Accurate mutation annotation and functional prediction enhance the applicability of -omics data in precision medicine

Clinical sequencing has been recognized as an effective approach for enhancing the accuracy and efficiency of cancer patient management and therefore achieve the goals of personalized therapy. However, the accuracy of large scale sequencing data in clinics has been constrained by many different aspects, such as clinical detection, annotation and interpretation of the variants that are observed in clinical sequencing data. In my Ph.D thesis work, I mainly investigated how to comprehensively and efficiently apply high dimensional -omics data to enhance the capability of precision cancer medicine. Following this motivation, my dissertation has been focused on two important topics in translational genomics. 1) Developing a computational approach to resolve ambiguities in existing clinical genomic annotations and to facilitate correct diagnostic and treatment decisions. I have developed a multi-level variant annotator, TransVar, to perform precise annotation at genomic, mRNA and protein levels. TransVar implements three main functions: 1) it performs an innovative “reverse annotation” function, which identifies the genomic variants that can be translated into a given protein variant through alternative splicing. This function significantly improves the accuracy of genomic testing in clinics and functional validation in genomic laboratories; 2) It performs “equivalence annotation”, which identifies the protein variants having identical genomic origins with a given protein variant. This function resolves annotation inconsistencies among variants imported from different data sources, and is crucial for precise mutation biomarker identification and functional prediction; 3) It improves “forward annotation” (i.e., translation of genomic variants to protein variants) over existing annotators by more rigorously implementing the Human Genome Variation Society (HGVS) nomenclature. Our study also tried to illustrate the ambiguities of annotation among different transcript databases and different mutation types. TransVar standardizes mutation annotation and enables precise characterization of genomic variants in the context of functional genomic studies and clinical decision support and will significantly advance genomic medicine. 2) Developing a statistical framework to precisely identify hotspot mutations and investigate their functional impact on tumorigenesis and drug therapeutic response using large-scale -omics data. I have proposed a statistical model, which utilizes characteristics of genomic data to nominate 702 cancer type-specific hotspot mutations in 549 genes. It models background mutation rate variations among different genes, mutation subtypes and di-nucleotide sequence contexts and effectively identifies hotspots that have more than the expected number of recurrent mutations. We then investigate the mutational signatures represented by the hotspot mutations and find they vary from one tumor type to another, suggesting distinct mutational positive selections during different cancer progressions. In addition, we build an integrative statistical framework by using transcriptomics, proteomics and pharmacogenomics data to investigate the diverse functions of each hotspot mutation under different disease and biological contexts and to associate the effects of mutations on RNA/protein expression, pathway activity, and drug sensitivity. We not only validate diverse functions of well-known hotspot mutations in different contexts, but also identify some novel hotspot mutations such as MAP3K4 A1199 deletion, NR1H2 R175 insertion, and GATA3 P409 insertion with different functional associations. Our study addresses a long-term challenge of explicitly distinguishing driver mutations from passengers, and nominates a set of putative driver mutations that possess diverse functional potentials. The translational genomics research I conducted in my Ph.D study will benefit the cancer research community. The tools I developed will answer translational genomics questions such as identification of biomarkers for clinical diagnostics and treatment, and promote our understanding of the biological function of driver mutations towards the realization of personalized medicine

novoBreak: local assembly for breakpoint detection in cancer genomes.

We present novoBreak, a genome-wide local assembly algorithm that discovers somatic and germline structural variation breakpoints in whole-genome sequencing data. novoBreak consistently outperformed existing algorithms on real cancer genome data and on synthetic tumors in the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge primarily because it more effectively utilized reads spanning breakpoints. novoBreak also demonstrated great sensitivity in identifying short insertions and deletions

Quantum Instruction Set Design for Performance

A quantum instruction set is where quantum hardware and software meet. We develop new characterization and compilation techniques for non-Clifford gates to accurately evaluate different quantum instruction set designs. We specifically apply them to our fluxonium processor that supports mainstream instruction $\mathrm{iSWAP}$ by calibrating and characterizing its square root $\mathrm{SQiSW}$. We measure a gate fidelity of up to $99.72\%$ with an average of $99.31\%$ and realize Haar random two-qubit gates using $\mathrm{SQiSW}$ with an average fidelity of $96.38\%$. This is an average error reduction of $41\%$ for the former and a $50\%$ reduction for the latter compared to using $\mathrm{iSWAP}$ on the same processor. This shows designing the quantum instruction set consisting of $\mathrm{SQiSW}$ and single-qubit gates on such platforms leads to a performance boost at almost no cost.Comment: 2 figures in main text and 21 figures in Supplementary Materials. This manuscript subsumes version 1 with significant improvements such as experimental demonstration and materials presentatio

Évaluation de polymorphismes de p22phox, RAGE et ALOX12 dans la survenue de la néphropathie diabétique chez le type 1 (projet NEPHRODIANOX)

Le stress oxydant est un des mécanismes clefs dans la physiopathologie de la néphropathie diabétique chez le patient type 1. Nous avons évalué l association de polymorphismes de trois gènes impliqués dans cette voie : C242T de CYBA (p22phox), -374T/A et -429T/C de RAGE, et Arg261Gln d ALOX12, dans le délai de survenue de la néphropathie microalbuminurique chez le patient diabétique de type 1. 162 patients type 1, ancienneté moyenne du diabète de 32,9 +/- 9 ans, inclus au CHU de Grenoble. 53 patients présentaient une microalbuminurie (> 30 mg/L) et 109 indemnes de néphropathie. Nous avons determiné pour chaque patient son statut vis-à-vis de chacun des polymorphysmes étudiés, et évalué leurs associations à la survenue de la microalbuminurie dans un modèle de cox. Le modèle de cox en analyse multi-variée retrouve quatre facteurs associés au délai de survenue de la néphroapthie diabétique : RAGE 374AA (HR 4.19 [1.84-9.58] (p=0.001)), p22phox TT+TC (HR 2.1 [1.16-3.8], p= 0.015), mais égalment le sexe masculin (HR 1.92 [1.07-3.43], p=0.028) et le diagnostique du diabète à l âge pédiatrique (HR 1.85 [1.03-3.32], p=0.039). Nous retrouvons également une association avec le délai de survenue de l IRCT (p= 0.028 pour p22phox TC+TT, et p=0.033 pour RAGE 374AA). Le polymorphisme C242T de p22phox semble indépendant de la rétinopathie. Conclusion : les polymorphismes C242T de p22phox et -374T/A de RAGE sont associés à une survenue plus précoce de la microalbuminurie dans une population de diabétiques de type 1 française. L indépendance de la rétinopathie ainsi que l association avec la survenue de l IRCT nous fournissent des arguments supplémentaires leur implication.Background: Oxidative stress is a key component of type 1 diabetic nephropathy. Therefore, we investigated the association between polymorphisms of three genes implicated in this pathway: C242T of CYBA (p22phox), -374T/A and -429T/C of RAGE, as Arg261Gln of ALOX 12, in the delay of microalbuminuria onset in type 1 diabetic patients. Methods: 162 diabetic type 1 patients with 32.9 +/- 9 years of diabetes duration were included at the Grenoble University Hospital. 53 presented a history of persistent microalbuminuria (> 30 mg/l) and 109 did not. Delay between microalbuminuria and diabetes diagnosis, as end stage renal disease (ESRD) onset and bio-clinical data, were recorded. Polymorphism status was determined and its association to microalbumuria was assessed with a Cox regression model. Results: All polymorphisms respect the Hardy Weinberg equilibrium. At univariate level, C242T dominant model (13.6% TT, 45.7% TC, 41.7% CC) and -374T/A (5.6% AA, 35.2% TA, 59% TT) were significantly correlated with microalbuminuria (p=0.038, 0.0021 respectively). The Cox regression model validated four significant variables: RAGE 374AA (HR 4.19 [1.84-9.58] (p=0.001)), p22phox TT+TC (HR 2.1 [1.16-3.8], p= 0.015), associated with male sex (HR 1.92 [1.07-3.43], p=0.028) and diabetes diagnosis at pediatric age (HR 1.85 [1.03-3.32], p=0.039). The same association was found with ESRD (p= 0.028 for p22phox TC+TT, and p=0.033 for RAGE 374AA). The C242T polymorphism was independent of retinopathy onset (66.7% of CC patients versus 63.6% of CT+TT p=0.6 for superiority and p=0.043 for non inferiority). Finally we suspected an increasing risk with polymorphism associations but it did not reach significant level. Conclusions: p22phox C242T, and RAGE-374T/A correlate with microalbuminuria onset in a type 1 diabetic French population. The same correlation with ESRD onset provides argument for the involvement of a genetic predisposition involving renal oxidative stress for diabetic nephropathy independently of retinopathy for C242T.GRENOBLE1-BU Médecine pharm. (385162101) / SudocSudocFranceF

Identify optimal HAP series scores for unresectable HCC patients undergoing TACE plus sorafenib: A Chinese multicenter observational study

BackgroundHepatoma arterial-embolization prognostic (HAP) series scores have been proposed for prognostic prediction in patients with unresectable hepatocellular carcinoma (uHCC) undergoing transarterial chemoembolization (TACE). However, their prognostic value in TACE plus sorafenib (TACE-S) remains unknown. Here, we aim to evaluate their prognostic performance in such conditions and identify the best model for this combination therapy.MethodsBetween January 2012 and December 2018, consecutive patients with uHCC receiving TACE-S were recruited from 15 tertiary hospitals in China. Cox regression analyses were used to investigate the prognostic values of baseline factors and every scoring system. Their prognostic performance and discriminatory performance were evaluated and confirmed in subgroup analyses.ResultsA total of 404 patients were enrolled. In the whole cohort, the median follow-up period was 44.2 (interquartile range (IQR), 33.2–60.7) months, the median overall survival (OS) time was 13.2 months, and 336 (83.2%) patients died at the end of the follow-up period. According to multivariate analyses, HAP series scores were independent prognostic indicators of OS. In addition, the C-index, Akaike information criterion (AIC) values, and time-dependent area under the receiver operating characteristic (ROC) curve (AUC) indicated that modified HAP (mHAP)-III had the best predictive performance. Furthermore, the results remained consistent in most subsets of patients.ConclusionHAP series scores exhibited good predictive ability in uHCC patients accepting TACE-S, and the mHAP-III score was found to be superior to the other HAP series scores in predicting OS. Future prospective high-quality studies should be conducted to confirm our results and help with treatment decision-making

Potential candidates for liver resection in liver-confined advanced HCC: a Chinese multicenter observational study

BackgroundAdvanced hepatocellular carcinoma (HCC) is characterized as symptomatic tumors [performance status (PS) score of 1-2], vascular invasion and extrahepatic spread, but patients with PS1 alone may be eliminated from this stage. Although liver resection is used for liver-confined HCC, its role in patients with PS1 alone remains controversial. Therefore, we aimed to explore its application in such patients and identify potential candidates.MethodsEligible liver-confined HCC patients undergoing liver resection were retrospectively screened in 15 Chinese tertiary hospitals, with limited tumor burden, liver function and PS scores. Cox-regression survival analysis was used to investigate the prognostic factors and develop a risk-scoring system, according to which patients were substratified using fitting curves and the predictive values of PS were explored in each stratification.ResultsFrom January 2010 to October 2021, 1535 consecutive patients were selected. In the whole cohort, PS, AFP, tumor size and albumin were correlated with survival (adjusted P<0.05), based on which risk scores of every patient were calculated and ranged from 0 to 18. Fitting curve analysis demonstrated that the prognostic abilities of PS varied with risk scores and that the patients should be divided into three risk stratifications. Importantly, in the low-risk stratification, PS lost its prognostic value, and patients with PS1 alone achieved a satisfactory 5-year survival rate of 78.0%, which was comparable with that PS0 patients (84.6%).ConclusionSelected patients with PS1 alone and an ideal baseline condition may benefit from liver resection and may migrate forward to BCLC stage A

Maternal microbe-specific modulation of the offspring microbiome and development during pregnancy and lactation

ABSTRACTThe maternal microbiome is essential for the healthy growth and development of offspring and has long-term effects later in life. Recent advances indicate that the maternal microbiome begins to regulate fetal health and development during pregnancy. Furthermore, the maternal microbiome continues to affect early microbial colonization via birth and breastfeeding. Compelling evidence indicates that the maternal microbiome is involved in the regulation of immune and brain development and affects the risk of related diseases. Modulating offspring development by maternal diet and probiotic intervention during pregnancy and breastfeeding could be a promising therapy in the future. In this review, we summarize and discuss the current understanding of maternal microbiota development, perinatal microbial metabolite transfer, mother-to-infant microbial transmission during/after birth and its association with immune and brain development as well as corresponding diseases

Steroid Receptor Coactivator 3 Is Required for Clearing Bacteria and Repressing Inflammatory Response in Escherichia coli-Induced Septic Peritonitis

National Natural Science Foundation of China [30600566, 30770455]; National Basic Research Program of China (973 Program) [2008CB517311, 2009CB522200]; Science Planning Program of Fujian Province [2009J1010]; National Institutes of Health [DK058242]Steroid receptor coactivator 3 (SRC-3) is a multifunctional protein that plays an important role in regulation of bacterial LPS-induced inflammation. However, its involvement in host defense against bacterial infection remains unclear. In this study, we used SRC-3 knockout mice to assess the role of SRC-3 in antibacterial defense in Escherichia coli-induced septic peritonitis. After E. coli bacteria were injected i.p., SRC-3-deficient mice exhibited excessive local and systemic inflammatory responses and more severe bacterial burdens, leading to a significantly higher mortality compared with wild-type mice. Peritoneal macrophages of SRC-3-deficient mice showed a decrease in bacterial phagocytosis in culture and an increase in apoptosis, which was consistent with the defective bacterial clearance observed in SRC-3-deficient mice. Accordingly, SRC-3 null macrophages expressed much lower levels of scavenger receptor A, the antioxidant enzyme catalase, and antiapoptotic gene Bcl-2. Collectively, our data demonstrate that SRC-3 is important not only in modulating the local and systemic inflammation but also in intensifying bacterial clearance, which highlights a pivotal role of SRC-3 in the host defense system against bacterial infection. The Journal of Immunology, 2010, 185: 5444-5452

MPP8 Governs the Activity of the LIF/STAT3 Pathway and Plays a Crucial Role in the Differentiation of Mouse Embryonic Stem Cells

Mouse embryonic stem cells (mESCs) possess the remarkable characteristics of unlimited self-renewal and pluripotency, which render them highly valuable for both fundamental research and clinical applications. A comprehensive understanding of the molecular mechanisms underlying mESC function is of the utmost importance. The Human Silence Hub (HUSH) complex, comprising FAM208A, MPP8, and periphilin, constitutes an epigenetic silencing complex involved in suppressing retroviruses and transposons during early embryonic development. However, its precise role in regulating mESC pluripotency and differentiation remains elusive. In this study, we generated homogenous miniIAA7-tagged Mpp8 mouse ES cell lines. Upon induction of MPP8 protein degradation, we observed the impaired proliferation and reduced colony formation ability of mESCs. Furthermore, this study unveils the involvement of MPP8 in regulating the activity of the LIF/STAT3 signaling pathway and Nanog expression in mESCs. Finally, we provide compelling evidence that degradation of the MPP8 protein impairs the differentiation of mESC