Identification of pathogenic CDK12 alterations in cell-free DNA (cfDNA) from patients with breast cancer

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Background: Cyclin dependent kinase 12 ( CDK12) has both tumor suppressive and proto-oncogenic potential in metastatic breast cancers (MBC). CDK12 may be an important biomarker and target in MBC. However, a comprehensive genomic analysis of CDK12 alterations from cfDNA in MBC has not been investigated and the genomic impact of CDK12 alterations across the MBC spectrum is unknown. The purpose of this study was to identify the incidence of CDK12 genomic alterations occurring in cfDNA from patients with MBC and elucidate which CDK12 alterations may impact CDK12 kinase activity. Methods: We queried 13,070 MBC samples from the Guardant Health database between April 2019 – November 2020 to identify the incidence of CDK12 alterations detected in cfDNA. We classified each alteration type as: missense mutations, indels, or truncations. Amino acid changes occurring at conserved regions across multiple species were identified. Three-dimensional biochemical in silico analyses with ChimeraX were used to determine which CDK12 alterations may impact CDK12 kinase activity. To gain further biologic insights into CDK12 altered MBC we made associations with CDK12 alterations and co-occurring mutated genes. Results: Nonsynonymous CDK12 alterations from the Guardant Health database were found in 317 samples from a cohort of 13,070 patients indicating an overall incidence of 2.43%. Alterations included: 239 (75.4%) missense mutations; 26 (8.2%) indels; and 52 (16.4%) truncations. We identified 62 alterations within the kinase domain with all occurring at highly conserved regions across species. The most frequent hotspot mutation identified was I76M/T, occurring in 11 unique breast cancers. Three-dimensional analyses indicate that CDK12 alterations within the hinge, HRD, DFG, catalytic spine, and regulatory spine may impact CDK12 kinase activity. The significantly co-occurring mutations from the Guardant Health breast cancer database in samples with CDK12 alterations were ARID1A, APC, RB1, and PTEN. Conclusions: A modest incidence of CDK12 genomic alterations occur in cfDNA from patients with breast cancer. Novel somatic alterations in CDK12 were identified from Guardant Health that were not detected in the public domain. A portion of these occurred at highly conserved regions across species suggesting these specific CDK12 mutations may impact CDK12 kinase expression and be actionable therapeutic targets in breast cancers. Three dimensional analyses of the CDK12 gene further illustrate which specific alterations may induce CDK12 kinase expression or lead to inactivation. Co-occurring mutations reveal a unique genotype associated with CDK12 alterations that may play a biologic role in CDK12-mediated breast cancer pathogenesis. Preclinical studies to determine the prognostic and therapeutic implication of CDK12 alterations in MBC are warranted.

Preclinical and Clinical Development of ABBV-8E12, a Humanized Anti-Tau Antibody, for Treatment of Alzheimer's Disease and Other Tauopathies

Tau neurofibrillary tangles are found in the brains of patients suffering from Alzheimer's disease and other tauopathies. The progressive spreading of tau pathology from one brain region to the next is believed to be caused by extracellular transsynaptic transmission of misfolded tau between neurons. Preclinical studies have shown that antibodies against tau can prevent this transfer of misfolded tau between cells. Thus, antibodies against tau have the potential to stop or slow the progression of tau pathology observed in human tauopathies. To test this hypothesis, a humanized anti-tau antibody (ABBV-8E12) was developed and a phase 1 clinical trial of this antibody has been completed. The double-blind, placebo-controlled phase 1 study tested single doses of ABBV-8E12 ranging from 2.5 to 50 mg/kg in 30 patients with progressive supranuclear palsy (PSP). ABBV-8E12 was found to have an acceptable safety profile with no clinically concerning trends in the number or severity of adverse events between the placebo and dosed groups. Pharmacokinetic modelling showed that the antibody has a plasma half-life and cerebrospinal fluid:plasma ratio consistent with other humanized antibodies, and there were no signs of immunogenicity against ABBV-8E12. Based on the acceptable safety and tolerability profile of single doses of ABBV-8E12, AbbVie is currently enrolling patients into two phase 2 clinical trials to assess efficacy and safety of multiple doses of ABBV-8E12 in patients with early Alzheimer's disease or PSP.

The Rules of Engagement: Perspectives on Secure Messaging From Experienced Ambulatory Patient Portal Users

Background

Patient portals have shown promise in engaging individuals in self-management of chronic conditions by allowing patients to input and track health information and exchange secure electronic messages with their providers. Past studies have identified patient barriers to portal use including usability issues, low health literacy, and concerns about loss of personal contact as well as provider concerns such as increased time spent responding to messages. However, to date, studies of both patient and provider perspectives on portal use have focused on the pre-implementation or initial implementation phases and do not consider how these issues may change as patients and providers gain greater experience with portals.

Objective

Our study examined the following research question: Within primary care offices with high rates of patient-portal use, what do experienced physician and patient users of the ambulatory portal perceive as the benefits and challenges of portal use in general and secure messaging in particular?

Methods

This qualitative study involved 42 interviews with experienced physician and patient users of an ambulatory patient portal, Epic’s MyChart. Participants were recruited from the Department of Family Medicine at a large Academic Medical Center (AMC) and included providers and their patients, who had been diagnosed with at least one chronic condition. A total of 29 patients and 13 primary care physicians participated in the interviews. All interviews were conducted by telephone and followed a semistructured interview guide. Interviews were transcribed verbatim to permit rigorous qualitative analysis. Both inductive and deductive methods were used to code and analyze the data iteratively, paying particular attention to themes involving secure messaging.

Results

Experienced portal users discussed several emergent themes related to a need for greater clarity on when and how to use the secure messaging feature. Patient concerns included worry about imposing on their physician’s time, the lack of provider compensation for responding to secure messages, and uncertainty about when to use secure messaging to communicate with their providers. Similarly, providers articulated a lack of clarity as to the appropriate way to communicate via MyChart and suggested that additional training for both patients and providers might be important. Patient training could include orienting patients to the “rules of engagement” at portal sign-up, either in the office or through an online tutorial.

Conclusions

As secure messaging through patient portals is increasingly being used as a method of physician-patient communication, both patients and providers are looking for guidance on how to appropriately engage with each other using this tool. Patients worry about whether their use is appropriate, and providers are concerned about the content of messages, which allow them to effectively manage patient questions. Our findings suggest that additional training may help address the concerns of both patients and providers, by providing “rules of engagement” for communication via patient portals.

Cryopreservation of Freshly Isolated Porcine Islet Cells

INTRODUCTION

The use of xenogenic islet cells may be a possibility to overcome the shortage of human donor organs to treat diabetes. Microencapsulation seems to be a promising method for immunoprotection. Since isolation, purification, encapsulation, and transplantation of islet cells are labor intensive, cryopreservation has emerged as an attractive system of islet banking. The aim of this study was to determine the influence of three different freezing media (FM) on viability of freshly isolated porcine islet cells (FIPIC).

METHODS

FIPIC were isolated using a modified Ricordi method and purification performed using a Lymphoprep density gradient. Viability of FIPIC prior to freezing and after thawing was determined using the MTT-based Cell Growth Determination Kit. Insulin production was detected using enzyme-linked immunosorbent assay. Three different FM containing dimethylsulfoxide (DMSO) or glycerol and sucrose were used for cryoprotection of FIPIC.

RESULTS

Isolation and purification of FIPIC resulted in 95% +/- 1.3% viability and 97% +/- 1.4% purity. Cryopreservation with FM I (containing DMEM, FCS, DMSO) yielded 98.4% and FM III (containing DMEM, FCS, glycerol) 93.1% viability, whereas only 85.6% were alive when cryoprotection is performed with FM II (containing DMSO, BM). Glucose stimulation revealed a loss of 2.8% and 1.9% of insulin secretion per microgram DNA when working with FM I and FM III, but a decrease in glucose-dependent insulin secretion of 7.8% (P < .05) when FIPIC were stored in FM II.

DISCUSSION

Low concentrations of DMSO or the use of glycerol and sucrose seem to be equivalent to cryopreserve FIPIC.

Pulsatile non-Newtonian flow characteristics in a three-dimensional human carotid bifurcation model

Numerical analysis of flow phenomena and wall shear stresses in the human carotid artery bifurcation has been carried out using a three-dimensional geometrical model. The primary aim of this study is the detailed discussion of non-Newtonian flow velocity and wall shear stress during the pulse cycle. A comparison of non-Newtonian and Newtonian results is also presented. The applied non-Newtonian behavior of blood is based on measured dynamic viscosity. In the foreground of discussion are the flow characteristics in the carotid sinus. The investigation shows complex flow patterns especially in the carotid sinus where flow separation occurs at the outer wall throughout the systolic deceleration phase. The changing sign of the velocity near the outer sinus wall results in oscillating shear stress during the pulse cycle. At the outer wall of the sinus at maximum diameter level the shear stress ranges from -1.92 N/m2 to 1.22 N/m2 with a time-averaged value of 0.04 N/m2. At the inner wall of the sinus at maximum diameter level the shear stress range is from 1.16 N/m2 to 4.18 N/m2 with a mean of 1.97 N/m2. The comparison of non-Newtonian and Newtonian results indicates unchanged flow phenomena and rather minor differences in the basic flow characteristics.

Wall shear stress distribution in the human carotid siphon during pulsatile flow

Wall shear stress distribution in the carotid siphon, which is a multiple curved segment of the internal carotid artery, is investigated numerically under physiological flow conditions. The computer simulation of flow through the model segment is based on the time-dependent, three-dimensional Navier-Stokes equations, solved numerically with a finite element method. The study shows the behavior of the wall shear stress-vector field and identifies the zones of high and low wall shear stress values during the cardiac cycle.

Numerical blood flow analysis: arterial bifurcation with a saccular aneurysm

The flow pattern and the paths of fluid particles in a saccular aneurysm located at the bifurcation of an intracranial arterial segment are investigated with a numerical method. A normal physiological flow pattern was assumed as input to the studied segment. The theoretical study is carried out for two different Reynolds numbers and two different geometries of the aneurysm. The governing equations for incompressible Newtonian fluid flow are solved using the finite element method. The results show the disturbed blood flow in the pathologically altered bifurcation and the flow activity in the aneurysms. It is particularly important that blood particles can circulate in a whirl within the aneurysm for a time which seems long enough to permit the generation of cell aggregates or/and blood clots.

Analysis of pulsatile blood flow: a carotid siphon model

Numerical results for axial and secondary flow velocity and pressure in a three-dimensional model of the human carotid siphon have been calculated; the investigations were carried out under physiologically relevant pulsatile flow conditions. Time-dependent, three-dimensional Navier-Stokes equations were solved numerically by using a special finite element method. The results of the computer simulation presented here concentrate on the secondary motion effect during the pulsatile flow cycle in multiple three-dimensional curvatures.

Calculation of pulsatile flow and particle paths in an aneurysm-model

The velocity field and the wall shear stress have been calculated numerically by the finite element method to the time-dependent Navier-Stokes equations for pulsatile flow in a model of an aneurysm. The results show a complex flow field with two eddies growing and disappearing during the cardiac cycle. Downstream at the outlet vessel high wall shear stress occurs, which may lead to a downstream-growing of the aneurysm. With the knowledge of a sufficiently accurate flow field, the calculation of several particle paths has been carried out. Starting points and starting time are varied. The paths demonstrate the time-dependent development, shift and disappearance of vortices during the pulsatile cycle and provide hints on zones of stasis. These are significant factors in thrombogenesis.