2021 White Paper on Recent Issues in Bioanalysis: ISR for Biomarkers, Liquid Biopsies, Spectral Cytometry, Inhalation/Oral & Multispecific Biotherapeutics, Accuracy/LLOQ for Flow Cytometry (Part 2 - Recommendations on Biomarkers/CDx Assays Development & Validation, Cytometry Validation & Innovation, Biotherapeutics PK LBA Regulated Bioanalysis, Critical Reagents & Positive Controls Generation).

The 15th edition of the Workshop on Recent Issues in Bioanalysis (15th WRIB) was held on 27 September to 1 October 2021. Even with a last-minute move from in-person to virtual, an overwhelmingly high number of nearly 900 professionals representing pharma and biotech companies, contract research organizations (CROs), and multiple regulatory agencies still eagerly convened to actively discuss the most current topics of interest in bioanalysis. The 15th WRIB included three Main Workshops and seven Specialized Workshops that together spanned 1 week in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccines. Moreover, in-depth workshops on biomarker assay development and validation (BAV) (focused on clarifying the confusion created by the increased use of the term "context of use" [COU]); mass spectrometry of proteins (therapeutic, biomarker and transgene); state-of-the-art cytometry innovation and validation; and critical reagent and positive control generation were the special features of the 15th edition. This 2021 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2021 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 2) covers the recommendations on ISR for Biomarkers, Liquid Biopsies, Spectral Cytometry, Inhalation/Oral & Multispecific Biotherapeutics, Accuracy/LLOQ for Flow Cytometry. Part 1A (Endogenous Compounds, Small Molecules, Complex Methods, Regulated Mass Spec of Large Molecules, Small Molecule, PoC), Part 1B (Regulatory Agencies' Inputs on Bioanalysis, Biomarkers, Immunogenicity, Gene & Cell Therapy and Vaccine) and Part 3 (TAb/NAb, Viral Vector CDx, Shedding Assays; CRISPR/Cas9 & CAR-T Immunogenicity; PCR & Vaccine Assay Performance; ADA Assay Comparability & Cut Point Appropriateness) are published in volume 14 of Bioanalysis, issues 9 and 11 (2022), respectively.

Test-retest Repeatability of the Ohio Contrast Cards.

SIGNIFICANCE: The Ohio Contrast Cards are a repeatable test of contrast sensitivity, and they reveal higher contrast sensitivity for low-vision patients than is shown by the Pelli-Robson chart. PURPOSE: This study aimed to compare the contrast sensitivity results and test/retest ±limits of agreement for the Ohio Contrast Cards and the Pelli-Robson letter contrast sensitivity chart on two challenging groups of participants, and to compare the Ohio Contrast Card results with grating acuity and the Pelli-Robson results with letter acuity. METHODS: The Ohio Contrast Card and Pelli-Robson tests were each performed twice by two different examiners within one visit on 40 elder patients in Primary Vision Care (>65 years old) and 23 to 27 low-vision school-aged students. Grating acuity was measured using the Teller Acuity Cards (all participants), and letter acuity was measured using ClearChart (elders) or the Bailey-Lovie chart (students). RESULTS: The ±95% limits of agreement were similar for the Ohio Contrast Cards and the Pelli-Robson chart. The elders' limits of agreement were ±0.27 (Ohio Contrast Cards) and ±0.28 (Pelli-Robson); the students' limits of agreement were ±0.42 (Ohio Contrast Cards) and ±0.51 (Pelli-Robson). However, Ohio Contrast Card results were 0.41 log10 Michelson units more sensitive than the Pelli-Robson chart (over one line on the Pelli-Robson chart) for the elders and 0.90 log10 Michelson units (three lines on the Pelli-Robson chart) more sensitive for the elders (0.11 and 0.6 log10 Weber units, respectively). The Pelli-Robson results were correlated with letter acuities and Ohio Contrast Card results for both groups, and the Ohio Contrast Card results were correlated with Teller Acuity Card acuities for the elders. CONCLUSIONS: The Ohio Contrast Cards and Pelli-Robson chart are similarly repeatable. Both contrast sensitivity tests can provide additional clinical information that is not available through visual acuity testing, and Ohio Contrast Card may provide additional information not available from the Pelli-Robson chart.

Technical Report: A New Method for Determining Image Distance for Stand Magnifiers.

SIGNIFICANCE: Low vision rehabilitation clinicians must sometimes evaluate stand magnifiers to determine their true optical properties. A novel method is described for measuring the image distance of stand magnifiers. PURPOSE: We describe a new method for determining the image distance of stand magnifiers, which has some advantages over previously described methods. METHODS: Diverging light emerging from a stand magnifier is brought to a focus on the ceiling or other flat surface using convex lenses placed on the top of the stand magnifier lens. Knowing the power of this convex lens and the distance from the magnifier lens to the imaging surface, one can calculate the degree to which the emerging light is diverging and, from that, the image distance. Each author evaluated three stand magnifiers using this method and compared our results with each other and with the values for image distance published by the manufacturer. RESULTS: Our method produced measurements that were consistent between three clinicians, with emerging divergence values differing by no more than 0.37 D and image distance differing by 0.6 to 3.1 cm for the three magnifiers evaluated. Our measured values also corresponded favorably with the published image distances listed in the manufacturer's catalog, deviating by a maximum of 3.7 cm and a mean of 1.3 cm. When the manufacturer's image distances were converted to dioptric divergence, our measurements varied by a maximum of 0.48 D and a mean of 0.17 D. CONCLUSIONS: Our method provides an expedient and clinically accurate way to evaluate the divergence and image distance of a stand magnifier. Knowing the image distance is valuable by itself, but the divergence of the emerging light is also critical in determining the stand magnifier's enlargement ratio.

Optometric Applications for Three-dimensional Printing: A Technical Report from Low Vision Rehabilitation Practice.

SIGNIFICANCE: Delivering personalized three-dimensional (3D)-printed solutions for our patients is easier now than it has ever been. This technological revolution makes things possible that it would be extremely challenging to achieve using traditional approaches. PURPOSE: The purpose of this study was to increase awareness among the optometric and vision science community of opportunities to apply 3D printing to enhance clinical practice and research. METHODS: A widely available fused deposition modeling 3D printing approach was used to fabricate several plastic items for use in optometric practice and low vision rehabilitation. RESULTS: The authors will share nine optometric extensions of 3D printing: (1) an attachment for glare-acuity testing, (2) a disposable cover paddle to limit infection spread for red-eye visits, (3) ophthalmic equipment repair/modification, (4) ophthalmic lens thickness calipers, (5) NoIR lens filter flipper, (6) Optivisor faceplate, (7) EasyPocket lanyard card holder, (8) dome magnifier handle, and (9) a phoropter near card holder. CONCLUSIONS: Designing customized solutions and problem-solving for our patients and offices are becoming easier to do using 3D printing every year. The possible applications for this technology are constantly being expanded. This technology allows for cost-effective production of solutions, some of which would not be feasible otherwise.

B-cell differentiation and IL-21 response in IL2RG/JAK3 SCID patients after hematopoietic stem cell transplantation.

Allogeneic hematopoietic stem cell transplant (HSCT) typically results in donor T-cell engraftment and function in patients with severe combined immunodeficiency (SCID), but humoral immunity, particularly when using donors other than matched siblings, is variable. B-cell function after HSCT for SCID depends on the genetic cause, the use of pre-HSCT conditioning, and whether donor B-cell chimerism is achieved. Patients with defects in IL2RG or JAK3 undergoing HSCT without conditioning often have poor B-cell function post-HSCT, perhaps as a result of impairment of IL-21 signaling in host-derived B cells. To investigate the effect of pre-HSCT conditioning on B-cell function, and the relationship of in vitro B-cell function to clinical humoral immune status, we analyzed 48 patients with IL2RG/JAK3 SCID who were older than 2 years after HSCT with donors other than matched siblings. T follicular helper cells (TFH) developed in these patients with kinetics similar to healthy young children; thus, poor B-cell function could not be attributed to a failure of TFH development. In vitro differentiation of B cells into plasmablasts and immunoglobulin secretion in response to IL-21 strongly correlated with the use of conditioning, donor B-cell engraftment, freedom from immunoglobulin replacement, and response to tetanus vaccine. Patients receiving immunoglobulin replacement who had normal serum immunoglobulin M showed poor response to IL-21 in vitro, similar to those with low serum IgM. In vitro response of B cells to IL-21 may predict clinically relevant humoral immune function in patients with IL2RG/JAK3 SCID after HSCT.

The Ohio Contrast Cards: Visual Performance in a Pediatric Low-vision Site.

SIGNIFICANCE: This report describes the first clinical use of the Ohio Contrast Cards, a new test that measures the maximum spatial contrast sensitivity of low-vision patients who cannot recognize and identify optotypes and for whom the spatial frequency of maximum contrast sensitivity is unknown. PURPOSE: To compare measurements of the Ohio Contrast Cards to measurements of three other vision tests and a vision-related quality-of-life questionnaire obtained on partially sighted students at Ohio State School for the Blind. METHODS: The Ohio Contrast Cards show printed square-wave gratings at very low spatial frequency (0.15 cycle/degree). The patient looks to the left/right side of the card containing the grating. Twenty-five students (13 to 20 years old) provided four measures of visual performance: two grating card tests (the Ohio Contrast Cards and the Teller Acuity Cards) and two letter charts (the Pelli-Robson contrast chart and the Bailey-Lovie acuity chart). Spatial contrast sensitivity functions were modeled using constraints from the grating data. The Impact of Vision Impairment on Children questionnaire measured vision-related quality of life. RESULTS: Ohio Contrast Card contrast sensitivity was always less than 0.19 log10 units below the maximum possible contrast sensitivity predicted by the model; average Pelli-Robson letter contrast sensitivity was near the model prediction, but 0.516 log10 units below the maximum. Letter acuity was 0.336 logMAR below the grating acuity results. The model estimated the best testing distance in meters for optimum Pelli-Robson contrast sensitivity from the Bailey-Lovie acuity as distance = 1.5 - logMAR for low-vision patients. Of the four vision tests, only Ohio Contrast Card contrast sensitivity was independently and statistically significantly correlated with students' quality of life. CONCLUSIONS: The Ohio Contrast Cards combine a grating stimulus, a looking indicator behavior, and contrast sensitivity measurement. They show promise for the clinical objective of advising the patient and his/her caregivers about the success the patient is likely to enjoy in tasks of everyday life.

Human HOIP and LUBAC deficiency underlies autoinflammation, immunodeficiency, amylopectinosis, and lymphangiectasia.

Inherited, complete deficiency of human HOIL-1, a component of the linear ubiquitination chain assembly complex (LUBAC), underlies autoinflammation, infections, and amylopectinosis. We report the clinical description and molecular analysis of a novel inherited disorder of the human LUBAC complex. A patient with multiorgan autoinflammation, combined immunodeficiency, subclinical amylopectinosis, and systemic lymphangiectasia, is homozygous for a mutation in HOIP, the gene encoding the catalytic component of LUBAC. The missense allele (L72P, in the PUB domain) is at least severely hypomorphic, as it impairs HOIP expression and destabilizes the whole LUBAC complex. Linear ubiquitination and NF-κB activation are impaired in the patient's fibroblasts stimulated by IL-1ß or TNF. In contrast, the patient's monocytes respond to IL-1ß more vigorously than control monocytes. However, the activation and differentiation of the patient's B cells are impaired in response to CD40 engagement. These cellular and clinical phenotypes largely overlap those of HOIL-1-deficient patients. Clinical differences between HOIL-1- and HOIP-mutated patients may result from differences between the mutations, the loci, or other factors. Our findings show that human HOIP is essential for the assembly and function of LUBAC and for various processes governing inflammation and immunity in both hematopoietic and nonhematopoietic cells.

A modified γ-retrovirus vector for X-linked severe combined immunodeficiency.

BACKGROUND: In previous clinical trials involving children with X-linked severe combined immunodeficiency (SCID-X1), a Moloney murine leukemia virus-based γ-retrovirus vector expressing interleukin-2 receptor γ-chain (γc) complementary DNA successfully restored immunity in most patients but resulted in vector-induced leukemia through enhancer-mediated mutagenesis in 25% of patients. We assessed the efficacy and safety of a self-inactivating retrovirus for the treatment of SCID-X1. METHODS: We enrolled nine boys with SCID-X1 in parallel trials in Europe and the United States to evaluate treatment with a self-inactivating (SIN) γ-retrovirus vector containing deletions in viral enhancer sequences expressing γc (SIN-γc). RESULTS: All patients received bone marrow-derived CD34+ cells transduced with the SIN-γc vector, without preparative conditioning. After 12.1 to 38.7 months of follow-up, eight of the nine children were still alive. One patient died from an overwhelming adenoviral infection before reconstitution with genetically modified T cells. Of the remaining eight patients, seven had recovery of peripheral-blood T cells that were functional and led to resolution of infections. The patients remained healthy thereafter. The kinetics of CD3+ T-cell recovery was not significantly different from that observed in previous trials. Assessment of insertion sites in peripheral blood from patients in the current trial as compared with those in previous trials revealed significantly less clustering of insertion sites within LMO2, MECOM, and other lymphoid proto-oncogenes in our patients. CONCLUSIONS: This modified γ-retrovirus vector was found to retain efficacy in the treatment of SCID-X1. The long-term effect of this therapy on leukemogenesis remains unknown. (Funded by the National Institutes of Health and others; ClinicalTrials.gov numbers, NCT01410019, NCT01175239, and NCT01129544.).

Ultra-low dose of Mycobacterium tuberculosis aerosol creates partial infection in mice.

A murine low dose (LD) aerosol model is commonly used to test tuberculosis vaccines. Doses of 50-400 CFU (24h lung CFU) infect 100% of exposed mice. The LD model measures progression from infection to disease based on organ CFU at defined time points. To mimic natural exposure, we exposed mice to an ultra-low dose (ULD) aerosol. We estimated the presented dose by sampling the aerosol. Female C57BL/6 mice were exposed to Mycobacterium tuberculosis H37Rv aerosol at 1.0, 1.1, 1.6, 5.4, and 11 CFU presented dose, infecting 27%, 36%, 36%, 100%, and 95% of mice, respectively. These data are compatible with a stochastic infection event (Poisson distribution, weighted R(2)=0.97) or with a dose-response relationship (sigmoid distribution, weighted R(2)=0.97). Based on the later assumption, the ID50 was 1.6CFU presented dose (95% confidence interval, 1.2-2.1). We compared organ CFU after ULD and LD aerosols (5.4 vs. 395CFU presented dose). Lung burden was 30-fold lower in the ULD model at 4 weeks (3.4 vs. 4.8 logs, p<0.001) and 18 weeks (≤3.6 vs. 5.0 logs, p=0.01). Mice exposed to ULD aerosols as compared to LD aerosols had greater within-group CFU variability. Exposure to ULD aerosols leads to infection in a subset of mice, and to persistently low organ CFU. The ULD aerosol model may resemble human pulmonary tuberculosis more closely than the standard LD model, and may be used to identify host or bacterial factors that modulate the initial infection event.

Sampling port for real-time analysis of bioaerosol in whole body exposure system for animal aerosol model development.

INTRODUCTION: Multiple factors influence the viability of aerosolized bacteria. The delivery of aerosols is affected by chamber conditions (humidity, temperature, and pressure) and bioaerosol characteristics (particle number, particle size distribution, and viable aerosol concentration). Measurement of viable aerosol concentration and particle size is essential to optimize viability and lung delivery. The Madison chamber is widely used to expose small animals to infectious aerosols. METHODS: A multiplex sampling port was added to the Madison chamber to measure the chamber conditions and bioaerosol characteristics. Aerosols of three pathogens (Bacillus anthracis, Yersinia pestis, and Mycobacterium tuberculosis) were generated under constant conditions and their bioaerosol characteristics were analyzed. Airborne microbes were captured using an impinger or BioSampler. The particle size distribution of airborne microbes was determined using an aerodynamic particle sizer (APS). Viable aerosol concentration, spray factor (viable aerosol concentration/inoculum concentration), and dose presented to the mouse were calculated. Dose retention efficiency and viable aerosol retention rate were calculated from the sampler titers to determine the efficiency of microbe retention in lungs of mice. RESULTS: B. anthracis, Y. pestis, and M. tuberculosis aerosols were sampled through the port. The count mean aerodynamic sizes were 0.98, 0.77, and 0.78 µm with geometric standard deviations of 1.60, 1.90, and 2.37, and viable aerosol concentrations in the chamber were 211, 57, and 1 colony-forming unit (CFU)/mL, respectively. Based on the aerosol concentrations, the doses presented to mice for the three pathogens were 2.5e5, 2.2e4 and 464 CFU. DISCUSSION: Using the multiplex sampling port we determined whether the animals were challenged with an optimum bioaerosol based on dose presented and respirable particle size.

Association between 16S-23S internal transcribed spacer sequence groups of Mycobacterium avium complex and pulmonary disease.

Organisms within the Mycobacterium avium complex (MAC) may have differential virulence. We compared 33 subjects with MAC pulmonary disease to 75 subjects with a single positive culture without disease. M. avium isolates were significantly more likely to be associated with MAC pulmonary disease (odds ratio = 5.14, 95% confidence interval = 1.25 to 22.73) than M. intracellulare.

Study of the role of CCR5 in a mouse model of intranasal challenge with Yersinia pestis.

CCR5 is a chemokine receptor used by HIV-1 to enter cells and has recently been found to act as a pathogen associated molecule pattern receptor. Current positive selection for the high frequency of a CCR5-Delta32 allele in humans has been attributed to resistance to HIV, smallpox, and plague infections. Using an intranasal mouse model of Y. pestis infection, we have found that lack of CCR5 does not enhance host resistance to Y. pestis infection and that CCR5-mediated responses might have a protective role. CCR5-/- mice exhibited higher levels of circulating RANTES and MIP-1alpha than those exhibited by wild-type mice at the baseline and throughout the course of Y. pestis infection. High levels of RANTES and MIP-1alpha, which are CCR5 ligands that mediate Natural Killer cell migration, may reflect compensation for the absence of CCR5 signaling.

Yersinia pestis kills Caenorhabditis elegans by a biofilm-independent process that involves novel virulence factors.

It is known that Yersinia pestis kills Caenorhabditis elegans by a biofilm-dependent mechanism that is similar to the mechanism used by the pathogen to block food intake in the flea vector. Using Y. pestis KIM 5, which lacks the genes that are required for biofilm formation, we show that Y. pestis can kill C. elegans by a biofilm-independent mechanism that correlates with the accumulation of the pathogen in the intestine. We used this novel Y. pestis-C. elegans pathogenesis system to show that previously known and unknown virulence-related genes are required for full virulence in C. elegans. Six Y. pestis mutants with insertions in genes that are not related to virulence before were isolated using C. elegans. One of the six mutants carried an insertion in a novel virulence gene and showed significantly reduced virulence in a mouse model of Y. pestis pathogenesis. Our results indicate that the Y. pestis-C. elegans pathogenesis system that is described here can be used to identify and study previously uncharacterized Y. pestis gene products required for virulence in mammalian systems.