Analytic validation of NeXT Dx™, a comprehensive genomic profiling assay

We describe the analytic validation of NeXT Dx, a comprehensive genomic profiling assay to aid therapy and clinical trial selection for patients diagnosed with solid tumor cancers. Proprietary methods were utilized to perform whole exome and whole transcriptome sequencing for detection of single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations (CNAs), and gene fusions, and determination of tumor mutation burden and microsatellite instability. Variant calling is enhanced by sequencing a patient-specific normal sample from, for example, a blood specimen. This provides highly accurate somatic variant calls as well as the incidental reporting of pathogenic and likely pathogenic germline alterations. Fusion detection via RNA sequencing provides more extensive and accurate fusion calling compared to DNA-based tests. NeXT Dx features the proprietary Accuracy and Content Enhanced technology, developed to optimize sequencing and provide more uniform coverage across the exome. The exome was validated at a median sequencing depth of >500x. While variants from 401 cancer-associated genes are currently reported from the assay, the exome/transcriptome assay is broadly validated to enable reporting of additional variants as they become clinically relevant. NeXT Dx demonstrated analytic sensitivities as follows: SNVs (99.4%), indels (98.2%), CNAs (98.0%), and fusions (95.8%). The overall analytic specificity was >99.0%.

Abstract 1334: A diagnostic platform for precision cancer therapy enabling composite biomarkers by combining tumor and immune features from an enhanced exome and transcriptome

There is an increasing need for more advanced, composite biomarkers that can model the complex systems biology driving response and resistance to cancer therapy. However, many cancer diagnostic platforms to date, with their focus on mutational changes in a relatively small panel of genes, provide limited data to support integrative, multidimensional biomarkers that can better predict immunotherapy response.

To enable the identification of composite biomarkers that combine tumor- and immune-related information from both DNA and RNA, we have developed ImmunoID NeXT, an enhanced exome/transcriptome-based diagnostic platform that can simultaneously profile the tumor and immune system from a single FFPE sample, across all of the approximately 20,000 genes. By co-optimizing assay and analytics design, we enable sensitive evaluation of clinically-relevant cancer biomarkers from >=25ng of co-extracted DNA/RNA, while also providing a broader evaluation of neoantigens, HLA typing and LOH, antigen processing machinery (APM), TCR/BCR repertoire, immune expression signatures, tumor-infiltrating lymphocytes (TILs), oncoviruses, and germline variants. Leveraging this expansive feature set, we developed methods that combine individual analytes to construct composite biomarker scores that correlate with immunotherapy response.

Validation of ImmunoID NeXT demonstrated high sensitivity and specificity to somatic and structural variants across ~20,000 genes at allelic fractions as low as 5%, with clinical diagnostic reporting on actionable mutations (SNVs, indels, CNAs, fusions) in 248 cancer-driver genes that have been boosted further for higher sensitivity, as well as reporting on TMB and MSI status. For neoantigen prediction, immuno-peptidomic data from monoallelic HLA-transfected cell lines were used to train neural networks to predict pMHC binding with higher precision than public tools. For TCRα/β analysis in FFPE tumor samples, strong correlation with targeted TCR kit results was shown (R^2>0.9 and >0.94). For TILs, we developed signatures for eight immune cell types, demonstrating concordance with orthogonal immunofluorescence methods. We achieved genotyping accuracy of 99.1% for HLA Class I, and 95% for HLA Class II, and have developed and verified the performance of a tool for HLA LOH detection. In a cohort of 55 late-stage melanoma patients, the integration of neoantigen burden, HLA LOH, and APM mutational data formed a composite neoantigen score that more accurately predicted response to checkpoint blockade than other markers such as TMB.

With ImmunoID NeXT, we have developed a broad diagnostic platform that can be leveraged for the development of advanced composite biomarkers (and novel resistance mechanisms) that combine both tumor and immune features from DNA and RNA; enabling more accurate stratification of patient response to immunotherapy. The platform has been validated and optimized for use with limited FFPE tissue samples, making it ideal for both research and clinical applications.

Citation Format: Robert Peter Power, Gabor Bartha, Jason Harris, Sean M. Boyle, Eric Levy, Pamela Milani, Prateek Tandon, Paul McNitt, Mandy Lee, Massimo Morra, Sejal Desai, Sebastian Salvidar, Michael J. Clark, Christian Haudenschild, Sekwon Jang, John West, Richard Chen. A diagnostic platform for precision cancer therapy enabling composite biomarkers by combining tumor and immune features from an enhanced exome and transcriptome [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1334.

Validation of an exome and transcriptome based diagnostic platform enabling clinical cancer therapy selection and emerging composite biomarkers for immunotherapy

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Background: While immunotherapy has become a pillar of cancer treatment, diagnostic biomarkers that consistently predict patient response to these therapies have remained elusive. There is an increasing need for the development of integrative, composite biomarkers that can model the complex biology driving response and/or resistance to immunotherapy more effectively than existing single-analyte approaches. However, the majority of current cancer diagnostic panels, with their focus on a small set of genes, provide limited ability to support these emerging advanced biomarkers. Methods: To address these limitations, we developed and validated NeXT Dx, a comprehensive enhanced exome and transcriptome based diagnostic platform designed to simultaneously characterize tumor and immune genomics from a single limited FFPE sample. To achieve higher accuracy and sensitivity for an exome scale diagnostic platform, we developed an augmented exome assay that improves uniformity of coverage across all ~20,000 genes, including boosted coverage of 248 clinically-relevant cancer genes. We validated this assay using genomic DNA and RNA extracted from tumor-derived cell-lines, constructs, clinical FFPE samples, and proficiency testing samples. The assay utilizes > = 25ng of co-extracted DNA and RNA which were sequenced using Illumina NovaSeq instruments at our CAP-accredited, CLIA-certified laboratory. Additional assay enhancements for HLA, immune repertoire, and oncoviruses were designed to further optimize the platform for immunotherapy biomarker discovery applications. Results: Validation of NeXT Dx demonstrated a performance of 99.5% sensitivity and 99.8% positive predictive value (PPV) for SNVs with > = 5% AF; 98.7% sensitivity and 97.4% PPV for indels with > = 10% AF; 97.2% sensitivity and 94.6% PPV for CNAs in samples with > = 30% tumor content; 94.9% sensitivity and 94.9% PPV for fusions; and a 2.1% error rate for MSI classification. TMB was calculated using gold-standard whole exome data from SNVs and indels. Typical median coverage depth was > 1,000X for 248 clinically-relevant genes, ~300X for the remaining (whole exome) footprint. Conclusions: With NeXT Dx, we demonstrate a exome/transcriptome scale diagnostic platform that can detect current clinical biomarkers with high sensitivity as well as support emerging, advanced biomarkers that integrate across both tumor and immune features.

Abstract A051: A comprehensive, highly accurate genomics platform for precision immunotherapy: Simultaneously characterize tumors and the TME from a single FFPE sample

Immunogenomic profiling of the tumor and the tumor microenvironment (TME) is critical for identifying new biomarkers of immunotherapy response, understanding resistance, and enabling the development of personalized immunotherapies. However, running a comprehensive array of biomarker assays for each patient sample is often impractical given limited sample quantity, processing complexity, and prohibitive cost. To address these challenges, we developed a novel, augmented exome and transcriptome-based platform that simultaneously characterizes the tumor and TME from a single FFPE sample. We co-optimized the design of our sequencing assays and analytics to increase performance for the detection of somatic SNVs, indels, CNAs, and fusions across ~20,000 genes, as well as the evaluation of neoantigens, expression signatures, HLA typing and LOH, TCR/BCR repertoires, oncoviruses, tumor-infiltrating lymphocytes (TILs), clinically-actionable mutations, tumor mutational burden (TMB), and MSI status. We developed novel methods to sequence difficult regions of the exome and to extend coverage to key immunogenomic biomarkers. Analytic pipelines were designed to utilize assay optimizations to achieve higher accuracy than with other platforms. We then validated the platform for diagnostic and therapeutic use. With as little as 50ng of DNA per FFPE sample and co-extracted RNA, this platform completely covers between 17% to 40% more genes compared to a non-augmented exome, thus increasing sensitivity to somatic mutations and putative neoantigens. For neoantigen performance, we generated immune-peptidomic data from mono-allelic HLA transfected cell-lines and trained neural networks to predict neoepitope binding to MHC, demonstrating a higher precision (0.88) across alleles than publicly available tools (<0.7). For TCR alpha and beta clonotype profiling in tumor samples, we demonstrate strong correlation with the results from a targeted TCR kit (R2>0.9 and >0.94, respectively). For TILs, we developed signatures for CD4, CD8 T-cells, and other immune cells, demonstrating concordance with synthetic and CyTOF-derived validation sets. For HLA typing, we achieve an accuracy of 99.1% for HLA Class I, and 95% for HLA Class II typing calls, and have developed a novel tool for HLA LOH detection. We demonstrate sensitive detection of HPV, EBV, HCV, HTLV, and KSHV in known samples, and accurate MSI and TMB assessment. Finally, for diagnostic reporting, we achieve high sensitivity and specificity for clinically-reportable mutations comparable with diagnostic cancer panels. With this platform, we have developed a novel immunogenomics platform that can characterize both the tumor and TME from a single sample. By co-optimizing our assay and analytics for immuno-oncology, we enhance biomarker sensitivity compared to non-optimized genomics assays. Validation of the platform extends its use to diagnostics and personalized immunotherapy development.

Citation Format: Robert Power, Gabor Bartha, Jason Harris, Sean Michael Boyle, Eric Levy, Pamela Milani, Prateek Tandon, Robin Li, Manjula Chinnappa, Paul McNitt, Rena McClory, Massimo Morra, Sebastian Saldivar, Michael Clark, Christian Haudenschild, Erin Newburn, Christelle Johnson, John West. A comprehensive, highly accurate genomics platform for precision immunotherapy: Simultaneously characterize tumors and the TME from a single FFPE sample [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A051. doi:10.1158/1535-7163.TARG-19-A051

Adhesion and Function of Rat Liver Cells Adherent to Silk Fibroin/Collagen Blend Films

Collagen is often used in bioartificial livers as a biomimetic coating to promote liver cell adhesion and differentiation. Animal proteins are expensive and expose the host to risks of cross-species infection due to contamination with prions. Silk fibroin (SF) is a biocompatible protein produced by Bombyx mori silk worms and possibly an alternative to collagen. We prepared SF-collagen blend films with different SF content adherent to the bottom of standard tissue culture dishes, and characterized their surface morphology by SEM, their wettability and examined them for their capacity to support rat liver cell adhesion and metabolism. Cell metabolism was characterized by estimating the rate at which cells eliminated ammonia and synthesized urea for up to 48h of culture. SF-containing films were smooth, clear and more wettable than collagen. Cells readily adhered, formed junctions and small size aggregates on all films. As many cells adhered on SF as on collagen films. Cell adhesion to high collagen content blend films could not be reliably estimated because cells dwelt in the large cavities in the film. The effect of SF on cell metabolism differed with the investigated metabolic pathway. However, cells on SF-containing films eliminated ammonia and synthesized urea at rates generally comparable to, for urea synthesis at times higher than, that of cells on collagen. These results suggest that silk fibroin is a suitable substratum for liver cell attachment and culture, and a potential alternative to collagen as a biomimetic coating.

A variant by any name: quantifying annotation discordance across tools and clinical databases

Background

Clinical genomic testing is dependent on the robust identification and reporting of variant-level information in relation to disease. With the shift to high-throughput sequencing, a major challenge for clinical diagnostics is the cross-identification of variants called on their genomic position to resources that rely on transcript- or protein-based descriptions.

Methods

We evaluated the accuracy of three tools (SnpEff, Variant Effect Predictor, and Variation Reporter) that generate transcript and protein-based variant nomenclature from genomic coordinates according to guidelines by the Human Genome Variation Society (HGVS). Our evaluation was based on transcript-controlled comparisons to a manually curated set of 126 test variants of various types drawn from data sources, each with HGVS-compliant transcript and protein descriptors. We further evaluated the concordance between annotations generated by Snpeff and Variant Effect Predictor and those in major germline and cancer databases: ClinVar and COSMIC, respectively.

Results

We find that there is substantial discordance between the annotation tools and databases in the description of insertions and/or deletions. Using our ground truth set of variants, constructed specifically to identify challenging events, accuracy was between 80 and 90% for coding and 50 and 70% for protein changes for 114 to 126 variants. Exact concordance for SNV syntax was over 99.5% between ClinVar and Variant Effect Predictor and SnpEff, but less than 90% for non-SNV variants. For COSMIC, exact concordance for coding and protein SNVs was between 65 and 88% and less than 15% for insertions. Across the tools and datasets, there was a wide range of different but equivalent expressions describing protein variants.

Conclusions

Our results reveal significant inconsistency in variant representation across tools and databases. While some of these syntax differences may be clear to a clinician, they can confound variant matching, an important step in variant classification. These results highlight the urgent need for the adoption and adherence to uniform standards in variant annotation, with consistent reporting on the genomic reference, to enable accurate and efficient data-driven clinical care.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-016-0396-7) contains supplementary material, which is available to authorized users.

A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories

PURPOSE

While the diagnostic success of genomic sequencing expands, the complexity of this testing should not be overlooked. Numerous laboratory processes are required to support the identification, interpretation and reporting of clinically significant variants. This study aimed to examine workflow and reporting procedures among US laboratories to highlight shared practices and identify areas in need of standardization.

METHODS

Surveys and follow-up interviews were conducted with laboratories offering exome and/or genome sequencing, to support a research program or for routine clinical services. The 73-item survey elicited multiple choice and free text responses, later clarified with phone interviews.

RESULTS

Twenty-one laboratories participated. Practices highly concordant across all groups included: consent documentation, multi-person case review, and enabling patient opt-out of incidental or secondary findings analysis. Noted divergence included use of phenotypic data to inform case analysis and interpretation, and reporting of case-specific quality metrics and methods. Few laboratory policies detailed procedures for data reanalysis, data sharing or patient access to data.

CONCLUSION

This study provides an overview of practices and policies of experienced exome and genome sequencing laboratories. The results enable broader consideration of which practices are becoming standard approaches, where divergence remains, and areas development of best practice guidelines may be helpful.

Abstract 4744: Solving genomic assay trade-offs with an optimized, extended cancer gene panel for research and clinical applications

Choosing a genomic assay for cancer research is complicated by trade-offs. Cancer gene panels are a common choice, but they target mutational hotspots in a relatively small number of genes, often for cancers that are most commonly tested and that have common genetic etiologies. A common alternative is exome sequencing, which includes all the coding genes but, due to its larger genomic footprint, cannot reach the same depths as panels and therefore is less able to deal with low tumor purity and heterogeneity. Whole genome sequencing trades off very shallow depth and coverage over vast regions of uninterpretable genomic sequence in exchange for the identification of intergenic variants and structural variant breakpoints. All of these assays can be supplemented with RNA sequencing in order to capture gene fusions, allelic expression, splice isoforms, and gene expression. RNAseq comes with its own costs: the need to extract RNA from the same tissue, the need to perform a second assay, and the need to analyze a very different type of data from DNA sequencing.

The trade-offs generally come down to three major issues: depth of sequencing, specific genes targeted, and cost. To solve these, we designed an extended, optimized cancer gene panel facilitating high depth sequencing at low cost. We started by identifying a comprehensive list of over 1,300 cancer genes. These genes were chosen through exhaustive cancer gene database and literature curation, and include genes from all major cancer pathways and from the Cancer Gene Census. We then took this gene list and applied an augmented targeting design strategy that we have previously used to create an augmented exome enrichment platform which fills in gaps that standard technical exomes miss.

To validate the panel and analysis, we identified test samples including well-described cancer cell lines, cell line mixtures with engineered cancer variations, and formalin-fixed neoplastic tissues. We then performed a series of tests with these samples to measure the panel's small variant sensitivity and specificity, gauge its limits of detection, validate the detection of gene fusions, and demonstrate its ability to identify copy number alterations and loss of heterozygosity. In engineered cell lines, we detected 100% of small variants down to 5% allele frequency. We also mixed the cancer cell lines in various ratios and found similarly high sensitivity as well as very high specificity for small variant detection. We further compared our structural variation calls in the DNA and our fusion calls in the RNA with known data and found that we had very high concordance with known variations.

These studies demonstrate that an extended, augmented cancer gene panel strategy solves many genomic assay trade-offs and leads to high accuracy and variant yield for cancer research applications.

Citation Format: Michael J. Clark, Sean M. Boyle, Elena Helman, Shujun Luo, Gabor Bartha, Massimo Morra, Anil Patwardhan, Christian Haudenschild, Mirian Karbelashvili, Parin Sripakdeevong, Jason Harris, Deanna Church, Stephen Chervitz, John West, Richard Chen. Solving genomic assay trade-offs with an optimized, extended cancer gene panel for research and clinical applications. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4744. doi:10.1158/1538-7445.AM2015-4744

Achieving high-sensitivity for clinical applications using augmented exome sequencing

Background

Whole exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet the variation of coverage and sensitivity over medically relevant parts of the genome remains poorly understood. Several sequencing-based assays continue to provide coverage that is inadequate for clinical assessment.

Methods

Using sequence data obtained from the NA12878 reference sample and pre-defined lists of medically-relevant protein-coding and noncoding sequences, we compared the breadth and depth of coverage obtained among four commercial exome capture platforms and whole genome sequencing. In addition, we evaluated the performance of an augmented exome strategy, ACE, that extends coverage in medically relevant regions and enhances coverage in areas that are challenging to sequence. Leveraging reference call-sets, we also examined the effects of improved coverage on variant detection sensitivity.

Results

We observed coverage shortfalls with each of the conventional exome-capture and whole-genome platforms across several medically interpretable genes. These gaps included areas of the genome required for reporting recently established secondary findings (ACMG) and known disease-associated loci. The augmented exome strategy recovered many of these gaps, resulting in improved coverage in these areas. At clinically-relevant coverage levels (100 % bases covered at ≥20×), ACE improved coverage among genes in the medically interpretable genome (>90 % covered relative to 10-78 % with other platforms), the set of ACMG secondary finding genes (91 % covered relative to 4-75 % with other platforms) and a subset of variants known to be associated with human disease (99 % covered relative to 52-95 % with other platforms). Improved coverage translated into improvements in sensitivity, with ACE variant detection sensitivities (>97.5 % SNVs, >92.5 % InDels) exceeding that observed with conventional whole-exome and whole-genome platforms.

Conclusions

Clinicians should consider analytical performance when making clinical assessments, given that even a few missed variants can lead to reporting false negative results. An augmented exome strategy provides a level of coverage not achievable with other platforms, thus addressing concerns regarding the lack of sensitivity in clinically important regions. In clinical applications where comprehensive coverage of medically interpretable areas of the genome requires higher localized sequencing depth, an augmented exome approach offers both cost and performance advantages over other sequencing-based tests.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-015-0197-4) contains supplementary material, which is available to authorized users.

Auto-antibody production and glomerulonephritis in congenic Slamf1-/- and Slamf2-/- [B6.129] but not in Slamf1-/- and Slamf2-/- [BALB/c.129] mice

Several genes in an interval of human and mouse chromosome 1 are associated with a predisposition for systemic lupus erythematosus. Congenic mouse strains that contain a 129-derived genomic segment, which is embedded in the B6 genome, develop lupus because of epistatic interactions between the 129-derived and B6 genes, e.g. in B6.129chr1b mice. If a gene that is located on chromosome 1 is altered through homologous recombination in 129-derived embryonic stem cells (ES cells) and if the resultant knockout mouse is backcrossed with B6, interpretation of the phenotype of the mutant mouse may be affected by epistatic interactions between the 129 and B6 genomes. Here, we report that knockout mice of two adjacent chromosome 1 genes, Slamf1(-/-) and Slamf2(-/-), which were generated with the same 129-derived ES cell line, develop features of lupus, if backcrossed on to the B6 genetic background. By contrast, Slamf1(-/-) [BALB/c.129] and Slamf2(-/-) [BALB/c.129] do not develop disease. Surprisingly, Slamf1(-/-) [B6.129] mice develop both auto-antibodies and glomerulonephritis between 3 and 6 months of age, while disease fully develops in Slamf1(-/-) [B6.129] mice after 9-14 months. Functional analyses of CD4(+) T cells reveals that Slamf2(-/-) T cells are resistant to tolerance induction in vivo. We conclude that the Slamf2(-/-) mutation may have a unique influence on T-cell tolerance and lupus.

Gene expression of markers of osteogenic differentiation of human mesenchymal cells on collagen I-modified microrough titanium surfaces

Microrough, doubly acid etched titanium surfaces (Ti) were further modified by amination and covalent coupling of fibrillar collagen type I (ColTi). Human Mesenchymal Cells (HMC) adhesion and growth, and relevant osteogenic differentiation in nonosteogenic (basal) medium were evaluated by fluorescence microscopy, scanning electron microscopy, and RT-PCR for a three-week period. Results show strongly enhanced HMC adhesion and cell density at short experimental time on ColTi, together with complete spreading of the cell body over the microrough surface topography. RT-PCR analysis of several genes involved in osteogenesis indicate, since the first week of culturing, significant progression of HMC on ColTi along the osteogenic pathway. These results indicate that the adopted process of surface immobilization of collagen, mandatory to impart collagenase resistance in implant sites, does not impair biospecific interactions between HMC and collagen. Thus, it is possible to upgrade properties arising from the control of Ti surfaces topography by surface-chemistry driven enhanced recruitment of precursor osteogenic cells and pro-osteogenic stimula.

IgA and IgG hypogammaglobulinemia in Waldenström's macroglobulinemia

BACKGROUND

Hypogammaglobulinemia is common in Waldenström's macroglobulinemia. The etiology of this finding remains unclear, but it has been speculated to be based on tumor-induced suppression of the 'uninvolved' immunoglobulin production

DESIGN AND METHODS

We evaluated the incidence of IgA and IgG hypogammaglobulinemia in 207 untreated patients with Waldenström's macroglobulinemia and investigated the associated clinicopathological findings and impact of therapy. We also sequenced eight genes (AICDA, BTK, CD40, CD154, NEMO, TACI, SH2D1A, UNG) implicated in immunoglobulin deficiency in 19 Waldenström's macroglobulinemia patients with IgA and/or IgG hypogammaglobulinemia.

RESULTS

At baseline 63.3%, 58.0% and 49.3% of the 207 patients had abnormally low serum levels of IgA, IgG, or both. No association between IgA and IgG hypogammaglobulinemia and disease burden, serum IgM levels, beta(2)-microglobulin, International Prognostic Scoring System score, or incidence of recurrent infections was observed, although the presence of adenopathy and/or splenomegaly was associated with a lower incidence of hypogammaglobulinemia. Lower IgA and IgG levels were associated with disease progression in patients managed with a 'watch and wait' strategy. IgA and/or IgG levels remained abnormally low despite response to treatment, including complete remissions. A missense mutation in the highly conserved catalytic site of UNG was observed in a patient with hypogammaglobulinemia, warranting further study of this pathway in Waldenström's macroglobulinemia.

CONCLUSIONS

IgA and IgG hypogammaglobulinemia is common in Waldenström's macroglobulinemia and persists despite therapeutic intervention and response. IgA and IgG hypogammaglobulinemia does not predict the risk of recurrent infections in patients with Waldenström's macroglobulinemia, although lower levels of serum IgA and IgG are associated with disease progression in Waldenström's macroglobulinemia patients being managed with a 'watch and wait' strategy.

Inhibition of LPS-induced proinflammatory responses of J774.2 macrophages by immobilized enzymatically tailored pectins

The surface of an implant device can be modified by immobilizing biological molecules on it to improve its integration into the host tissue. We have previously demonstrated that enzymatically tailored plant pectins are promising nanocoatings for biomaterials. This study investigates whether a coating of modified hairy region (rhamnogalacturonan-I) from apple pectin (MHR-alpha) which has anti-adhesive properties can inhibit the generation of inflammatory mediators by lipopolysaccharide (LPS)-activated macrophages. For that purpose, J774.2 murine macrophages were cultured for 24h on MHR-alpha-coated Petri dishes and tissue culture polystyrene controls, with and without LPS. Cell morphology, cell growth, nitrite and TNF-alpha secretion were studied. The results indicate that MHR-alpha coating inhibits the LPS-induced activation of macrophages.

Biomaterials surface characterization and modification

This paper presents several examples of recent work in the field of surface modification and characterization of biomaterials. Due to the explosion of techniques and approaches in this area, a complete review would be unmanageable in a single paper. Rather selected examples taken from such different areas as bone-contacting devices, drug eluting stents, and immobilization of novel biomolecules are presented. The aim is to place the existing and quickly developing background of analytical and synthetic biomaterial surface science into the current perspective of this rapidly evolving discipline.

Advancements in carbohydrate bioactivity and implications for the surface modification of biomaterials

This paper reviews recent advancements in the field of bioactive plant polysaccharides, and relevant implications forthe surface modification of medical devices. A number of complex plant polysaccharides exist, that display, for example, anti-inflammatoryactivity or specific effects on cultured mammalian cells. Advancements in the separation and purification of complex plant polysaccharides such as pectins, are paving the way for a conscious exploitation of some of these properties. Suitable immobilization methods and preliminary results on biological activity of surface-linked plant pectic polysaccharides are reviewed.

Effects of molecular weight and surface functionalization on surface composition and cell adhesion to Hyaluronan coated titanium

This paper describes the effect of surface functionalization on surface composition and cell adhesion to titanium samples by high and low molecular weight Hyaluronan (HA). HA was covalently linked to aminated Ti surfaces obtained by two different surface functionalization techniques, that is polyethyleneimine (PEI) adsorption and deposition from allylamine plasma. The two approaches yield very different surface densities of available amino groups, affecting this way the number and frequency of surface-HA bonds and the configurational freedom of the latter. Results of cell adhesion test are dependent on the surface functionalization approach adopted, low molecular weight HA coupled to PEI functionalized Ti does not yield the same degree of resistance to cell adhesion found on other samples. These results indicate that the details of the surface functionalization step are crucial for surface engineering of implant devices by biological molecules.

Physical-chemical and biological characterization of silk fibroin-coated porous membranes for medical applications

Membranes in artificial organs and scaffolds for tissue engineering are often coated with biomimetic molecules (e.g., collagen) to improve their biocompatibility and promote primary cell adhesion and differentiation. However, animal proteins are expensive and may be contaminated with prions. Silk fibroin (SF) made by Bombyx Mori silk worms, used as a scaffold or grafted to other polymers, reportedly promotes the adhesion and growth of many human cell types. This paper describes how commercial porous membranes were physically coated with SF, and their physical-chemical properties were characterized by SEM, AFM, tensile stress analysis and dynamic contact angle measurements. The effect of the SF coating on membrane biocompatibility and resistance to bacterial colonization is also examined. The proposed technique yields SF coats of different thickness that strengthen the membranes and make their surface remarkably more wettable. The SF coat is not cytotoxic, and promotes the adhesion and proliferation of an immortalized fibroblast cell line. Similarly to collagen, SF-coated membranes also exhibit a much better resistance to the adhesion of S. epidermidis bacteria than uncoated membranes. These preliminary results suggest that SF is a feasible alternative to collagen as a biomimetic coating for 3D scaffolds for tissue engineering or bioartificial (as well as artificial) prosthesis.

Biochemical modification of titanium surfaces: peptides and ECM proteins

This paper reviews current approaches to the enhancement of bone regeneration at the interface with implant devices, by immobilization of biomolecules to titanium surfaces. In particular, techniques based on surface linking of peptides or extracellular matrix (ECM) proteins are reviewed, trying to describe surface modification approaches and to present results of chemico-physical and biological evaluations, both in vitro and in vivo. Based on existing literature, surface modification by peptides or ECM proteins appears as an effective way to stimulate bone regeneration over that provided by titanium, as suggested by basic studies and in vitro results and confirmed by in vivo findings.

Elevated plasma homocysteine in acute stroke was not associated with severity and outcome: stronger association with small artery disease

Homocysteine increases in the acute phase of ischaemic stroke and from the acute to the convalescent phase, suggesting that hyper-homocysteinaemia may be a consequence rather than a causal factor. Therefore we measured homocysteine plasma levels in stroke patients in order to investigate possible correlations of homocysteine with stroke severity and clinical outcome. Further we looked for eventual differences in stroke subtypes. We prospectively studied plasma homocysteine levels in acute stroke patients admitted to the stroke unit of our department. Seven hundred and seventy-five ischaemic stroke patients, 39 cerebral haemorrhages and 421 healthy control subjects have been enrolled. Stroke severity and clinical outcome were measured with the Scandinavian Stroke Scale, the Rankin Scale and the Barthel Index. Stroke severity by linear stepwise regression analysis was not an independent determinant of plasma homocysteine levels. Homocysteine was not correlated with outcome measured by the Barthel Index. Mean plasma homocysteine of both ischaemic and haemorrhagic stroke was significantly higher than controls (p<0.05). Homocysteine had an adjusted odds ratios (OR) of 4.2 (95% CI 2.77-6.54) for ischaemic stroke and of 3.69 (95% CI 1.90-7.17) for haemorrhagic stroke. Compared with the lowest quartile, the upper quartile was associated with an adjusted OR of ischaemic stroke due to small artery disease of 17.4 (95% CI 6.8-44.3). Homocysteine in the acute phase of stroke was not associated with stroke severity or outcome. Elevated plasma homocysteine in the acute phase of stroke was associated with both ischaemic and haemorrhagic stroke. Higher levels are associated with higher risk of small artery disease subtype of stroke.

Collagen I-coated titanium surfaces: Mesenchymal cell adhesion andin vivo evaluation in trabecular bone implants

The goal of the study was the evaluation of the effect of modification of titanium implants by acrylic acid surface grafting-collagen I coupling. Tests were performed on titanium samples treated by galvanostatic anodization to create a porous surface topography. Surface characterization by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM) confirms the biochemical modification of the surface and shows a surface topography characterized by pores mostly below 1 mum diameter. In vitro evaluation involving human mesenchymal cells shows enhanced cell growth on collagen coated surfaces as compared to titanium ones. Four weeks in vivo evaluation of implants in rabbit femur trabecular bone shows improvements of bone-to-implant contact, while improvement of bone ingrowth is slightly not significant (p = 0.056), when compared to the control. Overall, these data indicate that integration in trabecular, or cancellous, bone can be enhanced by the surface collagen layer, confirming previous findings obtained by modification of machined surfaces by the same approach in cortical bone implants.

[The Dialysis Outcomes and Practice Patterns Study (DOPPS): results of the Italian cohort]

BACKGROUND

The Dialysis Outcomes and Practice Patterns Study (DOPPS) is an international prospective, longitudinal, observational study examining the relationship between dialysis unit practices and outcomes for hemodialysis (HD) patients in seven developed countries France, Germany, Italy, Spain, United Kingdom, Japan and the United States. Results of the DOPPS in Italy are the subject of this report.

METHODS

A national representative sample of 20 dialysis units (21 in Germany) was randomly selected in each of the European DOPPS countries (Euro-DOPPS). In these units, the HD in-center patients were included on a facility census, and their survival rates continuously monitored. A representative sample of incident (269 in Italy, 1553 in the Euro-DOPPS) and prevalent (600 in Italy, 3038 in the Euro-DOPPS) patients was randomly selected from the census for more detailed longitudinal investigation with regard to medical history, laboratory values and hospital admission.

RESULTS

Comparing the Italian and Euro-DOPPS cohorts we found comparable mean age for prevalent patients (61.4 vs. 59.5 yrs), but incident patients were older in Italy. Italian prevalent patients had less cardiovascular disease, more satisfactory nutritional status and more frequent use of native vascular access. These data were associated with a comparable mortality (15.7 vs. 16.3 deaths/100 patient yrs), but morbidity was lower in Italy. Kt/V levels were comparable in the two cohorts (1.32 vs. 1.37), but 35% of Italian patients showed a Kt/V below the recommended target. Moreover, hemoglobin levels were below 11 g/dL in 60% of Italian patients.

CONCLUSIONS

The DOPPS results bring to light several positive aspects and the opportunity for further possible improvements for Italian patients, but at the same time highlight some critical points that could represent a risk for dialysis quality.

Cutting Edge: The SLAM Family Receptor Ly108 Controls T Cell and Neutrophil Functions

Ly108, a glycoprotein of the signaling lymphocytic activation molecule family of cell surface receptors expressed by T, B, NK, and APCs has been shown to have a role in NK cell cytotoxicity and T cell cytokine responses. In this study, we describe that CD4(+) T cells from mice with a targeted disruption of exons 2 and 3 of Ly108 (Ly108(DeltaE2+3)) produce significantly less IL-4 than wild-type CD4(+) cells, as judged by in vitro assays and by in vivo responses to cutaneous infection with Leishmania mexicana. Surprisingly, neutrophil functions are controlled by Ly108. Ly108(DeltaE2+3) mice are highly susceptible to infection with Salmonella typhimurium, bactericidal activity of Ly108(DeltaE2+3) neutrophils is defective, and their production of IL-6, IL-12, and TNF-alpha is increased. The aberrant bactericidal activity by Ly108(DeltaE2+3) neutrophils is a consequence of severely reduced production of reactive oxygen species following phagocytosis of bacteria. Thus, Ly108 serves as a regulator of both innate and adaptive immune responses.

Defective B cell responses in the absence of SH2D1A

More than half of patients with X-linked lympho-proliferative disease, which is caused by a defect in the intracellular adapter protein SH2D1A, suffer from an extreme susceptibility to Epstein-Barr virus. One-third of these patients, however, develop dysgammaglobulenemia without an episode of severe mononucleosis. Here we show that in SH2D1A(-/-) mice, both primary and secondary responses of all Ig subclasses are severely impaired in response to specific antigens. Because germinal centers were absent in SH2D1A(-/-) mice upon primary immunization, and because SH2D1A was detectable in wt germinal center B cells, we examined whether SH2D1A(-/-) B cell functions were impaired. Using the adoptive cotransfer of B lymphocytes from hapten-primed SH2D1A(-/-) mice with CD4(+) T cells from primed wt mice into irradiated wt mice provided evidence that signal transduction events controlled by SH2D1A are essential for B cell activities resulting in antigen specific IgG production. Defects in naive SH2D1A(-/-) B cells became evident upon cotransfer with non-primed wt CD4(+) cells into Rag2(-/-) recipients. Thus, both defective T and B cells exist in the absence of SH2D1A, which may explain the progressive dysgammaglobulinemia in a subset of X-linked lympho-proliferative disease patients without involvement of Epstein-Barr virus.

New polymers for drug delivery systems in orthopaedics: in vivo biocompatibility evaluation

The use of biodegradable polymers for drug delivery systems excluded the need for a second operation to remove the carrier. However, the development of an avascular fibrous capsule, reducing drug release, has raised concern about these polymers in terms of tissue-implant reaction. Five novel polymers were evaluated in vivo after implantation in the rat dorsal subcutis and compared to the reference polycaprolactone (PCL). Poly(cyclohexyl-sebacate) (PCS), poly(L-lactide-b-1,5-dioxepan-2-one-b-L-lactide) (PLLA-PDXO-PLLA), two 3-hydroxybutyrate-co-3-hydroxyvalerate copolymers (D400G and D600G), and a poly(organo)phosphazene (POS-PheOEt:Imidazole) specimens were histologically evaluated in terms of the inflammatory tissue thickness and vascular density at 4 and 12 weeks from surgery. The highest values of inflammatory tissue thickness were observed in D600G (P < 0.01), PCS (P < 0.001) and PLLA-PDXO-PLLA (P < 0.001) at 4 weeks, while POP-PheOEt:Imidazole showed the lowest value of inflammatory tissue thickness (P < 0.05) at 12 weeks. D400G, D600G, PLLA-PDXO-PPLA and POP-PheOEt:Imidazole showed higher (P < 0.001) values of vascular density near the implants in comparison to PCL at 4 weeks. Finally, D400G and D600G increased their vessel densities while POP-PheOEt:Imidazole and the synthetic polyester PLLA-PDXO-PLLA presented similar vessel density values during experimental times. These different behaviours to improve neoangiogenesis without severe inflammatory tissue-responses could be further investigated with drugs in order to obtain time-programmable drug delivery systems for musculoskeletal therapy.

Adsorption of cationic antibacterial on collagen-coated titanium implant devices

Two different cationic antimicrobial molecules, chlorhexidine (CH) and poly(hexamethylenebiguanide) (PH), were adsorbed from aqueous solution to titanium implant devices surface-modified by the covalent coupling of collagen on a polyanionic acrylic acid overlayer. Results show that more antimicrobial was adsorbed on surface modified implants as compared to control titanium devices. Moreover, the kinetic of release was affected by the interaction between the polyanionic overlayer and the cationic antimicrobial, leading to slower kinetic of release in the case of CH and stable adsorption in the case of polycationic PH . These data indicate that biochemically modified collagen coated surfaces could be endowed also by antimicrobial properties, in the spirit of present researches on multifunctional implant surfaces.

The solid surface free energy calculation. I. In defense of the multicomponent approach

The acid-base approach to the calculation of solid surface free energy and liquid-liquid interfacial tensions is a practical example of application of correlation analysis, and thus it is an approximate approach. In these limits, and provided that wide and well-obtained sets of contact angles or interfacial tension data are used for their computation, surface tension components can be considered as material properties. Although their numerical value depends on the characteristics of the chosen reference material, their chemical meaning is independent on the selected scale. Contact angles contain accessible information about intermolecular forces; using surface tension component (STC) acid-base theory, one can extract this information only making very careful use of the mathematical apparatus of correlation analysis. The specific mathematical methods used to obtain these results are illustrated by using as an example a base of data obtained by the supporters of the equation-of-state theory (EQS). The achievements are appreciably good and the agreement between STC and EQS is discussed.

Surface engineering of titanium by collagen immobilization. Surface characterization and in vitro and in vivo studies

Collagen was covalently linked to the surface of Titanium (Ti) by a surface modification process involving deposition of a thin film from hydrocarbon plasma followed by acrylic acid grafting. The composition and properties of surface-modified Ti were investigated by a number of surface sensitive techniques: XPS, ATR-IR, atomic force microscopy and AFM force-separation curves. In vitro tests were performed to check samples cytotoxicity and the behavior of osteoblast-like SaOS-2 cells. In vivo experiments involved 12 weeks implants in rabbit muscle as general biocompatibility assessment and 1-month implants in rabbit bone to evaluate the effect of surface modification on osteointegration rate. Results of XPS measurements show how surface chemistry is affected throughout each step of the surface modification process, finally leading to a complete and homogeneous collagen overlayer on top of the Ti samples. AFM data clearly display the modification of the surface topography and of the surface area of the samples as a consequence of the grafting and coupling process. AFM force-distance curves show that the interfacial structure responds by shrinking or swelling to variations of ionic force of the surrounding aqueous environment, suggesting that the aqueous interface of the biochemically modified Ti samples has enhanced degrees of freedom as compared to the inorganic surface of plain Ti. As to biological evaluations, the biochemically modified Ti samples are safe in terms of cytotoxicity and in vivo biocompatibility assessment. SaOS-2 cells growth rate is lower on collagen modified surfaces, and no significant difference is detected in terms of alkaline phosphatase production as compared to control Ti. Importantly, implants in rabbit femur show a significant increase of bone growth and bone-to-implant contact in the case of the collagen modified samples, confirming that biochemical modifications of Ti surface can enhance the rate of bone healing as compared to plain Ti.

[Corrosion of titanium in presence of dental amalgams and fluorides]

AIM

The aim of this study was to evaluate the behaviour of titanium (Ti) in precipitant condition, and more precisely the resistance against corrosion of Ti in presence of fluorides and the electrochemical interaction between Ti- amalgam couples in fluorinated solution.

METHODS

The experimental test was made with the use of an electrochemical cell. The following materials were tested: commercially pure Ti and 2 types of amalgams, the Persistalloy (Prs) and the IQC. Palladium (IQC.P). The free corrosion potential of Ti and the amalgams, the polarization curves of both amalgams and the corrosion current of the Ti-amalgam couples in the measurements were performed in 3 different electrolytic solutions: Ringer solution, fluorinated neutral Ringer solution and acid fluorinated solution. The three corrosive media are described.

RESULTS

The results showed that Ti could be damaged by the presence of fluorides with an acid pH: Ti potential becomes more negative in acid fluorinated solution. The corrosion currents between Ti and amalgam couples were considered: the amalgams underwent anodic oxidation in neutral Ringer, but a reversal phenomenon occurred in the fluorinated acid solution: Ti was damaged and the amalgams both Prs and IQC.P became the cathodic partner of the couple. In neutral fluorinated solution the IQC.P amalgam induced a significantly higher corrosion of Ti, when compared to the Prs one.

CONCLUSION

Results clearly show the dependence of the Ti corrosion behaviour on the pH and composition of the solution and that the outcome of the damage is affected by the composition of other metals.

Analysis of SH2D1A mutations in patients with severe Epstein-Barr virus infections, Burkitt's lymphoma, and Hodgkin's lymphoma

Mutations or deletions in the SH2D1A (src homology 2 domain protein 1A) gene result in a severe immunodeficiency called X-linked lymphoproliferative (XLP) disease. XLP is primarily characterized by a defective immune response against the Epstein-Barr virus (EBV), resulting in an unusually severe and often fatal clinical course following EBV infection. The second major cause of death is the development of B cell lymphomas, both in EBV-infected and EBV-negative patients. To study whether the clinical manifestation of XLP gene defects and/or polymorphisms extends beyond the classically recognized phenotype, we analyzed patients for the presence of SH2D1A gene alterations who presented with fatal or nonfatal, yet unusually severe or chronic EBV infections, and other possibly EBV-associated diseases, such as Hodgkin's lymphomas or nonendemic Burkitt's lymphomas and Burkitt-type leukemias. We identified mutations of the SH2D1A gene only in the majority of patients presenting with fatal mononucleosis or an XLP family history, but not in any of the other patients studied. The only alteration determined was a polymorphism in the 5' region of the SH2D1A gene both in patient groups as well as in controls.

A spectrum of mutations in SH2D1A that causes X-linked lymphoproliferative disease and other Epstein-Barr virus-associated illnesses

X-linked lymphoproliferative disease (Duncan's Disease) was first encountered by David T. Purtilo in 1969. The first communication describing the disease was published in 1975. In 1989 the disease locus was mapped to Xq25. Ten years later the gene (SH2D1A, SAP, DSHP), which is absent or mutated in XLP patients was identified. Since that the protein crystal structure of this small, SH2-domain containing protein has been solved, target molecules of the protein have been identified, physiological and pathological protein/protein interactions have been characterized, and the mouse model of the gene mutation has been developed. That said, a complete understanding of the function of the normal SH2D1A protein in immunoregulation and of the altered immune responses in XLP patients is not yet at hand. Therein lies the legacy of Purtilo's discovery for, as with other primary immunodeficiencies, these "experiments of nature" offer a window on the beauty of the immune system. In due course, the manner by which this gene orchestrates an elegant response (akin to a Mozart divertimento) to EBV infection shall be defined.

A "three-pronged" binding mechanism for the SAP/SH2D1A SH2 domain: structural basis and relevance to the XLP syndrome

The SH2 domain protein SAP/SH2D1A, encoded by the X-linked lymphoproliferative (XLP) syndrome gene, associates with the hematopoietic cell surface receptor SLAM in a phosphorylation-independent manner. By screening a repertoire of synthetic peptides, the specificity of SAP/SH2D1A has been mapped and a consensus sequence motif for binding identified, T/S-x-x-x-x-V/I, where x represents any amino acid. Remarkably, this motif contains neither a Tyr nor a pTyr residue, a hallmark of conventional SH2 domain-ligand interactions. The structures of the protein, determined by NMR, in complex with two distinct peptides provide direct evidence in support of a "three-pronged" binding mechanism for the SAP/SH2D1A SH2 domain in contrast to the "two-pronged" binding for conventional SH2 domains. Differences in the structures of the two complexes suggest considerable flexibility in the SH2 domain, as further confirmed and characterized by hydrogen exchange studies. The structures also explain binding defects observed in disease-causing SAP/SH2D1A mutants and suggest that phosphorylation-independent interactions mediated by SAP/SH2D1A likely play an important role in the pathogenesis of XLP.

Identification and characterization of SF2000 and SF2001, two new members of the immune receptor SLAM/CD2 family

The SLAM family of human genes currently consists of seven related members of the immunoglobulin superfamily, membrane-associated proteins, including CD150 (SLAM), CD244 (2B4), CD84, CD229 ( Ly-9), BLAME, CD48, and 19A. These genes are expressed to varying degrees in subsets of immune cells (T, B, natural killer, and myeloid cells) and may function as ligands or receptors. This set of genes, related to CD2 and CD58 on Chromosome (Chr) 1p98, are found clustered close together in the human genome on Chr 1q22. Four of these family members (CD150, CD244, CD84, CD229) contain conserved tyrosine motifs in their cytoplasmic tails that enable them to bind intracellular signaling molecules SAP and EAT-2. SAP is mutated in human X-linked lymphoproliferative disease (XLP), and studies in XLP patients have shown that improper signaling via molecules that bind SAP contributes to the disease. We have identified two new members of the SLAM family (SF), which we term SF2000 and SF2001, which are expressed in immune cells and map in the SLAM gene cluster. SF2001 does not contain SAP-binding motifs in its short cytoplasmic tail. SF2000, which is co-expressed with SAP in T cells, binds both SAP and EAT-2. The data suggest that signaling through SF2000, together with CD150, CD244, CD84, and CD229, is controlled by SAP and therefore contributes to the pathogenesis of XLP.

Structural basis for the interaction of the free SH2 domain EAT-2 with SLAM receptors in hematopoietic cells

The T and natural killer (NK) cell-specific gene SAP (SH2D1A) encodes a 'free SH2 domain' that binds a specific tyrosine motif in the cytoplasmic tail of SLAM (CD150) and related cell surface proteins. Mutations in SH2D1A cause the X-linked lymphoproliferative disease, a primary immunodeficiency. Here we report that a second gene encoding a free SH2 domain, EAT-2, is expressed in macrophages and B lympho cytes. The EAT-2 structure in complex with a phosphotyrosine peptide containing a sequence motif with Tyr281 of the cytoplasmic tail of CD150 is very similar to the structure of SH2D1A complexed with the same peptide. This explains the high affinity of EAT-2 for the pTyr motif in the cytoplasmic tail of CD150 but, unlike SH2D1A, EAT-2 does not bind to non-phosphorylated CD150. EAT-2 binds to the phosphorylated receptors CD84, CD150, CD229 and CD244, and acts as a natural inhibitor, which interferes with the recruitment of the tyrosine phosphatase SHP-2. We conclude that EAT-2 plays a role in controlling signal transduction through at least four receptors expressed on the surface of professional antigen-presenting cells.

Characterization of SH2D1A missense mutations identified in X-linked lymphoproliferative disease patients

X-linked lymphoproliferative disease (XLP) is a primary immunodeficiency characterized by extreme susceptibility to Epstein-Barr virus. The XLP disease gene product SH2D1A (SAP) interacts via its SH2 domain with a motif (TIYXXV) present in the cytoplasmic tail of the cell-surface receptors CD150/SLAM, CD84, CD229/Ly-9, and CD244/2B4. Characteristically, the SH2D1A three-pronged interaction with Tyr(281) of CD150 can occur in absence of phosphorylation. Here we analyze the effect of SH2D1A protein missense mutations identified in 10 XLP families. Two sets of mutants were found: (i) mutants with a marked decreased protein half-life (e.g. Y7C, S28R, Q99P, P101L, V102G, and X129R) and (ii) mutants with structural changes that differently affect the interaction with the four receptors. In the second group, mutations that disrupt the interaction between the SH2D1A hydrophobic cleft and Val +3 of its binding motif (e.g. T68I) and mutations that interfere with the SH2D1A phosphotyrosine-binding pocket (e.g. C42W) abrogated SH2D1A binding to all four receptors. Surprisingly, a mutation in SH2D1A able to interfere with Thr -2 of the CD150 binding motif (mutant T53I) severely impaired non-phosphotyrosine interactions while preserving unaffected the binding of SH2D1A to phosphorylated CD150. Mutant T53I, however, did not bind to CD229 and CD224, suggesting that SH2D1A controls several critical signaling pathways in T and natural killer cells. Because no correlation is present between identified types of mutations and XLP patient clinical presentation, additional unidentified genetic or environmental factors must play a strong role in XLP disease manifestations.