Solving Missing Heritability in Patients With Familial Adenomatous Polyposis With DNA-RNA Paired Testing.

PURPOSE: Patients with germline pathogenic variants (PVs) in APC develop tens (attenuated familial adenomatous polyposis [AFAP]) to innumerable (classic FAP) adenomatous polyps in their colon and are at significantly increased lifetime risk of colorectal cancer. Up to 10% of FAP and up to 50% of patients with AFAP who have undergone DNA-only multigene panel testing (MGPT) do not have an identified PV in APC. We seek to demonstrate how the addition of RNA sequencing run concurrently with DNA can improve detection of germline PVs in individuals with a clinical presentation of AFAP/FAP. METHODS: We performed a retrospective query of individuals tested with paired DNA-RNA MGPT from 2021 to 2022 at a single laboratory and included those with a novel APC PV located in intronic regions infrequently covered by MGPT, a personal history of polyposis, and family medical history provided. All clinical data were deidentified in this institutional review board-exempt study. RESULTS: Three novel APC variants were identified in six families and were shown to cause aberrant splicing because of the creation of a deep intronic cryptic splice site that leads to an RNA transcript subject nonsense-mediated decay. Several carriers had previously undergone DNA-only genetic testing and had received a negative result. CONCLUSION: Here, we describe how paired DNA-RNA MGPT can be used to solve missing heritability in FAP families, which can have important implications in family planning and treatment decisions for patients and their families.

Functional analysis and clinical classification of 462 germline BRCA2 missense variants affecting the DNA binding domain.

Variants of uncertain significance (VUSs) in BRCA2 are a common result of hereditary cancer genetic testing. While more than 4,000 unique VUSs, comprised of missense or intronic variants, have been identified in BRCA2, the few missense variants now classified clinically as pathogenic or likely pathogenic are predominantly located in the region encoding the C-terminal DNA binding domain (DBD). We report on functional evaluation of the influence of 462 BRCA2 missense variants affecting the DBD on DNA repair activity of BRCA2 using a homology-directed DNA double-strand break repair assay. Of these, 137 were functionally abnormal, 313 were functionally normal, and 12 demonstrated intermediate function. Comparisons with other functional studies of BRCA2 missense variants yielded strong correlations. Sequence-based in silico prediction models had high sensitivity, but limited specificity, relative to the homology-directed repair assay. Combining the functional results with clinical and genetic data in an American College of Medical Genetics (ACMG)/Association for Molecular Pathology (AMP)-like variant classification framework from a clinical testing laboratory, after excluding known splicing variants and functionally intermediate variants, classified 431 of 442 (97.5%) missense variants (129 as pathogenic/likely pathogenic and 302 as benign/likely benign). Functionally abnormal variants classified as pathogenic by ACMG/AMP rules were associated with a slightly lower risk of breast cancer (odds ratio [OR] 5.15, 95% confidence interval [CI] 3.43-7.83) than BRCA2 DBD protein truncating variants (OR 8.56, 95% CI 6.03-12.36). Overall, functional studies of BRCA2 variants using validated assays substantially improved the variant classification yield from ACMG/AMP models and are expected to improve clinical management of many individuals found to harbor germline BRCA2 missense VUS.

In Vivo Restoration of Myocardial Conduction With Carbon Nanotube Fibers.

BACKGROUND: Impaired myocardial conduction is the underlying mechanism for re-entrant arrhythmias. Carbon nanotube fibers (CNTfs) combine the mechanical properties of suture materials with the conductive properties of metals and may form a restorative solution to impaired myocardial conduction. METHODS: Acute open chest electrophysiology studies were performed in sheep (n=3). Radiofrequency ablation was used to create epicardial conduction delay after which CNTf and then silk suture controls were applied. CNTfs were surgically sewn across the right atrioventricular junction in rodents, and acute (n=3) and chronic (4-week, n=6) electrophysiology studies were performed. Rodent toxicity studies (n=10) were performed. Electrical analysis of the CNTf-myocardial interface was performed. RESULTS: In all cases, the large animal studies demonstrated improvement in conduction velocity using CNTf. The acute rodent model demonstrated ventricular preexcitation during sinus rhythm. All chronic cases demonstrated resumption of atrioventricular conduction, but these required atrial pacing. There was no gross or histopathologic evidence of toxicity. Ex vivo studies demonstrated contact impedance significantly lower than platinum iridium. CONCLUSIONS: Here, we show that in sheep, CNTfs sewn across epicardial scar acutely improve conduction. In addition, CNTf maintain conduction for 1 month after atrioventricular nodal ablation in the absence of inflammatory or toxic responses in rats but only in the paced condition. The CNTf/myocardial interface has such low impedance that CNTf can facilitate local, downstream myocardial activation. CNTf are conductive, biocompatible materials that restore electrical conduction in diseased myocardium, offering potential long-term restorative solutions in pathologies interrupting efficient electrical transduction in electrically excitable tissues.

Detection of the tuberculosis biomarker mannose-capped lipoarabinomannan in human serum: Impact of sample pretreatment with perchloric acid.

The development of an accurate and rapid diagnostic test for tuberculosis (TB) to use at point of need is vital to efforts aimed at reducing the global burden from this disease. This paper builds on our previous studies of mannose-capped lipoarabinomannan (ManLAM) as a serum biomarker for active TB infection by means of a heterogeneous immunoassay. That work found that complexation with components in serum (e.g., proteins) sterically hindered the capture and/or labeling of ManLAM in an immunoassay at levels <10 ng mL-1, compromising the clinical utility of this biomarker for detection of active TB infection. We also showed that the acidification of ManLAM-containing serum samples with perchloric acid improved the detectability of ManLAM by 250× by complex disruption when compared to measurements of untreated serum. The present study examined what effects the PCA treatment of serum samples may have on the recovery and structural integrity of ManLAM, owing to its potential susceptibility to acid hydrolysis. Recovery was assessed with an enzyme-linked immunosorbent assay (ELISA). The possible impact of acid hydrolysis on the ManLAM structure was investigated by gas chromatography-mass spectrometry and carbohydrate chemical degradation methods. The ELISA study indicated that while the signal strength for ManLAM in the serum spike-in experiments was significantly stronger after PCA pretreatment when compared to untreated human serum, it was only ∼20% of the ManLAM measured in physiological buffer. This loss in detectability was shown by structural analysis to arise mainly from the acid-induced degradation of the arabinan domains of ManLAM that are targeted by antibodies used for antigen capture and/or tagging. The implications of these findings in terms of the detection of this important biomarker for TB are also discussed.

Gold Nanoparticle Labels and Heterogeneous Immunoassays: The Case for the Inverted Substrate.

This paper examines how the difference in the spatial orientation of the capture substrate influences the analytical sensitivity and limits of detection for immunoassays that use gold nanoparticle labels (AuNPs) and rely on diffusion in quiet solution in the antigen capture and labeling steps. Ideally, the accumulation of both reactants should follow a dependence governed by the rate in which diffusion delivers reactants to the capture surface. In other words, the accumulation of reactants should increase with the square root of the incubation time, i.e., t1/2. The work herein shows, however, that this expectation is only obeyed when the capture substrate is oriented to direct the gravity-induced sedimentation of the AuNP labels away from the substrate. Using an assay for human IgG, the results show that circumventing the sedimentation of the gold nanoparticle labels by substrate inversion enables the dependence of the labeling step on diffusion, reduces nonspecific label adsorption, and improves the estimated detection limit by ∼30×. High-density maps of the signal across the two types of substrates also demonstrate that inversion in the labeling step results in a more uniform distribution of AuNP labels across the surface, which translates to a greater measurement reproducibility. These results, which are supported by model simulations via the Mason-Weaver sedimentation-diffusion equation, and their potential implications when using other nanoparticle labels and related materials in diagnostic tests and other applications, are briefly discussed.

Influence of Carbon Nanotube Characteristics on Macroscopic Fiber Properties.

We study how intrinsic parameters of carbon nanotube (CNT) samples affect the properties of macroscopic CNT fibers with optimized structure. We measure CNT diameter, number of walls, aspect ratio, graphitic character, and purity (residual catalyst and non-CNT carbon) in samples from 19 suppliers; we process the highest quality CNT samples into aligned, densely packed fibers, by using an established wet-spinning solution process. We find that fiber properties are mainly controlled by CNT aspect ratio and that sample purity is important for effective spinning. Properties appear largely unaffected by CNT diameter, number of walls, and graphitic character (determined by Raman G/D ratio) as long as the fibers comprise thin few-walled CNTs with high G/D ratio (above ∼20). We show that both strength and conductivity can be improved simultaneously by assembling high aspect ratio CNTs, producing continuous CNT fibers with an average tensile strength of 2.4 GPa and a room temperature electrical conductivity of 8.5 MS/m, ∼2 times higher than the highest reported literature value (∼15% of copper's value), obtained without postspinning doping. This understanding of the relationship of intrinsic CNT parameters to macroscopic fiber properties is key to guiding CNT synthesis and continued improvement of fiber properties, paving the way for CNT fiber introduction in large-scale aerospace, consumer electronics, and textile applications.

Increased solubility and fiber spinning of graphenide dispersions aided by crown-ethers.

Graphenide solutions in NMP have been prepared by dispersing potassium intercalated graphite with the assistance of 18-crown-6. The highest graphenide solubility achieved is 1.5 mg mL-1. Graphenide solutions have been applied to spin graphene/SWCNT hybrid fibers.

Enlightening the ultrahigh electrical conductivities of doped double-wall carbon nanotube fibers by Raman spectroscopy and first-principles calculations.

Highly aligned, packed, and doped carbon nanotube (CNT) fibers with electrical conductivities approaching that of copper have recently become available. These fibers are promising for high-power electrical applications that require light-weight, high current-carrying capacity cables. However, a microscopic understanding of how doping affects the electrical conductance of such CNT fibers in a quantitative manner has been lacking. Here, we performed Raman spectroscopy measurements combined with first-principles calculations to determine the position of the average Fermi energy and to obtain the temperature of chlorosulfonic-acid-doped double-wall CNT fibers under high current. Due to the unique way in which double-wall CNT Raman spectra depend on doping, it is possible to use Raman data to determine the doping level quantitatively. The correspondence between the Fermi level shift and the carbon charge transfer is derived from a tight-binding model and validated by several calculations. For the doped fiber, we were able to associate an average Fermi energy shift of ∼-0.7 eV with a conductance increase by a factor of ∼5. Furthermore, since current induces heating, local temperature determination is possible. Through the Stokes-to-anti-Stokes intensity ratio of the G-band peaks, we estimated a temperature rise at the fiber surface of ∼135 K at a current density of 2.27 × 108 A m-2 identical to that from the G-band shift, suggesting that thermalization between CNTs is well achieved.

Frequency-Domain Approach To Determine Magnetic Address-Sensor Separation Distance Using the Harmonic Ratio Method.

In this work, we describe an approach to determine the distance separating a magnetic address from a scanning magnetoresistive sensor, a critical adjustable parameter for certain bioassay analyses where magnetic nanoparticles are used as labels. Our approach is leveraged from the harmonic ratio method (HRM), a method used in the hard drive industry to control the distance separating a magnetoresistive read head from its data platter with nanometer resolution. At the heart of the HRM is an amplitude comparison of a signal's fundamental frequency to that of its harmonics. When the signal is derived from the magnetic field pattern of a periodic array of magnetic addresses, the harmonic ratio contains the information necessary to determine the separation between the address array and the read head. The elegance of the HRM is that there is no need of additional components to the detection platform to determine a separation distance; the streaming "bit signal" contains all the information needed. In this work, we demonstrate that the tenets governing HRM used in the hard drive industry can be applied to the bioanalytical arena where submicrometer to 100 µm separations are required.

Macroscopic nanotube fibers spun from single-walled carbon nanotube polyelectrolytes.

In this work, single-walled carbon nanotube (SWCNT) fibers were produced from SWCNT polyelectrolyte dispersions stabilized by crown ether in dimethyl sulfoxide and coagulated into aqueous solutions. The SWCNT polyelectrolyte dispersions had concentrations up to 52 mg/mL and showed liquid crystalline behavior under polarized optical microscopy. The produced SWCNT fibers are neat (i.e., not forming composites with polymers) and showed a tensile strength up to 124 MPa and a Young's modulus of 14 GPa. This tensile strength is comparable to those of SWCNT fibers spun from strong acids. Conductivities on the order of 10(4) S/m were obtained by doping the fibers with iodine.

Large flake graphene oxide fibers with unconventional 100% knot efficiency and highly aligned small flake graphene oxide fibers.

Two types of graphene oxide fibers are spun from high concentration aqueous dopes. Fibers extruded from large flake graphene oxide dope without drawing show unconventional 100% knot efficiency. Fibers spun from small sized graphene oxide dope with stable and continuous drawing yield in good intrinsic alignment with a record high tensile modulus of 47 GPa.

Increased solubility, liquid-crystalline phase, and selective functionalization of single-walled carbon nanotube polyelectrolyte dispersions.

The solubility of single-walled carbon nanotube (SWCNT) polyelectrolytes [K(THF)]nSWCNT in dimethyl sulfoxide (DMSO) was determined by a combination of centrifugation, UV-vis spectral properties, and solution extraction. The SWCNT formed a liquid crystal at a concentration above 3.8 mg/mL. Also, crown ether 18-crown-6 was found to increase the solubility of the SWCNT polyelectrolytes in DMSO. Raman spectroscopy and near-infrared (NIR) fluorescence analyses were applied to study the functionalization of SWCNTs. Small-diameter SWCNTs were found to be preferentially functionalized when the SWCNT polyelectrolytes were dispersed in DMSO.

Graphene nanoribbons as an advanced precursor for making carbon fiber.

Graphene oxide nanoribbons (GONRs) and chemically reduced graphene nanoribbons (crGNRs) were dispersed at high concentrations in chlorosulfonic acid to form anisotropic liquid crystal phases. The liquid crystal solutions were spun directly into hundreds of meters of continuous macroscopic fibers. The relationship of fiber morphology to coagulation bath conditions was studied. The effects of colloid concentration, annealing temperature, spinning air gap, and pretension during annealing on the fibers' performance were also investigated. Heat treatment of the as-spun GONR fibers at 1500 °C produced thermally reduced graphene nanoribbon (trGNR) fibers with a tensile strength of 378 MPa, Young's modulus of 36.2 GPa, and electrical conductivity of 285 S/cm, which is considerably higher than that in other reported graphene-derived fibers. This better trGNR fiber performance was due to the air gap spinning and annealing with pretension that produced higher molecular alignment within the fibers, as determined by X-ray diffraction and scanning electron microscopy. The specific modulus of trGNR fibers is higher than that of the commercial general purpose carbon fibers and commonly used metals such as Al, Cu, and steel. The properties of trGNR fibers can be further improved by optimizing the spinning conditions with higher draw ratio, annealing conditions with higher pretensions, and using longer flake GONRs. This technique is a new high-carbon-yield approach to make the next generation carbon fibers based on solution-based liquid crystal phase spinning.

Strong, light, multifunctional fibers of carbon nanotubes with ultrahigh conductivity.

Broader applications of carbon nanotubes to real-world problems have largely gone unfulfilled because of difficult material synthesis and laborious processing. We report high-performance multifunctional carbon nanotube (CNT) fibers that combine the specific strength, stiffness, and thermal conductivity of carbon fibers with the specific electrical conductivity of metals. These fibers consist of bulk-grown CNTs and are produced by high-throughput wet spinning, the same process used to produce high-performance industrial fibers. These scalable CNT fibers are positioned for high-value applications, such as aerospace electronics and field emission, and can evolve into engineered materials with broad long-term impact, from consumer electronics to long-range power transmission.

High-performance carbon nanotube transparent conductive films by scalable dip coating.

Transparent conductive carbon nanotube (CNT) films were fabricated by dip-coating solutions of pristine CNTs dissolved in chlorosulfonic acid (CSA) and then removing the CSA. The film performance and morphology (including alignment) were controlled by the CNT length, solution concentration, coating speed, and level of doping. Using long CNTs (∼10 µm), uniform films were produced with excellent optoelectrical performance (∼100 Ω/sq sheet resistance at ∼90% transmittance in the visible), in the range of applied interest for touch screens and flexible electronics. This technique has potential for commercialization because it preserves the length and quality of the CNTs (leading to enhanced film performance) and operates at high CNT concentration and coating speed without using surfactants (decreasing production costs).

Direct imaging of carbon nanotubes spontaneously filled with solvent.

For the first time, cryo-TEM imaging is used to directly show spontaneous filling of carbon nanotubes immersed in a solvent in the native state at ambient conditions. Multi-walled carbon nanotubes are dissolved in chlorosulfonic acid, and the high contrast between the acid and the carbon shows the difference between filled and unfilled nanotubes.

Spontaneous dissolution of ultralong single- and multiwalled carbon nanotubes.

We report that chlorosulfonic acid is a true solvent for a wide range of carbon nanotubes (CNTs), including single-walled (SWNTs), double-walled (DWNTs), multiwalled carbon nanotubes (MWNTs), and CNTs hundreds of micrometers long. The CNTs dissolve as individuals at low concentrations, as determined by cryo-TEM (cryogenic transmission electron microscopy), and form liquid-crystalline phases at high concentrations. The mechanism of dissolution is electrostatic stabilization through reversible protonation of the CNT side walls, as previously established for SWNTs. CNTs with highly defective side walls do not protonate sufficiently and, hence, do not dissolve. The dissolution and liquid-crystallinity of ultralong CNTs are critical advances in the liquid-phase processing of macroscopic CNT-based materials, such as fibers and films.