Neoantigen Landscape Supports Feasibility of Personalized Cancer Vaccine for Follicular Lymphoma

Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that 'polyvalent' vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole exome sequencing (WES) and RNA sequencing (RNA-Seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-Seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by alignment of B-cell receptor (BCR) CDR3 regions from RNA-Seq data, grouping at the protein level, and comparison to the BCR repertoire from healthy individuals using RNA-Seq data. An average of 52 somatic mutations per patient (range: 2-172) were identified, and two or more (median: 15) high-quality neoantigens were predicted for 56 of 58 FL samples. The predicted neoantigen peptides were composed of missense mutations (77%), indels (9%), gene fusions (3%), and BCR sequences (11%). Building off of these preclinical analyses, we initiated a pilot clinical trial using personalized neoantigen vaccination combined with PD-1 blockade in patients with relapsed or refractory FL (#NCT03121677). Synthetic long peptide (SLP) vaccines targeting predicted high-quality neoantigens were successfully synthesized for and administered to all four patients enrolled. Initial results demonstrate feasibility, safety, and potential immunologic and clinical responses. Our study suggests that a genomics-driven personalized cancer vaccine strategy is feasible for patients with FL, and this may overcome prior challenges in the field.

Donor-Derived Follicular Lymphoma After Kidney Transplantation: A Case Report

Donor-derived follicular lymphoma after kidney transplant revealed by genomic profiling.

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC's functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.

Bilateral simultaneous extensor mechanism disruption following simultaneous bilateral total knee replacement

Extensor disruptions of the knee following the total knee replacements are uncommon. We describe a case of postoperative bilateral simultaneous extensor mechanism disruption following simultaneous bilateral total knee replacement. On both sides, the patient sustained open wounds. The extensor mechanism was successfully repaired on both sides, but the outcome is less than satisfactory.

Correlations between plasminogen activator inhibitor-1 and peritoneal transport in pediatric CCPD patients

OBJECTIVE

Plasminogen activator inhibitor-1 (PAI-1) is an important regulator of plasminogen activators and has been shown to be involved in the accumulation of extracellular matrix (ECM) in various tissues. Since peritoneal ECM is a resistance site for peritoneal transport, the production and release of PAI-1 in the peritoneum may affect the peritoneal transport of water and small solutes.

DESIGN

The linear correlations between the dialysate PAI-1 levels and the variables of peritoneal transport during peritoneal equilibration tests (PET) were examined.

SETTING

A tertiary university hospital.

PATIENTS

Six stable pediatric patients (age 10.8 +/- 4 years) undergoing continuous cycler-assisted peritoneal dialysis were included.

INTERVENTIONS

None.

RESULTS

All data are mean +/- SD. There was a positive correlation between the infused volume and the net ultrafiltration (UF, 198 +/- 127 mL, r = 0.82, p < 0.05). The dialysate PAI-1 levels increased during the dwell time (2.44 +/- 2.23 ng/mL or 2.46 +/- 1.72 micrograms at 4 hours vs 0.04 +/- 0.1 ng/mL or 0.04 +/- 0.09 micrograms at 0 hour, p < 0.05). The saturation indices (dialysate/plasma ratio) of PAI-1 and albumin at 4 hours were 1.05 +/- 1.21 and 0.028 +/- 0.004, respectively. The changes from 0 hour dwell to 4 hour dwell in the dialysate PAI-1 concentration (PAI4-0, 2.4 +/- 2.2 ng/mL) or amount corrected to body surface area (APAI4-0/BSA, 2.61 +/- 2.11 micrograms/m2) negatively correlated with UF or UF/body surface area and positively correlated with the number of episodes of peritonitis. There was no correlation between PAI4-0,APAI4-0/BSA, or plasma PAI-1 concentration and the mass transfer coefficient and clearance of either urea or creatinine.

CONCLUSIONS

The elevated PAI-1 level during the PET was likely from the local production and release of PAI-1. It had an inverse relationship with the amount of ultrafiltration. Repeated inflammation of the peritoneum was associated with an increased production and release of PAI-1 into the peritoneum.

Synthesis and biological studies on some organo-tin and lead halo and mixed halo-pseudohalo anionic complexes

Some new anionic complexes of organo-tin(IV) and lead (IV) isolated in combination of tetraorgano-ammonium phosphonium and stibonium cation(s). L[R4-nMXnY] and L2[R2MX2Y2], where R = C2H5, C4H9 or C6H5; M = Sn or Pb; X = Y = Cl = Br, I, N3, NCS; n = 1, 2 and L = R4M1 (M1 = N, P, Sb), whose structures were confirmed by correct elemental analyses, molar conductance values, van't Hoff factor and IR spectral studies, were synthesized and evaluated for anti-convulsant activity in vivo and antiviral and antibacterial activity in vitro. A few of them exhibited promising activity. In addition, the toxicity (ALD50) and effects on the central nervous system of these complexes have been studied in mice.

Radiographic assessment of cup migration in bipolar hip arthroplasty: intra-observer and interobserver errors and tolerance limits

Statistical methods were used to calculate the possible observer error in measuring cup migration in bipolar hip arthroplasty from follow-up radiographs. Finding the "tolerance limits" by such methods helped in assigning the true significance of any observed change.

Regression and recursive partition strategies in the analysis of medical survival data

Regression and clustering methods have both been used to explore the effects of explanatory variables on survival times for patients with cancer or other chronic diseases. This paper discusses effective and computationally feasible approaches for this task in situations where there are fairly large and complex data sets; the techniques stressed are all-subsets regression and a kind of recursive partition clustering. We compare the two approaches in a rather general way, in part by examining some survival data for patients with ovarian carcinoma, and conclude that both have strong points to recommend them.

Simulation and prediciton of uptake, distribution, and exhalation of organic solvents

Fiserova-Bergerova, Vera, Vlach, J., and Singhal, K. (1974).British Journal of Industrial Medicine,31, 45-52. Simulation and prediction of uptake, distribution, and exhalation of organic solvents. Presented here is a theory and mathematical solution of the uptake, distribution, and excretion of inhaled lipid soluble noxious gases, which embraces the effects of metabolism. An electrical analogue was employed to explain the theory, since the analogue is described by the same set of differential equations, and much knowledge is available for the mathematical treatment of electrical networks. The model is used to calculate the uptake and exhalation curves of vapours, to explain what happens to the inhaled vapours in the body, and to predict their cumulation in the body in periodic situations such as occur in industrial exposure.