Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics

Spatial transcriptomics (ST) technologies represent a significant advance in gene expression studies, aiming to profile the entire transcriptome from a single histological slide. These techniques are designed to overcome the constraints faced by traditional methods such as immunostaining and RNA in situ hybridization, which are capable of analyzing only a few target genes simultaneously. However, the application of ST in histopathological analysis is also limited by several factors, including low resolution, a limited range of genes, scalability issues, high cost, and the need for sophisticated equipment and complex methodologies. Seq-Scope-a recently developed novel technology-repurposes the Illumina sequencing platform for high-resolution, high-content spatial transcriptome analysis, thereby overcoming these limitations. Here we provide a detailed step-by-step protocol to implement Seq-Scope with an Illumina NovaSeq 6000 sequencing flow cell that allows for the profiling of multiple tissue sections in an area of 7 mm × 7 mm or larger. In addition to detailing how to prepare a frozen tissue section for both histological imaging and sequencing library preparation, we provide comprehensive instructions and a streamlined computational pipeline to integrate histological and transcriptomic data for high-resolution spatial analysis. This includes the use of conventional software tools for single cell and spatial analysis, as well as our recently developed segmentation-free method for analyzing spatial data at submicrometer resolution. Given its adaptability across various biological tissues, Seq-Scope establishes itself as an invaluable tool for researchers in molecular biology and histology.

A Greater Platelet Dose May Yield Better Clinical Outcomes for Platelet-Rich Plasma in the Treatment of Knee Osteoarthritis: A Systematic Review

PURPOSE

To determine whether the platelet dose administered during a platelet-rich plasma (PRP) injection for knee osteoarthritis (OA) affects clinical outcomes.

METHODS

A systematic review was performed by searching PubMed, Cochrane Library, and Embase for randomized controlled trials with at least 1 study arm using PRP for knee OA. Only studies that provided a platelet count, concentration, or dose with a minimum of 6-month outcome scores were included. Studies in which the PRP group had statistically significant positive outcomes were separated from those without statistical significance. The average platelet doses for studies with positive outcomes in the PRP group were compared with those without positive outcomes.

RESULTS

After exclusion criteria were applied, 29 studies were analyzed. Of the 29, there were 31 arms that used PRP as a treatment method, of which 28 had statistically significant positive outcomes at 6 months compared with the control group. The mean platelet dose in the 28 with a positive outcome was 5,500 ± 474 × 106, whereas the 3 that had no positive difference had a mean platelet dose of 2,302 ± 437 × 106 (P < .01). There were 18 studies with 12-month outcomes, with 16 of 18 having positive outcomes. The positive studies had an average platelet dose of 5,464 ± 511, whereas the studies that had no statistical difference had an average platelet dose of 2,253 ± 753 × 106 (P < .05).

CONCLUSIONS

Improved clinical outcomes from PRP injections for knee OA may be related to a greater platelet dose.

LEVEL OF EVIDENCE

Level II, systematic review of Level I and II studies.

Willingness to work among males on parole: A quantitative and qualitative analysis

This study investigated employment attitudes of adult males who were recently released from prison and onto parole. The study investigated the role of willingness to work entry-level jobs, an understudied variable in career development of justice-involved persons. We hypothesized that criminal thinking and perception of barriers would each have a direct effect on job search self-efficacy and a direct and indirect effect on willingness to work entry-level jobs, through job search self-efficacy. We also predicted that criminal thinking and perception of barriers would each have an indirect effect on career aspirations within a job, through job search self-efficacy and willingness to work entry-level jobs. Results confirmed these hypotheses. Results of two serial mediation analyses indicated that perceiving more barriers to work predicted less job search self-efficacy, less job search self-efficacy predicted less willingness to work entry-level jobs, and less willingness to work entry-level jobs predicted lower career aspirations. Similarly, higher reactive criminal thinking predicted less job search self-efficacy, less job search self-efficacy predicted less willingness to work entry-level jobs, and less willingness to work entry-level jobs predicted lower career aspirations. Results of qualitative analysis indicated that the vast majority of parolees planned to work in entry-level jobs within the first few months of release from prison. The study sheds light on the work attitudes of males who leave prison and what factors may influence their willingness to work entry-level jobs. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Entrepreneurship and Criminal Justice Populations: A Social Cognitive Perspective

A criminal record limits employment opportunities of those released from prison. Entrepreneurship, or starting one's own business venture, has been suggested as a way to overcome the employment barriers of a criminal record, given that many justice-involved persons have entrepreneurship experiences, often through illegal ventures. Sparse research has investigated how legal or illegal business experience translates to legal entrepreneurship attitudes. Using social cognitive career theory-career theory (SCCT), and concepts from the Risk Need Responsivity (RNR) model, the role of illegal and legal business exposure were investigated. Findings indicated that both legal and illegal business exposure had a positive influence on entrepreneurship goals through entrepreneurship self-efficacy and entrepreneurship outcome expectations. Legal experiences had a stronger influence. Criminal thinking, a significant risk factor for return to criminal behavior, was investigated in its role in entrepreneurship attitudes. Findings indicated that criminal thinking had an indirect effect on entrepreneurship goals through entrepreneurship self-efficacy.

Correction: Evolution and consequences of individual responses during the COVID-19 outbreak

[This corrects the article DOI: 10.1371/journal.pone.0273964.].

The role of civil society organizations (CSOs) in the COVID-19 response across the Global South: A multinational, qualitative study

Despite receiving less attention than high-income countries, low- and middle-income countries (LMICs) experienced more than 85% of global excess deaths during the first two years of the COVID-19 pandemic. Due to the unprecedented speed and scale of the COVID-19 pandemic, which placed large demands on government capacity, many LMICs relied on civil society organizations (CSOs) to assist in implementing COVID-19 response programs. Yet few studies have examined the critical role CSOs played in mitigating the effects of the COVID-19 pandemic in low resource settings. This study explored the CSO response to COVID-19 in five of the most heavily impacted LMICs in the Global South. Interviews were conducted from May to August 2021 with a purposive sample of CSO key informants within each of the five countries. A total of 52 CSOs were selected from which 53 key informants were interviewed either via Zoom or by phone. Interviews were coded and analyzed using NVivo or MAXQDA2020. Out of the 52 CSOs selected, 24 were national organizations, 8 were regional, and 20 were local. CSOs fell into six categories: community-based organizations, non-governmental organizations, unions/professional organizations, campaigns/social movements, research organizations/think tanks, and networks/coalitions. CSOs across all five countries adapted their missions, stretched their resources, and performed a wide range of activities that fit into five programmatic areas: food security and livelihood support, public health and medical care, cash transfer programs, risk communication and community education, and needs assessment. This qualitative analysis demonstrates the critical role CSOs played in supplementing government emergency aid response by delivering necessary resources and supporting highly vulnerable populations during the COVID-19 pandemic, as well as the primary challenges they faced in doing so. Given the generally weak state of public capacity in the LMICs studied, this role was vital to responding to the pandemic.

Mitochondrial matrix protein LETMD1 maintains thermogenic capacity of brown adipose tissue in male mice

Brown adipose tissue (BAT) has abundant mitochondria with the unique capability of generating heat via uncoupled respiration. Mitochondrial uncoupling protein 1 (UCP1) is activated in BAT during cold stress and dissipates mitochondrial proton motive force generated by the electron transport chain to generate heat. However, other mitochondrial factors required for brown adipocyte respiration and thermogenesis under cold stress are largely unknown. Here, we show LETM1 domain-containing protein 1 (LETMD1) is a BAT-enriched and cold-induced protein required for cold-stimulated respiration and thermogenesis of BAT. Proximity labeling studies reveal that LETMD1 is a mitochondrial matrix protein. Letmd1 knockout male mice display aberrant BAT mitochondria and fail to carry out adaptive thermogenesis under cold stress. Letmd1 knockout BAT is deficient in oxidative phosphorylation (OXPHOS) complex proteins and has impaired mitochondrial respiration. In addition, BAT-specific Letmd1 deficient mice exhibit phenotypes identical to those observed in Letmd1 knockout mice. Collectively, we demonstrate that the BAT-enriched mitochondrial matrix protein LETMD1 plays a tissue-autonomous role that is essential for BAT mitochondrial function and thermogenesis.

Surface ID: A Geometry-aware System for Protein Molecular Surface Comparison

MOTIVATION

A protein can be represented in several forms, including its 1D sequence, 3D atom coordinates, and molecular surface. A protein surface contains rich structural and chemical features directly related to the protein's function such as its ability to interact with other molecules. While many methods have been developed for comparing similarity of proteins using the sequence and structural representations, computational methods based on molecular surface representation are limited.

RESULTS

Here, we describe "Surface ID", a geometric deep learning system for high-throughput surface comparison based on geometric and chemical features. Surface ID offers a novel grouping and alignment algorithm useful for clustering proteins by function, visualization, and in-silico screening of potential binding partners to a target molecule. Our method demonstrates top performance in surface similarity assessment, indicating great potential for protein functional annotation, a major need in protein engineering and therapeutic design.

AVAILABILITY

Source code for the Surface ID model, trained weights and inference script are available under an open-source (Apache Version 2.0) license at https://github.com/Sanofi-Public/LMR-SurfaceID.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Mechanistic incorporation of FcRn binding in plasma and endosomes in a whole body PBPK model for large molecules

Monoclonal antibodies, endogenous IgG, and serum albumin bind to FcRn in the endosome for salvaging and recycling after pinocytotic uptake, which prolongs their half-life. This mechanism has been broadly recognized and is incorporated in currently available PBPK models. Newer types of large molecules have been designed and developed, which also bind to FcRn in the plasma space for various mechanistic reasons. To incorporate FcRn binding affinity in PBPK models, binding in the plasma space and subsequent internalisation into the endosome needs to be explicitly represented. This study investigates the large molecules model in PK-Sim^® and its applicability to molecules with FcRn binding affinity in plasma. With this purpose, simulations of biologicals with and without plasma binding to FcRn were performed with the large molecule model in PK-Sim^®. Subsequently, this model was extended to ensure a more mechanistic description of the internalisation of FcRn and the FcRn-drug complexes. Finally, the newly developed model was used in simulations to explore the sensitivity for FcRn binding in the plasma space, and it was fitted to an in vivo dataset of wild-type IgG and FcRn inhibitor plasma concentrations in Tg32 mice. The extended model demonstrated a strongly increased sensitivity of the terminal half-life towards the plasma FcRn binding affinity and could successfully fit the in vivo dataset in Tg32 mice with meaningful parameter estimates.

International comparability of reference unit costs of education services: when harmonizing methodology is not enough (PECUNIA project)

BACKGROUND

Health problems can lead to costs in the education sector. However, these costs are rarely incorporated in health economic evaluations due to the lack of reference unit costs (RUCs), cost per unit of service, of education services and of validated methods to obtain them. In this study, a standardized unit cost calculation tool developed in the PECUNIA project, the PECUNIA RUC Template for services, was applied to calculate the RUCs of selected education services in five European countries.

METHODS

The RUCs of special education services and of educational therapy were calculated using the information collected via an exploratory gray literature search and contact with service providers.

RESULTS

The RUCs of special education services ranged from €55 to €189 per school day. The RUCs of educational therapy ranged from €6 to €25 per contact and from €5 to €35 per day. Variation was observed in the type of input data and measurement unit, among other.

DISCUSSION

The tool helped reduce variability in the RUCs related to costing methodology and gain insights into other aspects that contribute to the variability (e.g. data availability). Further research and efforts to generate high quality input data are required to reduce the variability of the RUCs.

Predictive Role of Aortic Valve Calcium score on post-procedural outcomes and mortality after Transcatheter aortic valve replacement

Introduction

Extent of aortic valve (AV) calcium increases as degenerative aortic valve stenosis progresses. Initial studies postulated AV calcium (AVC) score to be a predictor of complications such as need for pacemaker implantation, paravalvular regurgitation and mortality after Trans-catheter Aortic valve Replacement (TAVR). However, evidence regarding the impact of AVC score as a predictor of post-procedural complications and mortality has been conflicting.

Objective

This study aimed to determine the prognostic impact of AVC as predictor of post-procedural outcomes and mortality in patients with severe aortic stenosis (AS) who underwent TAVR.

Methods

We retrospectively abstracted the records of 497 patients with severe AS who underwent TAVR between January 2016 and July 2019 at our institution. All patients underwent a non-contrast cardiac CT scan on a Siemens Somatom Definition Flash 128 slice scanner. AVC score using the Agatston method was obtained retrospectively. Patients were divided into two groups: 1) Non-severe AVC score group [women &lt;1200 Agatston unit (AU) and men &lt;2000 AU]; 2) Severe AV Calcium Score group [women &gt;1200 AU and men &gt;2000 AU]. Primary outcome was 1-year mortality.

Results

Among 466 patients included in the analysis, 352 patients were included severe AVC group while 114 patients were in the non-severe AVC group. Patients in the severe AVC group were older (81±8 vs 79±8 years), were predominantly males (79% vs 71%), and had less diabetes mellitus (31% vs 42%, p=0.02). Post-TAVR AV dimensionless index (0.58±0.13 vs 0.58±0.12, p=0.8) and AV mean gradient (9.5±4.9 vs 9.2±5.4 mmHg) were not statistically different between both groups. There was no statistical difference in the need for PPM (12% vs 7%, p=0.16), post-TAVR stroke (1.5% vs 0%), post-TAVR major complications (17.4% vs 10%, p=0.07), 30 day (3.7% vs 4.4%), and 1-year mortality (13.6 vs 11.4, p=0.6) between both groups.

Conclusion

Our study report that the severity of AVC score does not have a prognostic impact on major post-procedural outcomes and mortality after TAVR.

Funding Acknowledgement

Type of funding sources: None.

Sex-based differences of the impact of aortic valve calcium score on mortality and post-procedural outcomes after trans-catheter aortic valve replacement

Introduction

Sex based differences exist in the presentation, outcomes, and management of cardiovascular diseases. Although aortic valve calcium (AVC) score has been postulated to be associated with post-procedural outcomes after transcatheter aortic valve replacement (TAVR), data on the impact of AVC score on procedural outcomes after TAVR based on sex have been scarce.

Objective

The aim of the present study was to elucidate sex related differences in the prognostic impact of AVC score as a predictor of post-procedural outcomes and mortality in patients with severe aortic stenosis (AS) who underwent TAVR.

Methods

We retrospectively abstracted the records of 497 patients with severe AS who underwent TAVR between January 2016 and July 2019 at our institution. All patients underwent a non-contrast cardiac CT scan on a Siemens Somatom Definition Flash 128 slice scanner. AVC score using the Agatston method was calculated retrospectively. Primary outcome was 1-year mortality. Patients were divided into two groups: 1) Non-severe AVC score group [women &lt;1200 Agatston unit (AU) and men &lt;2000 AU]; 2) Severe AVC Score group [women &gt;1200 AU and men &gt;2000 AU]. Cox-regression model was used to predict effect of variables on 1-year mortality in male and female patients.

Results

Among 466 patients included, 268 patients were male and 198 were female (57.5% vs 42.5%). When compared with males, female patients had significantly lower AVC score (p&lt;0.001), aortic valve area (AVA) (p&lt;0.001), obstructive CAD (p&lt;0.001), and history of previous PCI (p&lt;0.004), and CABG (&lt;0.001) but had a significantly higher STS score (6.7±3.2 vs 5.8±3.3 P=0.01). There was no difference between need for permanent pacemaker (PPM) implantation (11% vs 9.6%, p=0.4), major complications (16% vs 15%, p=0.9), stroke (0.8% vs 1.6%, p=0.7), 30-day (3.7% vs 4%, p=0.9), and 1-year mortality (14% vs 12%, p=0.6) between males and females, respectively. Female patients required smaller bio-prosthetic valves compared with males (26±3.2 vs 30±3, p&lt;0.001). Cox regression analysis for female patients showed BMI, hemoglobin level, and AVA independently predicted 1-year mortality, while there was no impact of severe AVC score (&gt;1200 AU) on 1-year mortality in females. Similarly, Cox regression analysis for male patients showed there was no impact of severe AVC score (&gt;2000 AU) on 1-year mortality in males. When males in the severe AVC group were compared with female patients in the severe AVC group, there was no difference in 30 day (4.3% vs 3.3%, p=0.82) and 1-year mortality (14.2% vs 13.3%, p=0.77). Similarly, in the severe AVC group there was no difference between need for PPM implantation (12.8% vs 12.1%, p=0.9), major complications (19.7% vs 15.8%, p=0.4), and stroke (2.2% vs 1%, p=0.6) between males and females, respectively.

Conclusion

There were no sex differences in the impact of AVC score on mortality and post-procedural outcomes after TAVR.

Funding Acknowledgement

Type of funding sources: None.

Evolution and consequences of individual responses during the COVID-19 outbreak

In a long-lasting major disease outbreak such as that of COVID-19, the challenge for public health authorities is to keep people motivated and keen on following safety guidelines. In this study, a compartmental model with a heterogeneous transmission rate (based on awareness) is utilized to hypothesize about the public adoption of preventive guidelines. Three subsequent outbreaks in South Korea, Pakistan, and Japan were analyzed as case studies. The transmission, behavior change, and behavioral change ease rates of the disease were measured in these countries. The parameters were estimated using the maximum likelihood method with an additional identifiability analysis performed to determine the uniqueness of the estimated parameters for quantitatively comparing them during the first three waves of COVID-19. The mathematical analysis and simulation results show that individual responses had a significant effect on the outbreak. Individuals declining to follow the public health guidelines in Korea and Japan between the second and third waves contributed to making the third peak the highest of the three peaks. In Pakistan, however, individual responses to following public health guidelines were maintained between the second and third waves, resulting in the third peak being lower than the first, rather than being associated with the highest transmission rate. Thus, maintaining a high level of awareness is critical for containing the spread. Improvised public health campaigns are recommended to sustain individual attention and maintain a high level of awareness.

Accuracy of the Breast Cancer Surveillance Consortium Model Among Women with LCIS

PURPOSE

The Breast Cancer Surveillance Consortium (BCSC) model predicts risk of invasive breast cancer risk based on age, race, family history, breast density, and history of benign breast disease, including lobular carcinoma in situ (LCIS). However, validation studies for this model included few women with LCIS. We sought to evaluate the accuracy of the BCSC model among this cohort.

METHODS

Women with LCIS diagnosed between 1983 and 2017 were identified from a prospectively maintained database. The BCSC score was calculated; those with prior breast cancer, unknown breast density, age < 35 years or > 74 years, or with history of chemoprevention use were excluded. The Kaplan-Meier method was used to estimate incidence rates. Time-dependent receiver operating characteristic (ROC) analysis was used to analyze the discriminative capacity of the model.

RESULTS

1302 women with LCIS were included. At a median follow-up of 7 years, 152 women (12%) developed invasive cancer (6 with bilateral disease). Cumulative incidences of invasive breast cancer were 7.1% (95% CI 5.6-8.7) and 13.3% (95% CI 10.9-15.6), respectively, and the median BCSC risk scores were 4.9 and 10.4, respectively, at 5 and 10 years. The median 10-year BCSC score was significantly lower than the 10-year Tyrer-Cuzick score (10.4 vs 20.8, p < 0.001). The ROC curve scores (AUC) for BCSC at 5 and 10 years were 0.59 (95% CI 0.52-0.66) and 0.58 (95% CI 0.52-0.64), respectively.

CONCLUSION

The BCSC model has moderate accuracy in predicting invasive breast cancer risk among women with LCIS with fair discrimination for risk prediction between individuals.

Atypical jobs in psychology: An interview with Dr. McCarthy

This article summarizes the career of Dr. McCarthy, who is Dean of the College of Sciences and Humanities at Ball State University. She came from humble roots as the oldest of 10 children and is therefore grateful she was able to attend college. That experience gave her insight into the possible challenges of those pursuing a degree in higher education. This, coupled with her education in psychology, has helped her passionately serve both her students and faculty members in several public service roles, including her current position as dean. Through this interview, Dr. McCarthy was able to describe her background training, daily tasks, and the strategies she employs to effectively spark change at both the individual and institutional levels. She also discussed the rewards and challenges of her career. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Comparison of Outcomes for Classic-Type Lobular Carcinoma In Situ Managed with Surgical Excision After Core Biopsy Versus Observation

BACKGROUND

Studies report low upgrade rates following excision for classic-type lobular carcinoma in situ (LCIS) with radiologic-pathologic concordance. Thus, in the absence of other high-risk lesions, observation has become standard. We report long-term outcomes of excision versus observation following a core biopsy diagnosis of classic-type LCIS.

METHODS

Women with LCIS treated from 2013-2020 and managed with excision or observation were identified from a prospective database. Women with cancer upgrade at excision or history of cancer were excluded. We compared rates and characteristics of subsequent breast cancers by clinical management strategy.

RESULTS

Of 312 women, 170 (54%) underwent excision and 142 (46%) were managed with observation. Among the excision group, 36 of 170 (21%) had radiologic-pathologic concordant LCIS without other high-risk lesions, mass, or symptoms (concordant LCIS excision group). Overall, at 3.1 years median follow-up, 11 (6.5%) women managed with excision and 11 (7.7%) women managed with observation developed cancer. Cancer development was not associated with management choice (overall excision cohort vs. observation group [p = 0.8]) and did not differ between the concordant LCIS excision and observation groups (p > 0.9). The 5-year cancer development rate was 8.9% (95% confidence interval [CI]: 2.3-31.6%) in the concordant LCIS excision group and 10.3% (95% CI 5.5-18.6%) in the observation group.

CONCLUSIONS

No difference in breast cancer rates existed among women with a core-biopsy diagnosis of classic-type LCIS managed with excision or observation. These data support management of LCIS as a risk factor, with consideration of chemoprophylaxis, rather than as an indication for surgical excision.

Eyelash trichomegaly: a systematic review of acquired and congenital aetiologies of lengthened lashes

Long eyelashes have been popularized and many commercially available products exist to achieve eyelash growth as a desired cosmetic effect. Eyelash trichomegaly may be induced by medications, procedures, or be related to medical conditions; however, the exact mechanisms that govern eyelash growth are not well elucidated. This study aims to identify and summarize aetiologies associated with eyelash trichomegaly. We report a systematic review of 148 clinical trials, prospective and retrospective studies, and case reports describing all evidence-based potential aetiologies of eyelash trichomegaly obtained from the Medline/PubMed and Cochrane Library through January 2021. Inclusion criteria were defined as (i) human studies involving congenital and acquired diseases in which eyelash trichomegaly is a characteristic or (ii) assessment of trichomegaly as an adverse or desired effect of a medication or procedure. Exclusion criteria included: animal studies, articles not available in English, outcomes unrelated to eyelash trichomegaly, and secondary review articles. Pharmacologic agents associated with eyelash trichomegaly included prostaglandin analogues (15-keto fluprostenol isopropyl ester, bimatoprost, latanoprost, and travoprost), epidermal growth factor receptor inhibitors (cetuximab, erlotinib, and panitumumab), interferon-alpha, and calcineurin inhibitors (tacrolimus and cyclosporine). Surgical procedures of the eyelid, as well as allergic rhinitis, atopic dermatitis, HIV, ichthyosis vulgaris (IV), uveitis, and vernal keratoconjunctivitis were also associated with increased eyelash growth. Congenital disorders associated with lengthened eyelashes included Cantú syndrome, CHOPS syndrome, Coffin-Siris syndrome, congenital heart disease, Cornelia de Lange syndrome, Costello syndrome, familial trichomegaly, Floating Harbor syndrome, Hermansky-Pudlak syndrome, Kabuki-Makeup syndrome, KBG syndrome, Oliver-McFarlane syndrome, Rubinstein-Taybi syndrome, and Smith-Magenis syndrome. While the most common cause of eyelash trichomegaly is topical bimatoprost use, better understanding of pathways implicated in eyelash trichomegaly may lead to the discovery of additional medications to stimulate eyelash growth and create avenues for future therapeutic interventions.

Development of an integrated structural biology platform specialized for sub-100 kDa protein complexes to support biologics discovery and rational engineering

Background

Developing a biologic medicine requires successful decision making during selection and optimization in addition to the pool of candidates at early research stages. Knowing structural information and binding patterns between drug target and discovery candidates greatly increases the probability of success.

Methods

With the cryo-EM resolution revolution and rapid development of computational software, we have evaluated and integrated various tools in structural biology and the computation field and established a highly cost-effective platform which allows us to obtain fast and accurate structural information for nearly all our biologics projects with a close to 100% success rate and as fast as weeks turn-around time.

Results

Here we report four case studies selected from 38 different protein structures and share how we integrate cryo-EM structure determination, computational structure modeling, and molecular dynamics simulation. With proper decision making and strategic planning, the platform allows us to obtain quality results within days to weeks, including sub-100 kDa complexes which are usually considered a challenge due to their small size.

Conclusions

Our utilization of this differential approach and multiple software packages allows us to manage priorities and resources to achieve goals quickly and efficiently. We demonstrate how to effectively overcome particle orientation bias by altering complex composition. In several of our examples, we use glycan density to facilitate interpretation of low-resolution 3D reconstruction and epitope mapping. Protein information plays an important role in our cryo-EM projects, especially in cases where we see significant challenges in obtaining high-resolution 3D maps.

Engineered Fc-glycosylation switch to eliminate antibody effector function

Antibodies mediate effector functions through Fcγ receptor (FcγR) interactions and complement activation, causing cytokine release, degranulation, phagocytosis, and cell death. They are often undesired for development of therapeutic antibodies where only antigen binding or neutralization would be ideal. Effector elimination has been successful with extensive mutagenesis, but these approaches can potentially lead to manufacturability and immunogenicity issues. By switching the native glycosylation site from position 297 to 298, we created alternative antibody glycosylation variants in the receptor interaction interface as a novel strategy to eliminate the effector functions. The engineered glycosylation site at Asn298 was confirmed by SDS-PAGE, mass spectrometry, and X-ray crystallography (PDB code 6X3I). The lead NNAS mutant (S298N/T299A/Y300S) shows no detectable binding to mouse or human FcγRs by surface plasmon resonance analyses. The effector functions of the mutant are completely eliminated when measured in antibody-dependent cell-meditated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC) assays. In vivo, the NNAS mutant made on an antibody against a human lymphocyte antigen does not deplete T cells or B cells in transgenic mice, in contrast to wild-type antibody. Structural study confirms the successful glycosylation switch to the engineered Asn298 site. The engineered glycosylation would clash with approaching FcγRs based on reported Fc-FcγR co-crystal structures. In addition, the NNAS mutants of multiple antibodies retain binding to antigens and neonatal Fc receptor, exhibit comparable purification yields and thermal stability, and display normal circulation half-life in mice and non-human primate. Our work provides a novel approach for generating therapeutic antibodies devoid of any ADCC and CDC activities with potentially lower immunogenicity.

Application of an integrated computational antibody engineering platform to design SARS-CoV-2 neutralizers

As the COVID-19 pandemic continues to spread, hundreds of new initiatives including studies on existing medicines are running to fight the disease. To deliver a potentially immediate and lasting treatment to current and emerging SARS-CoV-2 variants, new collaborations and ways of sharing are required to create as many paths forward as possible. Here, we leverage our expertise in computational antibody engineering to rationally design/engineer three previously reported SARS-CoV neutralizing antibodies and share our proposal towards anti-SARS-CoV-2 biologics therapeutics. SARS-CoV neutralizing antibodies, m396, 80R and CR-3022 were chosen as templates due to their diversified epitopes and confirmed neutralization potency against SARS-CoV (but not SARS-CoV-2 except for CR3022). Structures of variable fragment (Fv) in complex with receptor binding domain (RBD) from SARS-CoV or SARS-CoV-2 were subjected to our established in silico antibody engineering platform to improve their binding affinity to SARS-CoV-2 and developability profiles. The selected top mutations were ensembled into a focused library for each antibody for further screening. In addition, we convert the selected binders with different epitopes into the trispecific format, aiming to increase potency and to prevent mutational escape. Lastly, to avoid antibody-induced virus activation or enhancement, we suggest application of NNAS and DQ mutations to the Fc region to eliminate effector functions and extend half-life.

A platform-agnostic, function first-based antibody discovery strategy using plasmid-free mammalian expression of antibodies

Hybridoma technology has been valuable in the development of therapeutic antibodies. More recently, antigen-specific B-cell selection and display technologies are also gaining importance. A major limitation of these approaches used for antibody discovery is the extensive process of cloning and expression involved in transitioning from antibody identification to validating the function, which compromises the throughput of antibody discovery. In this study, we describe a process to identify and rapidly re-format and express antibodies for functional characterization. We used two different approaches to isolate antibodies to five different targets: 1) flow cytometry to identify antigen-specific single B cells from the spleen of immunized human immunoglobulin transgenic mice; and 2) panning of phage libraries. PCR amplification allowed recovery of paired V_H and V_L sequences from 79% to 96% of antigen-specific B cells. All cognate V_H and V_L transcripts were formatted into transcription and translation compatible linear DNA expression cassettes (LEC) encoding whole IgG or Fab. Between 92% and 100% of paired V_H and V_L transcripts could be converted to LECs, and nearly 100% of them expressed as antibodies when transfected into Expi293F cells. The concentration of IgG in the cell culture supernatants ranged from 0.05 µg/ml to 145.8 µg/ml (mean = 18.4 µg/ml). Antigen-specific binding was displayed by 78–100% of antibodies. High throughput functional screening allowed the rapid identification of several functional antibodies. In summary, we describe a plasmid-free system for cloning and expressing antibodies isolated by different approaches, in any format of choice for deep functional screening that can be applied in any research setting during antibody discovery.

Myonectin inhibits adipogenesis in 3T3-L1 preadipocytes by regulating p38 MAPK pathway

In current times, obesity is a major health problem closely associated with metabolic disease such as diabetes, dyslipidemia, and cardiovascular disease. The direct cause of obesity is known as an abnormal increase in fat cell size and the adipocyte pool. Hyperplasia, the increase in number of adipocytes, results from adipogenesis in which preadipocytes differentiate into mature adipocytes. Adipogenesis is regulated by local and systemic cues that alter transduction pathways and subsequent control of adipogenic transcription factors. Therefore, the regulation of adipogenesis is an important target for preventing obesity. Myonectin, a member of the CTRP family, is a type of myokine released by skeletal muscle cells. Although several studies have shown that myonectin is associated with lipid metabolism, the role of myonectin during adipogenesis is not known. Here, we demonstrate the role of myonectin during adipocyte differentiation of 3T3-L1 cells. We found that myonectin inhibits the adipogenesis of 3T3-L1 preadipocytes with a reduction in the expression of adipogenic transcription factors such as C/EBPα, β and PPARγ. Furthermore, we show that myonectin has an inhibitory effect on adipogenesis through the regulation of the p38 MAPK pathway and CHOP. These findings suggest that myonectin may be a novel therapeutic target for the prevention of obesity.

Noninvasive Monitoring of Mantle Cell Lymphoma by Immunoglobulin Gene Next-Generation Sequencing in a Phase 2 Study of Sequential Chemoradioimmunotherapy Followed by Autologous Stem-Cell Rescue

Limited information exists in mantle cell lymphoma (MCL) on the performance of next-generation sequencing–based assay of immunoglobulin gene rearrangements for minimal residual disease (MRD) assessment. Posttreatment peripheral blood samples were collected from 16 MCL patients and analyzed with the Adaptive Biotechnologies MRD assay, which identified early molecular relapse. We observed more sensitivity in the cellular versus acellular compartment.

GATA3 induces the upregulation of UCP-1 by directly binding to PGC-1α during adipose tissue browning

OBJECTIVE

Obesity is recognized as the cause of multiple metabolic diseases and is rapidly increasing worldwide. As obesity is due to an imbalance in energy homeostasis, the promotion of energy consumption through browning of white adipose tissue (WAT) has emerged as a promising therapeutic strategy to counter the obesity epidemic. However, the molecular mechanisms of the browning process are not well understood. In this study, we investigated the effects of the GATA family of transcription factors on the browning process.

METHODS

We used qPCR to analyze the expression of GATA family members during WAT browning. In order to investigate the function of GATA3 in the browning process, we used the lentivirus system for the ectopic expression and knockdown of GATA3. Western blot and real-time qPCR analyses revealed the regulation of thermogenic genes upon ectopic expression and knockdown of GATA3. Luciferase reporter assays, co-immunoprecipitation, and chromatin immunoprecipitation were performed to demonstrate that GATA3 interacts with proliferator-activated receptor-γ co-activator-1α (PGC-1α) to regulate the promoter activity of uncoupling protein-1 (UCP-1). Enhanced energy expenditure by GATA3 was confirmed using oxygen consumption assays, and the mitochondrial content was assessed using MitoTracker. Furthermore, we examined the in vivo effects of lentiviral GATA3 overexpression and knockdown in inguinal adipose tissue of mice.

RESULTS

Gata3 expression levels were significantly elevated in the inguinal adipose tissue of mice exposed to cold conditions. Ectopic expression of GATA3 enhanced the expression of UCP-1 and thermogenic genes upon treatment with norepinephrine whereas GATA3 knockdown had the opposite effect. Luciferase reporter assays using the UCP-1 promoter region showed that UCP-1 expression was increased in a dose-dependent manner by GATA3 regardless of norepinephrine treatment. GATA3 was found to directly bind to the promoter region of UCP-1. Furthermore, our results indicated that GATA3 interacts with the transcriptional coactivator PGC-1α to increase the expression of UCP-1. Taken together, we demonstrate that GATA3 has an important role in enhancing energy expenditure by increasing the expression of thermogenic genes both in vitro and in vivo.

CONCLUSION

GATA3 may represent a promising target for the prevention and treatment of obesity by regulating thermogenic capacity.

Evaluation of COVID-19 epidemic outbreak caused by temporal contact-increase in South Korea

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Widespread COVID-19 infection occurred in South Korea after February 18 because of the mass infections in the Shincheonji Church of Jesus.

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The mean transmission rate has increased by approximately 20 times since the mass infections from the 31 st confirmed patient occurred on February 9.

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Voluntary prevention actions were fairly implemented, and, consequently, the effective reproduction number on February 28 has remained below unity after identifying the 31 st confirmed patient on February 18.

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We aim for the voluntary participation by citizens in active prevention activities until vaccines or treatments are developed in the countries that are presently suffering from COVID-19.

Objectives

On March 15, 2020, 61.3% of the confirmed cases of COVID-19 infection in South Korea are associated with the worship service that was organized on February 9 in the Shincheonji Church of Jesus in Daegu. We aim to evaluate the effects of mass infection in South Korea and assess the preventive control intervention.

Method

Using openly available data of daily cumulative confirmed cases and deaths, the basic and effective reproduction numbers was estimated using a modified susceptible–exposed–infected–recovered-type epidemic model.

Results

The basic reproduction number was estimated to be  R0=1.77. The effective reproduction number increased approximately 20 times after the mass infections from the 31 st patient, which was confirmed on February 9 in the Shincheonji Church of Jesus, Daegu. However, the effective reproduction number decreased to less than unity after February 28 owing to the implementation of high-level preventive control interventions in South Korea, coupled with voluntary prevention actions by citizens.

Conclusion

Preventive action and control intervention were successfully established in South Korea.

A mathematical model for assessing the effectiveness of controlling relapse in Plasmodium vivax malaria endemic in the Republic of Korea

Malaria has persisted as an endemic near the Demilitarized Zone in the Republic of Korea since the re-emergence of Plasmodium vivax malaria in 1993. The number of patients affected by malaria has increased recently despite many controls tools, one of the reasons behind which is the relapse of malaria via liver hypnozoites. Tafenoquine, a new drug approved by the United States Food and Drug Administration in 2018, is expected to reduce the rate of relapse of malaria hypnozoites and thereby decrease the prevalence of malaria among the population. In this work, we have developed a new transmission model for Plasmodium vivax that takes into account a more realistic intrinsic distribution from existing literature to quantify the current values of relapse parameters and to evaluate the effectiveness of the anti-relapse therapy. The model is especially suitable for estimating parameters near the Demilitarized Zone in Korea, in which the disease follows a distinguishable seasonality. Results were shown that radical cure could significantly reduce the prevalence level of malaria. However, eradication would still take a long time (over 10 years) even if the high-level treatment were to persist. In addition, considering that the vector's behavior is manipulated by the malaria parasite, relapse repression through vector control at the current level may result in a negative effect in containing the disease. We conclude that the use of effective drugs should be considered together with the increased level of the vector control to reduce malaria prevalence.

Do Body Mass Index and Breast Density Impact Cancer Risk Among Women with Lobular Carcinoma In Situ?

PURPOSE

Both body mass index (BMI) and breast density impact breast cancer risk in the general population. Whether obesity and density represent additive risk factors in women with lobular carcinoma in situ (LCIS) is unknown.

METHODS

Patients diagnosed with LCIS from 1988 to 2017 were identified from a prospectively maintained database. BMI was categorized by World Health Organization classification. Density was captured as the mammographic Breast Imaging Reporting and Data System (BIRADS) value. Other covariates included age at LCIS diagnosis, menopausal status, family history, chemoprevention, and prophylactic mastectomy. Cancer-free probability was estimated using the Kaplan-Meier method, and Cox regression models were used for univariable and multivariable analyses.

RESULTS

A total of 1222 women with LCIS were identified. At a median follow-up of 7 years, 179 women developed breast cancer (121 invasive, 58 ductal carcinoma in situ); 5- and 10-year cumulative incidences of breast cancer were 10% and 17%, respectively. In multivariable analysis, increased breast density (BIRADS C/D vs. A/B) was significantly associated with increased hazard of breast cancer (hazard ratio [HR] 2.42, 95% confidence interval [CI] 1.52-3.88), whereas BMI was not. On multivariable analysis, chemoprevention use was associated with a significantly decreased hazard of breast cancer (HR 0.49, 95% CI 0.29-0.84). Exploratory analyses did not demonstrate significant interaction between BMI and menopausal status, BMI and breast density, BMI and chemoprevention use, or breast density and chemoprevention.

CONCLUSIONS

Breast cancer risk among women with LCIS is impacted by breast density. These results aid in personalizing risk assessment among women with LCIS and highlight the importance of chemoprevention counseling for risk reduction.

The Role of Adipose Tissue Mitochondria: Regulation of Mitochondrial Function for the Treatment of Metabolic Diseases

: Mitochondria play a key role in maintaining energy homeostasis in metabolic tissues, including adipose tissues. The two main types of adipose tissues are the white adipose tissue (WAT) and the brown adipose tissue (BAT). WAT primarily stores excess energy, whereas BAT is predominantly responsible for energy expenditure by non-shivering thermogenesis through the mitochondria. WAT in response to appropriate stimuli such as cold exposure and β-adrenergic agonist undergoes browning wherein it acts as BAT, which is characterized by the presence of a higher number of mitochondria. Mitochondrial dysfunction in adipocytes has been reported to have strong correlation with metabolic diseases, including obesity and type 2 diabetes. Dysfunction of mitochondria results in detrimental effects on adipocyte differentiation, lipid metabolism, insulin sensitivity, oxidative capacity, and thermogenesis, which consequently lead to metabolic diseases. Recent studies have shown that mitochondrial function can be improved by using thiazolidinedione, mitochondria-targeted antioxidants, and dietary natural compounds; by performing exercise; and by controlling caloric restriction, thereby maintaining the metabolic homeostasis by inducing adaptive thermogenesis of BAT and browning of WAT. In this review, we focus on and summarize the molecular regulation involved in the improvement of mitochondrial function in adipose tissues so that strategies can be developed to treat metabolic diseases.

The Tyrer-Cuzick Model Inaccurately Predicts Invasive Breast Cancer Risk in Women With LCIS

BACKGROUND

The Tyrer-Cuzick model has been shown to overestimate risk in women with atypical hyperplasia, although its accuracy among women with lobular carcinoma in situ (LCIS) is unknown. We evaluated the accuracy of the Tyrer-Cuzick model for predicting invasive breast cancer (IBC) development among women with LCIS.

METHODS

Women with LCIS participating in surveillance from 1987 to 2017 were identified from a prospectively maintained database. Tyrer-Cuzick score (version 7) was calculated near the time of LCIS diagnosis. Patients with prior or concurrent breast cancer, a BRCA mutation, receiving chemoprevention, or with pleomorphic LCIS were excluded. Invasive cancer-free probability was estimated using the Kaplan-Meier method.

RESULTS

A total of 1192 women with a median follow-up of 6 years (interquartile range [IQR] 2.5-9.9) were included. Median age at LCIS diagnosis was 49 years (IQR 45-55), 88% were white; 37% were postmenopausal, 28% had ≥ 1 first-degree family member with breast cancer, and 13% had ≥ 2 second-degree family members with breast cancer. In total, 128 patients developed an IBC; median age at diagnosis was 54 years (IQR 49-61). Five- and 10-year cumulative incidences of invasive cancer were 8% (95% confidence interval [CI] 6-9%) and 14% (95% CI 12-17%), respectively. The median Tyrer-Cuzick 10-year risk score was 20.1 (IQR 17.4-24.3). Discrimination measured by the C-index was 0.493, confirming that the Tyrer-Cuzick model is not well calibrated in this patient population.

CONCLUSIONS

The Tyrer-Cuzick model is not accurate and may overpredict IBC risk for women with LCIS, and therefore should not be used for breast cancer risk assessment in this high-risk population.

Antibody Fc engineering for enhanced neonatal Fc receptor binding and prolonged circulation half-life

The neonatal Fc receptor (FcRn) promotes antibody recycling through rescue from normal lysosomal degradation. The binding interaction is pH-dependent with high affinity at low pH, but not under physiological pH conditions. Here, we combined rational design and saturation mutagenesis to generate novel antibody variants with prolonged half-life and acceptable development profiles. First, a panel of saturation point mutations was created at 11 key FcRn-interacting sites on the Fc region of an antibody. Multiple variants with slower FcRn dissociation kinetics than the wildtype (WT) antibody at pH 6.0 were successfully identified. The mutations were further combined and characterized for pH-dependent FcRn binding properties, thermal stability and the FcγRIIIa and rheumatoid factor binding. The most promising variants, YD (M252Y/T256D), DQ (T256D/T307Q) and DW (T256D/T307W), exhibited significantly improved binding to FcRn at pH 6.0 and retained similar binding properties as WT at pH 7.4. The pharmacokinetics in human FcRn transgenic mice and cynomolgus monkeys demonstrated that these properties translated to significantly prolonged plasma elimination half-life compared to the WT control. The novel variants exhibited thermal stability and binding to FcγRIIIa in the range comparable to clinically validated YTE and LS variants, and showed no enhanced binding to rheumatoid factor compared to the WT control. These engineered Fc mutants are promising new variants that are widely applicable to therapeutic antibodies, to extend their circulation half-life with obvious benefits of increased efficacy, and reduced dose and administration frequency.