., Utz, P. J., Habtezion, A., Khatri, P. 2022


    Current understanding of histone post-translational modifications (histone modifications) across immune cell types in patients with inflammatory bowel disease (IBD) during remission and flare is limited. The study aimed to quantify histone modifications at a single-cell resolution in IBD patients during remission and flare and how they differ compared to healthy controls.We performed a case-control study of 94 subjects (83 IBD patients and 11 healthy controls). IBD patients had either UC (n=38) or CD (n=45) in clinical remission or flare. We used epigenetic profiling by time-of-flight (EpiTOF) to investigate changes in histone modifications within peripheral blood mononuclear cells from IBD patients.We discovered substantial heterogeneity in histone modifications across multiple immune cell types in IBD patients. They had a higher proportion of less differentiated CD34 + hematopoietic progenitors, and a subset of CD56 bright NK cells and γδ T cells characterized by distinct histone modifications associated with the gene transcription. The subset of CD56 bright NK cells had increased several histone acetylations. An epigenetically defined subset of NK was associated with higher levels of CRP in peripheral blood. CD14+ monocytes from IBD patients had significantly decreased cleaved H3T22, suggesting they were epigenetically primed for macrophage differentiation.We describe the first systems-level quantification of histone modifications across immune cells from IBD patients at a single-cell resolution revealing the increased epigenetic heterogeneity that is not possible with traditional ChIP-seq profiling. Our data open new directions in investigating the association between histone modifications and IBD pathology using other epigenomic tools.

    View details for DOI 10.1093/ecco-jcc/jjac194

    View details for PubMedID 36571819

  • The Tumor Immune Microenvironment in Pancreatic Ductal Adenocarcinoma: Neither Hot nor Cold. Cancers Rubin, S. J., Sojwal, R. S., Gubatan, J., Rogalla, S. 2022; 14 (17)


    Pancreatic ductal adenocarcinoma (PDAC) is the most common pancreatic tumor and is associated with poor prognosis and treatment response. The tumor microenvironment (TME) is recognized as an important factor in metastatic progression across cancers. Despite extensive study of the TME in PDAC, the cellular and molecular signaling networks remain poorly understood, largely due to the tremendous heterogeneity across tumors. While earlier work characterized PDAC as an immunologically privileged tumor poorly recognized by the immune system, recent studies revealed the important and nuanced roles of immune cells in the pathogenesis of PDAC. Distinct lymphoid, myeloid, and stromal cell types in the TME exert opposing influences on PDAC tumor trajectory, suggesting a more complex organization than the classical "hot" versus "cold" tumor distinction. We review the pro- and antitumor immune processes found in PDAC and briefly discuss their leverage for the development of novel therapeutic approaches in the field.

    View details for DOI 10.3390/cancers14174236

    View details for PubMedID 36077772

  • Metalloendopeptidase ADAM-like Decysin 1 (ADAMDEC1) in Colonic Subepithelial PDGFRalpha+ Cells Is a New Marker for Inflammatory Bowel Disease. International journal of molecular sciences Ha, S. E., Jorgensen, B. G., Wei, L., Jin, B., Kim, M., Poudrier, S. M., Singh, R., Bartlett, A., Zogg, H., Kim, S., Baek, G., Kurahashi, M., Lee, M., Kim, Y., Choi, S., Sasse, K. C., Rubin, S. J., Gottfried-Blackmore, A., Becker, L., Habtezion, A., Sanders, K. M., Ro, S. 2022; 23 (9)


    Metalloendopeptidase ADAM-Like Decysin 1 (ADAMDEC1) is an anti-inflammatory peptidase that is almost exclusively expressed in the gastrointestinal (GI) tract. We have recently found abundant and selective expression of Adamdec1 in colonic mucosal PDGFRalpha+ cells. However, the cellular origin for this gene expression is controversial as it is also known to be expressed in intestinal macrophages. We found that Adamdec1 mRNAs were selectively expressed in colonic mucosal subepithelial PDGFRalpha+ cells. ADAMDEC1 protein was mainly released from PDGFRalpha+ cells and accumulated in the mucosal layer lamina propria space near the epithelial basement membrane. PDGFRalpha+ cells significantly overexpressed Adamdec1 mRNAs and protein in DSS-induced colitis mice. Adamdec1 was predominantly expressed in CD45- PDGFRalpha+ cells in DSS-induced colitis mice, with only minimal expression in CD45+ CD64+ macrophages. Additionally, overexpression of both ADAMDEC1 mRNA and protein was consistently observed in PDGFRalpha+ cells, but not in CD64+ macrophages found in human colonic mucosal tissue affected by Crohn's disease. In summary, PDGFRalpha+ cells selectively express ADAMDEC1, which is localized to the colon mucosa layer. ADAMDEC1 expression significantly increases in DSS-induced colitis affected mice and Crohn's disease affected human tissue, suggesting that this gene can serve as a diagnostic and/or therapeutic target for intestinal inflammation and Crohn's disease.

    View details for DOI 10.3390/ijms23095007

    View details for PubMedID 35563399

  • Disease exacerbation is common in inflammatory bowel disease patients treated with immune checkpoint inhibitors for malignancy. World journal of clinical cases Rubin, S. J., Balabanis, T., Gubatan, J., Habtezion, A. 2022; 10 (6): 1787-1794


    Colitis is a known potential toxicity of immune checkpoint inhibitors (ICIs). Studies evaluating the risk of disease exacerbation following ICI treatment in patients with pre-existing inflammatory bowel disease (IBD) are limited.To assess the clinical characteristics of IBD patients treated with ICIs and determine prevalence of subsequent IBD exacerbations.We conducted a retrospective cohort study of all patients in the Stanford Research Repository database with pre-existing IBD who were exposed to ICIs.The prevalence of IBD exacerbation following ICI was 36.8% amongst 19 patients meeting inclusion criteria. Patients with exacerbations had more gastrointestinal-related hospitalizations (4 of 7) than patients without exacerbations (0 of 12; P = 0.0090).The prevalence of IBD exacerbations following ICI was higher than reported rates of ICI-induced colitis and diarrhea in the general population and was associated with hospitalization.

    View details for DOI 10.12998/wjcc.v10.i6.1787

    View details for PubMedID 35317167

    View details for PubMedCentralID PMC8891792

  • Antimicrobial peptides and the gut microbiome in inflammatory bowel disease. World journal of gastroenterology Gubatan, J., Holman, D. R., Puntasecca, C. J., Polevoi, D., Rubin, S. J., Rogalla, S. 2021; 27 (43): 7402-7422


    Antimicrobial peptides (AMP) are highly diverse and dynamic molecules that are expressed by specific intestinal epithelial cells, Paneth cells, as well as immune cells in the gastrointestinal (GI) tract. They play critical roles in maintaining tolerance to gut microbiota and protecting against enteric infections. Given that disruptions in tolerance to commensal microbiota and loss of barrier function play major roles in the pathogenesis of inflammatory bowel disease (IBD) and converge on the function of AMP, the significance of AMP as potential biomarkers and novel therapeutic targets in IBD have been increasingly recognized in recent years. In this frontier article, we discuss the function and mechanisms of AMP in the GI tract, examine the interaction of AMP with the gut microbiome, explore the role of AMP in the pathogenesis of IBD, and review translational applications of AMP in patients with IBD.

    View details for DOI 10.3748/wjg.v27.i43.7402

    View details for PubMedID 34887639

    View details for PubMedCentralID PMC8613745

  • Antimicrobial peptides and the gut microbiome in inflammatory bowel disease WORLD JOURNAL OF GASTROENTEROLOGY Gubatan, J., Holman, D. R., Puntasecca, C. J., Polevoi, D., Rubin, S. S., Rogalla, S. 2021; 27 (43): 7402-7422
  • Novel circulating and tissue monocytes as well as macrophages in pancreatitis and recovery. Gastroenterology Manohar, M., Jones, E. K., Rubin, S. J., Subrahmanyam, P. B., Swaminathan, G., Mikhail, D., Bai, L., Singh, G., Wei, Y., Sharma, V., Siebert, J. C., Maecker, H. T., Husain, S. Z., Park, W. G., Pandol, S. J., Habtezion, A. 2021


    BACKGROUND AND AIMS: Acute pancreatitis (AP) is an inflammatory disease with mild to severe course that is associated with local and systemic complications and significant mortality. Uncovering inflammatory pathways that lead to progression and recovery will inform ways to monitor and/or develop effective therapies.METHODS: We performed single-cell mass cytometry (CyTOF) analysis to identify pancreatic and systemic inflammatory signals during mild (referred as AP), severe AP (SAP) and recovery using two independent experimental models and blood from AP and recurrent AP (RAP) patients. Flowcytometric validation of monocytes subsets identified by CyTOF analysis was performed independently.RESULTS: Ly6C+ inflammatory monocytes were most altered cells in the pancreas during experimental AP, recovery, and SAP. Deep profiling uncovered heterogeneity among pancreatic and blood monocytes and identified seven novel subsets during AP and recovery, and six monocyte subsets during SAP. Notably, a dynamic shift in pancreatic CD206+ macrophage population was observed during AP and recovery. Deeper profiling of the CD206+ macrophage identified seven novel subsets during AP, recovery and SAP. DE analysis of these novel monocyte and CD206+ macrophage subsets revealed significantly altered surface (CD44, CD54, CD115, CD140a, CD196, PDPN) and functional markers (IFN-gamma, IL-4, IL-22, LAP-TGF-beta, TNF-alpha, T-bet, RoRgammat) that were associated with recovery and SAP. Moreover, a targeted functional analysis further revealed distinct expression of pro- and anti-inflammatory cytokines by pancreatic CD206+ macrophage subsets as the disease either progressed or resolved. Similarly, we identified heterogeneity among circulating classical inflammatory monocytes (CD14+CD16-) and novel subsets in patients with AP and RAP.CONCLUSION: We identified several novel monocyte/macrophage subsets with unique phenotype and functional characteristics that are associated with AP, recovery, and SAP. Our findings highlight differential innate immune responses during AP progression and recovery that can be leveraged for future disease monitoring and targeting.

    View details for DOI 10.1053/j.gastro.2021.08.033

    View details for PubMedID 34450180

  • Anti-Integrins for the Treatment of Inflammatory Bowel Disease: Current Evidence and Perspectives. Clinical and experimental gastroenterology Gubatan, J., Keyashian, K., Rubin, S. J., Wang, J., Buckman, C. A., Sinha, S. 2021; 14: 333-342


    Leukocyte trafficking to the gastrointestinal tract is recognized to play a role in the pathogenesis of inflammatory bowel disease (IBD). Integrins are expressed on immune cells and interact with cell adhesion molecules (CAM) to mediate leukocyte trafficking. Blockade of the gut-tropic integrin α4β7 and its subunits has been exploited as a therapeutic target in IBD. Natalizumab (anti-α4) is approved for moderate to severe Crohn's disease (CD), but its use is limited due to potential risk of progressive multifocal leukoencephalopathy. Vedolizumab (anti-α4β7) is approved for the treatment of ulcerative colitis (UC) and CD. It is the most widely used anti-integrin therapy in IBD and has been shown to be effective in both induction and maintenance therapy, with a favorable safety profile. Several models incorporating clinical, genetic, immune, gut microbial, and vitamin D markers to predict response to vedolizumab in IBD have been developed. Etrolizumab (anti-β7) blocks leukocyte trafficking via α4β7 and cell adhesion via αEβ7 integrins. Large phase 3 clinical trials evaluating efficacy of etrolizumab in the induction and maintenance of patients with IBD are underway. Other investigational anti-integrin therapies include abrilumab (anti-α4β7 IgG2), PN-943 (orally administered and gut-restricted α4β7 antagonist peptide), AJM300 (orally active small molecule inhibitor of α4), and ontamalimab (anti-MAdCAM-1 IgG).

    View details for DOI 10.2147/CEG.S293272

    View details for PubMedID 34466013

    View details for PubMedCentralID PMC8402953

  • Novel Circulating and Tissue Monocytes As Well As Macrophages in Pancreatitis and Recovery Manohar, M., Jones, E. K., Rubin, S. S., Subrahmanyam, P. B., Mikhail, D., Bai, L., Singh, G., Wei, Y., Sharma, V., Swaminathan, G., Siebert, J. C., Maecker, H. T., Park, W., Pandol, S. J., Husain, S., Habtezion, A. LIPPINCOTT WILLIAMS & WILKINS. 2021: 1079-1080
  • Immune checkpoint inhibitor-mediated colitis in gastrointestinal malignancies and inflammatory bowel disease. World journal of gastrointestinal oncology Weingarden, A. R., Rubin, S. J., Gubatan, J. 2021; 13 (8): 772-798


    Immune checkpoint inhibitors (ICI) have markedly changed the landscape of cancer therapy. By re-invigorating the immune system against tumors, ICI provide novel therapeutic options for a broad variety of malignancies, including many gastrointestinal (GI) cancers. However, these therapies can also induce autoimmune-like side effects in healthy tissue across the body. One of the most common of these side effects is ICI-mediated colitis and diarrhea (IMC). Here, we review the incidence and risk of IMC in ICI therapy, with a focus on what is known regarding IMC in patients with GI malignancies. We also discuss data available on the use of ICI and risk of IMC in patients with pre-existing inflammatory bowel disease, as these patients may have increased risk of IMC due to their underlying intestinal pathology.

    View details for DOI 10.4251/wjgo.v13.i8.772

    View details for PubMedID 34457186

    View details for PubMedCentralID PMC8371513

  • Vitamin D is Associated with α4β7+ Immunophenotypes and Predicts Vedolizumab Therapy Failure in Patients with Inflammatory Bowel Disease. Journal of Crohn's & colitis Gubatan, J., Rubin, S. J., Bai, L., Haileselassie, Y., Levitte, S., Balabanis, T., Patel, A., Sharma, A., Sinha, S. R., Habtezion, A. 2021


    Vitamin D downregulates the in vitro expression of the gut-tropic integrin α4β7 on immune cells. The clinical relevance of this finding in patients with inflammatory bowel disease (IBD) is unclear. We tested the hypothesis that vitamin D is associated with α4β7 immunophenotypes and risk of vedolizumab (anti- α4β7) failure in IBD.We performed single-cell immunophenotyping of peripheral and intestinal immune cells using mass cytometry (CyTOF) in vedolizumab-naïve patients with IBD (N=48). We analyzed whole-genome mucosal gene expression (GSE73661) from GEMINI I and GEMINI long-term safety (LTS) to determine the association between vitamin D receptor (VDR) and integrin alpha-4 (ITGA4) and beta-7 (ITGB7) genes. We estimated the odds of vedolizumab failure with low pre-treatment vitamin D in a combined retrospective and prospective IBD cohort (N= 252) with logistic regression.Immunophenotyping revealed that higher 25(OH)D was associated with decreased α4β7+ peripheral blood mononuclear cells (R = -0.400, P < 0.01) and α4β7+ intestinal leukocytes (R = -0.538, P= 0.03). Serum 25(OH)D was inversely associated with α4β7+ peripheral B cells and natural killer (NK) cells and α4β7+ intestinal B cells, NK cells, monocytes, and macrophages. Mucosal expression of VDR was inversely associated with ITGA4 and ITGB7 expression. In multivariate analysis, 25(OH)D < 25 ng/mL was associated with increased vedolizumab primary non-response during induction (OR 26.10, 95% CI 14.30-48.90, P<0.001) and failure at 1-year follow-up (OR 6.10, 95% CI 3.06-12.17, P<0.001).Low serum 25(OH)D is associated with α4β7+ immunophenotypes and predicts future vedolizumab failure in patients with IBD.

    View details for DOI 10.1093/ecco-jcc/jjab114

    View details for PubMedID 34180967

  • Anti-Integrins for the Treatment of Inflammatory Bowel Disease: Current Evidence and Perspectives CLINICAL AND EXPERIMENTAL GASTROENTEROLOGY Gubatan, J., Keyashian, K., Rubin, S. S., Wang, J., Buckman, C. A., Sinha, S. 2021; 14: 333-342
  • Engineering "Antimicrobial Peptides" and Other Peptides to Modulate Protein-Protein Interactions in Cancer. Current topics in medicinal chemistry Rubin, S. J., Qvit, N. 2020


    Antimicrobial peptides (AMPs) are a class of peptides found across a wide array of organisms that play key roles in host defense. AMPs induce selective death in target cells and orchestrate specific or nonspecific immune responses. Many AMPs exhibit native anticancer activity in addition to antibacterial activity, and others have been engineered as antineoplastic agents. We discuss the use of AMPs in detection and treatment of cancer as well as mechanisms of AMPinduced cell death. We present key examples of cathelicidins and transferrins, which are major AMP families. Further, we discuss the critical roles of protein-protein interactions (PPIs) in cancer and how AMPs are well suited to target PPIs based on their unique druglike properties not exhibited by small molecules or antibodies. While peptides including AMPs can have limited stability and bioavailability, these issues can be overcome by peptide backbone cyclization or stapling and by the use of delivery systems such as cell-penetrating peptides (CPPs), respectively. We discuss approaches for optimizing drug properties of peptide and peptidomimetic leads, providing examples of promising techniques that may be applied to AMPs. These molecules represent an exciting resource as anticancer agents with unique therapeutic advantages that can target challenging mechanisms involving PPIs. Indeed, AMPs are suitable drug leads for further development of cancer therapeutics, and many studies to this end are underway.

    View details for DOI 10.2174/1568026620666201021141401

    View details for PubMedID 33087030

  • Effects of processing conditions on stability of immune analytes in human blood. Scientific reports Gottfried-Blackmore, A., Rubin, S. J., Bai, L., Aluko, S., Yang, Y., Park, W., Habtezion, A. 2020; 10 (1): 17328


    Minimizing variability in collection and processing of human blood samples for research remains a challenge. Delaying plasma or serum isolation after phlebotomy (processing delay) can cause perturbations of numerous analytes. Thus, a comprehensive understanding of how processing delay affects major endpoints used in human immunology research is necessary. Therefore, we studied how processing delay affects commonly measured cytokines and immune cell populations. We hypothesized that short-term time delays inherent to human research in serum and plasma processing impact commonly studied immunological analytes. Blood from healthy donors was subjected to processing delays commonly encountered in sample collection, and then assayed by 62-plex Luminex panel, 40-parameter mass cytometry panel, and 540,000 transcript expression microarray. Variance for immunological analytes was estimated using each individual's baseline as a control. In general, short-term processing delay led to small changes in plasma and serum cytokines (range-10.8 to 43.5%), markers and frequencies of peripheral blood mononuclear cell phenotypes (range 0.19 to 3.54 fold), and whole blood gene expression (stable for>20K genes)-with several exceptions described herein. Importantly, we built an open-access web application allowing investigators to estimate the degree of variance expected from processing delay for measurements of interest based on the data reported here.

    View details for DOI 10.1038/s41598-020-74274-8

    View details for PubMedID 33060628

  • Clinical characteristics associated with COVID-19 severity in California. Journal of clinical and translational science Rubin, S. J., Falkson, S. R., Degner, N. R., Blish, C. 2020; 5 (1): e3


    Given the rapidly progressing coronavirus disease 2019 (COVID-19) pandemic, this report on a US cohort of 54 COVID-19 patients from Stanford Hospital and data regarding risk factors for severe disease obtained at initial clinical presentation is highly important and immediately clinically relevant. We identified low presenting oxygen saturation as predictive of severe disease outcomes, such as diagnosis of pneumonia, acute respiratory distress syndrome, and admission to the intensive care unit, and also replicated data from China suggesting an association between hypertension and disease severity. Clinicians will benefit by tools to rapidly risk stratify patients at presentation by likelihood of progression to severe disease.

    View details for DOI 10.1017/cts.2020.40

    View details for PubMedID 34192044

    View details for PubMedCentralID PMC7274026

  • Clinical characteristics associated with COVID-19 severity in California Journal of Clinical and Translational Science Rubin, S. J., Falkson, S. R., Degner, N. R., Blish, C. A. 2020

    View details for DOI 10.1017/cts.2020.40

  • Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity. Immunity Fenton, T. M., Jørgensen, P. B., Niss, K. n., Rubin, S. J., Mörbe, U. M., Riis, L. B., Da Silva, C. n., Plumb, A. n., Vandamme, J. n., Jakobsen, H. L., Brunak, S. n., Habtezion, A. n., Nielsen, O. H., Johansson-Lindbom, B. n., Agace, W. W. 2020


    The intestine contains some of the most diverse and complex immune compartments in the body. Here we describe a method for isolating human gut-associated lymphoid tissues (GALTs) that allows unprecedented profiling of the adaptive immune system in submucosal and mucosal isolated lymphoid follicles (SM-ILFs and M-ILFs, respectively) as well as in GALT-free intestinal lamina propria (LP). SM-ILF and M-ILF showed distinct patterns of distribution along the length of the intestine, were linked to the systemic circulation through MAdCAM-1+ high endothelial venules and efferent lymphatics, and had immune profiles consistent with immune-inductive sites. IgA sequencing analysis indicated that human ILFs are sites where intestinal adaptive immune responses are initiated in an anatomically restricted manner. Our findings position ILFs as key inductive hubs for regional immunity in the human intestine, and the methods presented will allow future assessment of these compartments in health and disease.

    View details for DOI 10.1016/j.immuni.2020.02.001

    View details for PubMedID 32160523

  • Peptide Therapeutics: Scientific Approaches, Current Development Trends, and Future Directions. Current topics in medicinal chemistry Qvit, N., Rubin, S. J. 2020; 20 (32): 2903

    View details for DOI 10.2174/156802662032201118092318

    View details for PubMedID 33297905

  • Safety of ACE-I and ARB medications in COVID-19: A retrospective cohort study of inpatients and outpatients in California Journal of Clinical and Translational Science Rubin, S. J., Falkson, S. R., Degner, N. R., Blish, C. A. 2020: e8


    There is significant interest in the use of angiotensin converting enzyme inhibitors (ACE-I) and angiotensin II receptor blockers (ARB) in coronavirus disease 2019 (COVID-19) and concern over potential adverse effects since these medications upregulate the severe acute respiratory syndrome coronavirus 2 host cell entry receptor ACE2. Recent studies on ACE-I and ARB in COVID-19 were limited by excluding outpatients, excluding patients by age, analyzing ACE-I and ARB together, imputing missing data, and/or diagnosing COVID-19 by chest computed tomography without definitive reverse transcription polymerase chain reaction (RT-PCR), all of which are addressed here.We performed a retrospective cohort study of 1023 COVID-19 patients diagnosed by RT-PCR at Stanford Hospital through April 8, 2020 with a minimum follow-up time of 14 days to investigate the association between ACE-I or ARB use with outcomes.Use of ACE-I or ARB medications was not associated with increased risk of hospitalization, intensive care unit admission, or death. Compared to patients with charted past medical history, there was a lower risk of hospitalization for patients on ACE-I (odds ratio (OR) 0.43; 95% confidence interval (CI) 0.19-0.97; P = 0.0426) and ARB (OR 0.39; 95% CI 0.17-0.90; P = 0.0270). Compared to patients with hypertension not on ACE-I or ARB, patients on ARB medications had a lower risk of hospitalization (OR 0.09; 95% CI 0.01-0.88; P = 0.0381).These findings suggest that the use of ACE-I and ARB is not associated with adverse outcomes and may be associated with improved outcomes in COVID-19, which is immediately relevant to care of the many patients on these medications.

    View details for DOI 10.1017/cts.2020.489

    View details for PubMedCentralID PMC7605244

  • Mass cytometry reveals systemic and local immune signatures that distinguish inflammatory bowel diseases. Nature communications Rubin, S. J., Bai, L., Haileselassie, Y., Garay, G., Yun, C., Becker, L., Streett, S. E., Sinha, S. R., Habtezion, A. 2019; 10 (1): 2686


    Inflammatory bowel disease (IBD) includes Crohn's disease and ulcerative colitis. Each disease is characterized by a diverse set of potential manifestations, which determine patients' disease phenotype. Current understanding of phenotype determinants is limited, despite increasing prevalence and healthcare costs. Diagnosis and monitoring of disease requires invasive procedures, such as endoscopy and tissue biopsy. Here we report signatures of heterogeneity between disease diagnoses and phenotypes. Using mass cytometry, we analyze leukocyte subsets, characterize their function(s), and examine gut-homing molecule expression in blood and intestinal tissue from healthy and/or IBD subjects. Some signatures persist in IBD despite remission, and many signatures are highly represented by leukocytes that express gut trafficking molecules. Moreover, distinct systemic and local immune signatures suggest patterns of cell localization in disease. Our findings highlight the importance of gut tropic leukocytes in circulation and reveal that blood-based immune signatures differentiate clinically relevant subsets of IBD.

    View details for DOI 10.1038/s41467-019-10387-7

    View details for PubMedID 31217423

  • B cell checkpoints in autoimmune rheumatic diseases NATURE REVIEWS RHEUMATOLOGY Rubin, S. S., Bloom, M. S., Robinson, W. H. 2019; 15 (5): 303–15
  • B cell checkpoints in autoimmune rheumatic diseases. Nature reviews. Rheumatology Rubin, S. J., Bloom, M. S., Robinson, W. H. 2019


    B cells have important functions in the pathogenesis of autoimmune diseases, including autoimmune rheumatic diseases. In addition to producing autoantibodies, B cells contribute to autoimmunity by serving as professional antigen-presenting cells (APCs), producing cytokines, and through additional mechanisms. B cell activation and effector functions are regulated byimmune checkpoints, including both activating and inhibitory checkpoint receptors that contribute to the regulation of B cell tolerance, activation, antigen presentation, T cell help, classswitching, antibody production and cytokine production. The various activating checkpoint receptors include B cell activating receptors that engage with cognate receptors on T cells or other cells, as well as Toll-like receptors that can provide dual stimulation to B cells via co-engagement with the B cell receptor. Furthermore, various inhibitory checkpoint receptors, including B cell inhibitory receptors, have important functions in regulating B cell development, activation and effector functions. Therapeutically targeting B cell checkpoints represents a promising strategy for the treatment of a variety of autoimmune rheumatic diseases.

    View details for PubMedID 30967621

  • Immunomodulatory receptors are differentially expressed in B and T cell subsets relevant to autoimmune disease. Clinical immunology (Orlando, Fla.) Murphy, K. A., Bhamidiphati, K. n., Rubin, S. J., Kipp, L. n., Robinson, W. H., Lanz, T. V. 2019: 108276


    Inhibitory cell-surface receptors on lymphocytes, often called immune checkpoints, are powerful targets for cancer therapy. Despite their direct involvement in autoimmune pathology, they are currently not exploited therapeutically for autoimmune diseases. Understanding the receptors' expression patterns in health and disease is essential for targeted drug design. Here, we designed three 23-colour flow cytometry panels for peripheral-blood T cells, including 15 lineage-defining markers and 21 immunomodulatory cell-surface receptors, and a 22-marker panel for B cells. Blood samples from healthy individuals, multiple sclerosis (MS), and lupus (SLE) patients were included in the study. Several receptors show differential expression on regulatory T cells (Treg) compared to T helper (Th) 1 and Th17 cells, and functional relevance of this difference could be shown for BTLA and CD5. Unbiased multiparametric analysis revealed a subset of activated CD8+ T cells and a subset of unswitched memory B cells that are diminished in MS and SLE, respectively.

    View details for DOI 10.1016/j.clim.2019.108276

    View details for PubMedID 31669582

  • Backbone-Cyclized Peptides: a Critical Review. Current topics in medicinal chemistry Rubin, S. J., Qvit, N. 2018


    Backbone-cyclized peptides and peptidomimetics integrate the biological activity and pharmacological features necessary for successful research tools and therapeutics. In general, these structures demonstrate improved maintenance of bioactive conformation, stability and cell permeability compared to their linear counterparts, while maintaining support for a variety of side chain chemistries. We explain how backbone cyclization and cycloscan techniques allow scientists to cyclize linear peptides with retained or enhanced biological activity and improved drug-like features. We discuss head-to-tail (C-terminus to N-terminus), building unit-to-tail, building unit-to-side chain, building unit-to-building unit, and building unit-to-head backbone cyclization, with examples of building blocks, such as Nalpha-(omega-thioalkylene), Nalpha-(omega-aminoalkylene) and Nalpha-(omega-carboxyalkylene) units. We also present several methods for recombinant expression of backbone-cyclized peptides, including backbone cyclic peptide synthesis using recombinant elements (bcPURE), phage display and induced peptidyl-tRNA drop-off. Moreover, natural backbone-cyclized peptides are also produced by cyanobacteria, plants and other organisms; several of these compounds have been developed and commercialized for therapeutic applications, which we review. Backbone-cyclized peptides and peptidomimetics comprise a growing share of the pharmaceutical industry and will be applied to additional problems in the near future.

    View details for PubMedID 29773062

  • Conversion of Protein Active Regions into Peptidomimetic Therapeutic Leads using Backbone Cyclization and Cycloscan - How to Do It Yourself. Current topics in medicinal chemistry Rubin, S. J., Tal-Gan, Y., Gilon, C., Qvit, N. 2018


    Protein-protein interactions (PPIs) are particularly important for controlling both physiologic and pathologic biological processes but are difficult to target due to their large and/or shallow interaction surfaces unsuitable for small molecules. Linear peptides found in nature interact with some PPIs, and protein active regions can be used to design synthetic peptide compounds for inhibition of PPIs. However, linear peptides are limited therapeutically by poor metabolic and conformational stability, which can compromise their bioactivity and half-life. Cyclic peptidomimetics (modified peptides) can be used to overcome these challenges because they are more resistant to metabolic degradation and can be engineered to adopt desired conformations. Backbone cyclization is a strategy that we developed to improve drug-like properties of linear peptide leads without jeopardizing the integrity of functionally relevant side-chains. Here, we provide the first description of an entire approach for developing backbone cyclized peptide compounds, based upon two straightforward 'ABC' and 'DEF' processes. We present practical examples throughout our discussion of revealing active regions important for PPIs and identifying critical pharmacophores, as well as developing backbone cyclized peptide libraries and screening them using cycloscan. Finally, we review the impact of these advances and provide a summary of current ongoing work in the field.

    View details for PubMedID 29773063

  • Cyclic Peptides for Protein-Protein Interaction Targets CURRENT TOPICS IN MEDICINAL CHEMISTRY Qvit, N., Rubin, S. S. 2018; 18 (7): 525

    View details for PubMedID 30014801

  • Backbone-cyclized Peptides: A Critical Review CURRENT TOPICS IN MEDICINAL CHEMISTRY Rubin, S. S., Qvit, N. 2018; 18 (7): 526-555
  • Conversion of Protein Active Regions into Peptidomimetic Therapeutic Leads Using Backbone Cyclization and Cycloscan - How to Do it Yourself! CURRENT TOPICS IN MEDICINAL CHEMISTRY Rubin, S. S., Tal-Gan, Y., Gilon, C., Qvit, N. 2018; 18 (7): 556-565
  • Gravity-Drawn Silicone Filaments: Production, Characterization, and Wormlike Chain Dynamics ACS APPLIED MATERIALS & INTERFACES Kiessling, R., Rubin, S. S., Zehner, J., Barraugh, C., Snell, K., Fukushima, C., Mulligan, M., Keckley, M., Bosshardt, A., Cook, W., Sanii, B. 2017; 9 (46): 39916–20


    We introduce a method to produce continuous polydimethylsiloxane (PDMS) silicone filaments on the order of 0.5 m long and 100 μm in diameter. The approach overcomes traditional limitations in silicone drawing by partially precuring the polymer and drawing through a tube furnace. We characterize the filaments' mechanical properties, and their ability to switch hydrophobicity by UV-ozone and corona discharge patterning. The flexible filaments' dynamic properties were evaluated by way of athermal acoustic excitation at the air-water interface, revealing conformational reconfigurability consistent with a wormlike chain model. We envision applications in rapid prototyping and as a platform for model foldamer studies.

    View details for DOI 10.1021/acsami.7b11972

    View details for Web of Science ID 000416614600006

    View details for PubMedID 29111635

  • Peptidomimetic therapeutics: scientific approaches and opportunities. Drug discovery today Qvit, N., Rubin, S. J., Urban, T. J., Mochly-Rosen, D., Gross, E. R. 2017; 22 (2): 454-462


    Natural endogenously occurring peptides exhibit desirable medicinal properties, but are often limited in application by rapid proteolysis and inadequate membrane permeability. However, editing naturally occurring peptide sequences to develop peptidomimetic analogs created a promising class of therapeutics that can augment or inhibit molecular interactions. Here, we discuss a variety of chemical modifications, including l to d isomerization, cyclization, and unnatural amino acid substitution, as well as design strategies, such as attachment to cell-penetrating peptides, which are used to develop peptidomimetics. We also provide examples of approved peptidomimetics and discuss several compounds in clinical trials.

    View details for DOI 10.1016/j.drudis.2016.11.003

    View details for PubMedID 27856346

  • Exceptional running and turning performance in a mite JOURNAL OF EXPERIMENTAL BIOLOGY Rubin, S., Young, M. H., Wright, J. C., Whitaker, D. L., Ahn, A. N. 2016; 219 (5): 676-685


    The Southern California endemic mite Paratarsotomus macropalpis was filmed in the field on a concrete substrate and in the lab to analyze stride frequency, gait and running speed under different temperature conditions and during turning. At ground temperatures ranging from 45 to 60 °C, mites ran at a mean relative speed of 192.4 ± 2.1 body lengths (BL) s(-1), exceeding the highest previously documented value for a land animal by 12.5%. Stride frequencies were also exceptionally high (up to 135 Hz), and increased with substrate temperature. Juveniles exhibited higher relative speeds than adults and possess proportionally longer legs, which allow for greater relative stride lengths. Although mites accelerated and decelerated rapidly during straight running (7.2 ± 1.2 and -10.1 ± 2.1 m s(-2), respectively), the forces involved were comparable to those found in other animals. Paratarsotomus macropalpis employs an alternating tetrapod gait during steady running. Shallow turns were accomplished by a simple asymmetry in stride length. During tight turns, mites pivoted around the tarsus of the inside third leg (L3), which thus behaved like a grappling hook. Pivot turns were characterized by a 42% decrease in turning radius and a 40% increase in angular velocity compared with non-pivot turns. The joint angle amplitudes of the inner L2 and L3 were negligible during a pivot turn. While exceptional, running speeds in P. macropalpis approximate values predicted from inter-specific scaling relationships.

    View details for DOI 10.1242/jeb.128652

    View details for Web of Science ID 000371134700016

    View details for PubMedID 26787481

  • Cyclic Peptides for Protein-Protein Interaction Targets: Applications to Human Disease CRITICAL REVIEWS IN EUKARYOTIC GENE EXPRESSION Rubin, S., Qvit, N. 2016; 26 (3): 199-221


    Protein-protein interactions (PPIs) represent a significant portion of functionally relevant biological interactions, and therefore potential therapeutic targets. Small molecules were traditionally used to target PPIs. However, many PPI surfaces lack binding pockets due to their large and flat structures. Antibodies can also be used to modulate PPIs, but they are expensive and not cell permeable. Linear peptides are less expensive to produce than antibodies and are generally more selective than small molecules, but they are limited by decreased stability and poor permeability. Modified peptides (peptidomimetics, e.g., cyclic peptides) can overcome these obstacles. Advantages of using cyclic peptidomimetics to modulate PPIs derive from their conformational constraint, which supports target specificity, cell permeability, and metabolic stability. Methods for rational design coupled with high-throughput techniques continue to support advances in the field. Further development of cyclic peptidomimetics to modulate PPIs will improve treatment of human diseases, such as cancer, infection, neurodegeneration, and autoimmunity. Here we describe several cyclic peptidomimetics that are currently used as drugs and many potential cyclic peptides PPI inhibitors in different stages of pre-clinical and clinical development. Further development of cyclic peptidomimetics to modulate PPIs will continue to improve treatment of human diseases, such as cancer, infection, neurodegeneration, and autoimmunity.

    View details for DOI 10.1615/CritRevEukaryotGeneExpr.2016016525

    View details for Web of Science ID 000385947400002

    View details for PubMedID 27650985

  • Exceptional locomotory performance in Paratarsotomus macropalpis mites Rubin, S., Wright, J., Young, M., Whitaker, D., Ahn, A. FEDERATION AMER SOC EXP BIOL. 2014