Privacy-preserving cancer type prediction with homomorphic encryption.

Cancer genomics tailors diagnosis and treatment based on an individual's genetic information and is the crux of precision medicine. However, analysis and maintenance of high volume of genetic mutation data to build a machine learning (ML) model to predict the cancer type is a computationally expensive task and is often outsourced to powerful cloud servers, raising critical privacy concerns for patients' data. Homomorphic encryption (HE) enables computation on encrypted data, thus, providing cryptographic guarantees to protect privacy. But restrictive overheads of encrypted computation deter its usage. In this work, we explore the challenges of privacy preserving cancer type prediction using a dataset consisting of more than 2 million genetic mutations from 2713 patients for several cancer types by building a highly accurate ML model and then implementing its privacy preserving version in HE. Our solution for cancer type inference encodes somatic mutations based on their impact on the cancer genomes into the feature space and then uses statistical tests for feature selection. We propose a fast matrix multiplication algorithm for HE-based model. Our final model achieves 0.98 micro-average area under curve improving accuracy from 70.08 to 83.61% , being 550 times faster than the standard matrix multiplication-based privacy-preserving models. Our tool can be found at https://github.com/momalab/octal-candet .

CRISPR/Cas9 encouraged CAR-T cell immunotherapy reporting efficient and safe clinical results towards cancer.

CRISPR is a customized genome-editing tool that snips DNA in a simpler, cheaper and more precise way than any other gene editing tool. In recent years CRISPR/Cas has completely transformed an existing discipline of genetic engineering. This 'review' focuses on the generations and modifications in CAR-T as an advanced cancer therapeutic tool and CAR-T-approved products. It also highlights three path-breaking successful autologous and allogenic ex vivo CAR-T clinical trials in treating cancer using CRISPR/Cas9 which reported successful results despite the controversies regarding the safety of this technique. Outcomes from the first successful clinical trial showed the beneficial long-term effect on genetically modified T-cells in targeting cancer cells which opens the door for CRISPR to be the most preferred technique to help treat cancer and other diseases in the future. We searched the MEDLINE, EMBASE and PUBMED databases for original studies and meta-analysis on the use of CRISPR/Cas9 to edit T-cells until 2021. We finally selected 15 pre-clinical and 26 clinical studies for the review.

Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption.

The recent advances in genome sequencing technologies provide unprecedented opportunities to understand the relationship between human genetic variation and diseases. However, genotyping whole genomes from a large cohort of individuals is still cost prohibitive. Imputation methods to predict genotypes of missing genetic variants are widely used, especially for genome-wide association studies. Accurate genotype imputation requires complex statistical methods. Due to the data and computing-intensive nature of the problem, imputation is increasingly outsourced, raising serious privacy concerns. In this work, we investigate solutions for fast, scalable, and accurate privacy-preserving genotype imputation using Machine Learning (ML) and a standardized homomorphic encryption scheme, Paillier cryptosystem. ML-based privacy-preserving inference has been largely optimized for computation-heavy non-linear functions in a single-output multi-class classification setting. However, having a large number of multi-class outputs per genome per individual calls for further optimizations and/or approximations specific to this application. Here we explore the effectiveness of linear models for genotype imputation to convert them to privacy-preserving equivalents using standardized homomorphic encryption schemes. Our results show that performance of our privacy-preserving genotype imputation method is equivalent to the state-of-the-art plaintext solutions, achieving up to 99% micro area under curve score, even on real-world large-scale datasets up to 80,000 targets.

Erratic journey of CRISPR/Cas9 in oncology from bench-work to successful-clinical therapy.

CRISPR is a customized molecular scissor, comprising genetic guide made of RNA and an enzyme, Cas9 which snips DNA in simpler, cheaper and more precise way than any other gene editing tools. In recent years CRISPR/Cas has taken the research world by storm being go-to genome editor for potential gene therapy to fix cancer as well as several hereditary disorders. This review explores the literature around the mechanism of Nobel winning CRISPR/Cas9 and its journey from its discovery to various pre-clinical and clinical trials in oncology, focusing mostly on PD-1 knockout CAR-T cell therapy. It also discusses the hurdles and ethical dispute associated with CRISPR, such as unintended on-target and off-target cuts, embryonic germ-line editing. Despite the controversies regarding the safety of this technique, many studies reported promising results on targeting cancer and other diseases using CRISPR/Cas9. Outcomes from the first successful clinical trial showed the beneficial long term effect on genetically modified T-cells in targeting cancer cells which opens the door for CRISPR to be the most preferred technique to help treating cancer and other diseases in future. As far as germ-line editing is concerned, further studies are needed to support the safety of this technique in humans fixing genetic disorders and mutations. Therefore till date only somatic cell editing is ethically approved.

In vitro Effect of Chlorquine and Picroliv on Plasmodium Berghei Induced Alterations in the Activity of Adenosine Triphosphatase, Aryl Hyrocarbon Hydroxylase Enzymes and Malondialdehyde in Spleen Explant Culture.

BACKGROUND: In recent years, great progress has been made in reducing the high level of malaria suffering worldwide. There is a great need to evaluate drug resistance reversers and consider new medicines against malaria. There are many approaches to the development of antimalarial drugs. Specific concerns must be taken into account in these approaches, in particular the requirement for inexpensive and simple new therapies and the need to limit drug discovery expenses. Important ongoing efforts are the optimisation of treatment with available medications, including the use of combination therapy, the production of analogs of known agents and the identification of natural products, the use of compounds originally developed against other diseases, the assessment of overcoming drug resistance and the consideration of new therapeutic targets. Liver and spleen are the important organs which are directly associated with malarial complications. AIM: An analysis of the Activity of Adenosine Triphosphatase, Aryl Hyrocarbon Hydroxylase Enzymes and Malondialdehyde in spleen Explant Culture. OBJECTIVE: To determine in vitro effectof Chlorquine and Picroliv on Plasmodium Berghei induced alterations in the Activity of Adenosine Triphosphatase, Aryl Hyrocarbon Hydroxylase Enzymes and Malondialdehyde in spleen Explant Culture. MATERIALS AND METHODS: 1-Histological preparation of spleen explants for paraplast embedding. 2- Biochemicalstudies (Enzymes (Atpase, ALP&GST) and the level of protein, Malondialdehyde (MDA). RESULTS: Splenomegalyis isone of the three main diagnostic parameters of malaria infection besides fever and anaemia. Many enzymes present in the liver and spleen may also be altered or liberated under different pathological conditions. Enzymes (ATPase, ALP&GST) and the level of protein, Malondialdehyde (MDA) content was found to increase in the liver and spleen explants during malarial infection. In the liver and spleen derived from parasitized CQ treated animals, the activity of all the above enzymes (ATPase, ALP&GST) and the level of protein & MDA of liver/spleen reversed towards the normal for all the 4 or 3 days of incubations. Picroliv efficacy decreased with the increment of parasitaemia and at 60% parasitaemia. CONCLUSION: Alkalinephosphatase (ALP) was found to increase with increasing parasitaemia. After the addition of Picroliv to the medium, a decrement in the activity was observed up to day 4 of culture. A similar positive effect of Picroliv was observed on the ATPase and ALP activity of spleen explants. DNA and protein contents also increased in the parasitized liver cultured in the presence of picroliv. On the contrary, in the spleen explants DNA, protein and MDA content were found to decrease after Picroliv supplementation to the culture medium.

First-in-Human Randomized Study to Assess the Safety and Immunogenicity of an Investigational Respiratory Syncytial Virus (RSV) Vaccine Based on Chimpanzee-Adenovirus-155 Viral Vector-Expressing RSV Fusion, Nucleocapsid, and Antitermination Viral Proteins in Healthy Adults.

BACKGROUND: Respiratory syncytial virus (RSV) disease is a major cause of infant morbidity and mortality. This Phase I, randomized, observer-blind, placebo- and active-controlled study evaluated an investigational vaccine against RSV (ChAd155-RSV) using the viral vector chimpanzee-adenovirus-155, encoding RSV fusion (F), nucleocapsid, and transcription antitermination proteins. METHODS: Healthy 18-45-year-old adults received ChAd155-RSV, a placebo, or an active control (Bexsero) at Days (D) 0 and 30. An escalation from a low dose (5 × 109 viral particles) to a high dose (5 × 1010 viral particles) occurred after the first 16 participants. Endpoints were solicited/unsolicited and serious adverse events (SAEs), biochemical/hematological parameters, cell-mediated immunogenicity by enzyme-linked immunospot, functional neutralizing antibodies, anti RSV-F immunoglobin (Ig) G, and ChAd155 neutralizing antibodies. RESULTS: There were 7 participants who received the ChAd155-RSV low dose, 31 who received the ChAd155-RSV high dose, 19 who received the placebo, and 15 who received the active control. No dose-related toxicity or attributable SAEs at the 1-year follow-up were observed. The RSV-A neutralizing antibodies geometric mean titer ratios (post/pre-immunization) following a high dose were 2.6 (D30) and 2.3 (D60). The ratio of the fold-rise (D0 to D30) in anti-F IgG over the fold-rise in RSV-A-neutralizing antibodies was 1.01. At D7 after the high dose of the study vaccine, the median frequencies of circulating B-cells secreting anti-F antibodies were 133.3/106 (IgG) and 16.7/106 (IgA) in peripheral blood mononuclear cells (PBMCs). The median frequency of RSV-F-specific interferon γ-secreting T-cells after a ChAd155-RSV high dose was 108.3/106 PBMCs at D30, with no increase after the second dose. CONCLUSIONS: In adults previously naturally exposed to RSV, ChAd155-RSV generated increases in specific humoral and cellular immune responses without raising significant safety concerns. CLINICAL TRIALS REGISTRATION: NCT02491463.

A simple immunofixation test for induced C3 degradation in disease states (including C3 nephritic factor) and its correlation with kidney biopsy.

Complement dysregulation from an uncontrolled activation of the alternate pathway can be mediated by C3 Nephritic Factor and results in C3 glomerulopathy. Identification of C3 degradation products C3c and C3d in patient serum provides evidence of uncontrolled complement activation. It is possible to detect C3c and C3d in patient serum by an immunofixation assay which induces in vitro C3 degradation. The clinical performance of the immunofixation assay has been assessed by comparing the assay results with findings from immunostaining of kidney biopsies. The immunofixation assay is a simple and reliable technique for detection of C3 degradation on a widely available platform and can be used to provide corroborative evidence of acquired complement dysregulation in patients with C3 glomerulopathy.

Abnormalities of serum-free light chain in patients with primary antibody deficiency in the absence of B lymphocyte clonality.

AIMS: A review of practice to determine whether serum-free light chain (SFLC) assays are helpful in detecting underlying clonal B-cell disorders or amyloidosis in patients with primary antibody deficiency (PAD) and recurrent infection. METHODS: SFLC were assayed by nephelometry (BN2 nephelometer, Siemens; FREELITE assay, Binding Site). We reviewed SFLC test results recorded in our regional laboratory over a 4-year time period; 20 adults with PAD were identified as having been tested on at least two occasions. RESULTS: Of 20 patients, 4 with PAD had abnormal serum-free kappa/lambda (K/L) ratios but no evidence of B-cell clonality. We also found extremely low levels of kappa and or lambda (below the limits of reliable detection) in 19/20 PAD cases (mostly common variable immunodeficiency), such that in many, ratios were not calculable. CONCLUSIONS: The data suggest that the abnormal ratios are generated by an inability to produce and/or secrete SFLCs, particularly kappa FLC. In this small initial study, we seek to highlight PAD cases where a suspicious K/L ratio, typically with very low absolute quantities of SFLCs, most likely points to B-cell dysfunction, rather than to B lymphocyte clonality.

Increased incidence of infections following the late introduction of mycophenolate mofetil in renal transplant recipients.

BACKGROUND: Late introduction of mycophenolate mofetil (MMF) is used in renal transplant patients to allow calcineurin inhibitor (CNI) withdrawal. This change in treatment may alter the immunosuppressive load predisposing patients to infections. To assess this we have analysed infection rates in 30 consecutive patients with chronic allograft nephropathy commenced on MMF for CNI withdrawal. Methods and results. The study period was from 12 months pre-commencement to 12 months post-commencement. At commencement, patient mean age was 51.2 +/- 12.9 years and mean time post-transplant was 3170 +/- 2130 days. Estimated glomerular filtration rate (eGFR) at the start of the study period and at conversion was 30.7 +/- 12.1 ml/min and 23.1 +/- 9.9 ml/min, respectively. The mean dose of MMF post-conversion was 1575 +/- 428 mg/day. Estimated GFR had stabilized at 12 months post-conversion to 25.3 +/- 12.2 ml/min. There was a significant increase in infections following conversion: pre-conversion, 26.7% (8/30); post-conversion, 66.6% (20/30) (chi(2) = 24.5, P < 0.0005). There was an inverse correlation between eGFR at conversion and infection rates post-conversion (r = -0.379, P = 0.039). There were no hospitalizations for infection pre-conversion and 6 patients (20%) were hospitalized post-conversion, for a total of 285 days (7-107). CONCLUSION: There is significant morbidity associated with an increased incidence of infection after late introduction of MMF at standard doses in renal transplant recipients. This risk may be related to GFR at the time of conversion.