Publications by authors named "Jonathan Lopez"

66 Publications

Oropharyngeal squamous cell carcinoma: p16/p53 immunohistochemistry as a strong predictor of HPV tumor status.

Histopathology 2021 Feb 9. Epub 2021 Feb 9.

Department of Pathology, Institut de Pathologie Multisite, Groupement Hospitalier Sud, Pierre-Bénite, Hospices Civils de Lyon.

Aims: Oropharyngeal squamous cell carcinomas (OPSCC) related to human papillomavirus (HPV) infection have a better prognosis than those without HPV infection. Although p16 overexpression is used as a surrogate marker for HPV infection, 5%-20% of p16-positive OPSCC are described as being unrelated to HPV infection, with worse overall survival compared to OPSCC-related HPV. There is, therefore, a risk of undertreating a proportion of OPSCC patients falsely considered as HPV-driven because of p16 positivity. TP53 mutations are highly prevalent in OPSCC driven by mutagens in tobacco and alcohol. We describe herein a combined p16/p53 algorithm to predict HPV tumor status in OPSCC.

Methods And Results: 110 OPSCC were identified in the database of the pathology department and were studied using p16 and p53 immunohistochemistry. For p16-positive or p16-negative/wild-type patterns-p53 (WT-p53) cases (n = 63), DNA in-situ hybridization for high-risk HPV was performed and if negative, the HPV status was controlled by HPV DNA PCR (n=19). A significant association between TP53 mutation and pattern of p53 expression was found (WT-p53, 7/16, P<0.001). The p16-positive/WT-p53 was significantly associated with HPV+ tumor status (p16-positive/WT-p53, 50/110, P<0.001). Interestingly, a subset of p16-positive OPSCC was unrelated to HPV (13.5%, 8/59) and showed mutant-type staining of p53 expression.

Conclusions: The p16 protein immunopositivity in conjunction with the mutant-type pattern of p53 staining helped to reclassify a subset of p16-positive OPSCC as OPSCC-unrelated HPV. This approach could be routinely applied by pathologists involved in the management of OPSCC, because of their potential therapeutic implications.
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http://dx.doi.org/10.1111/his.14350DOI Listing
February 2021

Two Missense CACNA1A Variants in a Single Family with Variable Neurobehavioral, Cerebellar, Epileptic, and Oculomotor Features.

Neuropediatrics 2021 Jan 14. Epub 2021 Jan 14.

Division of Pediatric Neurology, Department of Neurology, University of Washington, Seattle, Washington, United States.

We describe two novel missense variants in segregating in a family with variable severity of ataxia/oculomotor dysfunction, neurobehavioral impairments, and epilepsy. The most severe outcome occurred in a compound heterozygous proband, which could represent variable expression of the paternal allele or biallelic modulation of calcium channel function. Acetazolamide and lamotrigine were effective for seizure control.
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http://dx.doi.org/10.1055/s-0040-1721686DOI Listing
January 2021

BRD4-mediated repression of p53 is a target for combination therapy in AML.

Nat Commun 2021 01 11;12(1):241. Epub 2021 Jan 11.

Paul O'Gorman Leukemia Research Centre, Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.

Acute myeloid leukemia (AML) is a typically lethal molecularly heterogeneous disease, with few broad-spectrum therapeutic targets. Unusually, most AML retain wild-type TP53, encoding the pro-apoptotic tumor suppressor p53. MDM2 inhibitors (MDM2i), which activate wild-type p53, and BET inhibitors (BETi), targeting the BET-family co-activator BRD4, both show encouraging pre-clinical activity, but limited clinical activity as single agents. Here, we report enhanced toxicity of combined MDM2i and BETi towards AML cell lines, primary human blasts and mouse models, resulting from BETi's ability to evict an unexpected repressive form of BRD4 from p53 target genes, and hence potentiate MDM2i-induced p53 activation. These results indicate that wild-type TP53 and a transcriptional repressor function of BRD4 together represent a potential broad-spectrum synthetic therapeutic vulnerability for AML.
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http://dx.doi.org/10.1038/s41467-020-20378-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801601PMC
January 2021

RAS/TP53 co-Mutation is Associated with Worse Survival after Concurrent Resection of Colorectal Liver Metastases and Extrahepatic Disease.

Ann Surg 2020 Dec 18;Publish Ahead of Print. Epub 2020 Dec 18.

Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA Department of Surgical Oncology, CHU Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France EMR 3738, CICLY, Université Claude Bernard Lyon 1, Lyon, France Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France / Department of Biochemistry and Molecular Biology, Lyon University Hospital, Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Lyon, France.

Objective: To determine if tumor genetics are associated with overall survival (OS) after concurrent resection of colorectal liver metastases (CLM) and extrahepatic disease (EHD).

Summary Background Data: The prognosis for patients who undergo concurrent resection of CLM/EHD is unclear and the impact of somatic mutations has not been reported.

Methods: Patients undergoing concurrent resection of CLM and EHD from 2007-2017 were identified from two academic centers. From 1 center, patients were selected from a pre-existing database of patients undergoing cytoreductive surgery with hyperthermic intraperitoneal chemotherapy (HIPEC). The Kaplan-Meier method was used to construct survival curves, compared using the log-rank test. Multivariable Cox analysis for OS was performed.

Results: One hundred nine patients were included. Most common EHD sites included lung (33 patients), peritoneum (32), and portal lymph nodes (14). TP53 mutation was the most common mutation, identified in 75 patients (69%), and RAS/TP53 co-mutation was identified in 31 patients (28%). The median OS was 49 months (IQR, 24-125), and 3- and 5-year OS rates were 66% and 44%, respectively. Compared to patients without RAS/TP53 co-mutation, patients with RAS/TP53 co-mutation had lower median OS: 39 vs. 51 months (P = .02). On multivariable analysis, lung EHD (hazard ratio [HR], 0.7; 95% CI, 0.3-1.4), peritoneal EHD (HR, 2.2; 95% CI, 1.1-4.2) and RAS/TP53 co-mutation (HR, 2.8; 95% CI, 1.1-7.2) were independently associated with OS.

Conclusions: RAS/TP53 co-mutation is associated with worse OS after concurrent CLM/EHD resection. Mutational status and site of EHD should be included in the evaluation of patients considered for concurrent resection.
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http://dx.doi.org/10.1097/SLA.0000000000004672DOI Listing
December 2020

[Hobnail variant of papillary thyroid carcinoma].

Ann Pathol 2021 Apr 4;41(2):201-206. Epub 2020 Dec 4.

Service d'anatomie et cytologie pathologiques, CHU de Lyon-Sud, chemin du Grand-Revoyet, 69495 Pierre-Bénite cedex, France; Inserm1052 CNRS5286, Cancer Research Center of Lyon, Lyon 1 University, Lyon, France.

We report the case of a hobnail variant of papillary thyroid carcinoma revealed by a cervical mass in a 67 years-old patient. This new entity in the 2017 WHO classification is rare. Histopathological diagnosis is based on four main criteria, present in≥30% of tumor cells: a discohesive tumor, micropapillary structures and loss of cell polarity and hobnail cells. This tumor expresses markers of thyroid differentiation. The most widely described molecular alteration is BRAF V600E mutation associated with other alterations, especially p53 mutations. This reflects the agressivness of this variant. It is important to recognize the hobnail variant of papillary thyroid carcinoma and to specify it in the pathological report because of its more pejorative prognosis, with local invasion, lymph node and distant metastasis, and deacreased survival. No specific management is recommended, but a close follow up seems necessary.
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http://dx.doi.org/10.1016/j.annpat.2020.10.004DOI Listing
April 2021

Awake Mapping of the Auditory Cortex during Tumor Resection in an Aspiring Musical Performer: A Case Report.

Pediatr Neurosurg 2020 1;55(6):351-358. Epub 2020 Dec 1.

Department of Neurosurgery, Seattle Children's Hospital, Seattle, Washington, USA.

Introduction: Preoperative functional MRI (fMRI) and intraoperative awake cortical mapping are established strategies to identify and preserve critical language structures during neurosurgery. There is growing appreciation for the need to similarly identify and preserve eloquent tissue critical for music production.

Case Report: A 19-year-old female musician, with a 3- to 4-year history of events concerning for musicogenic seizures, was found to have a right posterior temporal tumor, concerning for a low-grade glial neoplasm. Preoperative fMRI assessing passive and active musical tasks localized areas of activation directly adjacent to the tumor margin. Cortical stimulation during various musical tasks did not identify eloquent tissue near the surgical site. A gross total tumor resection was achieved without disruption of singing ability. At 9-month follow-up, the patient continued to have preserved musical ability with full resolution of seizures and without evidence of residual lesion or recurrence.

Conclusion: A novel strategy for performing an awake craniotomy, incorporating preoperative fMRI data for music processing with intraoperative cortical stimulation, interpreted with the assistance of a musician expert and facilitated gross total resection of the patient's tumor without comprising her musical abilities.
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http://dx.doi.org/10.1159/000509328DOI Listing
December 2020

ctDNA in neuroendocrine carcinoma of gastroenteropancreatic origin or of unknown primary: the CIRCAN-NEC pilot study.

Neuroendocrinology 2020 Oct 23. Epub 2020 Oct 23.

Introduction: Gastroenteropancreatic neuroendocrine carcinomas (GEPNEC) are characterised by a heterogeneous molecular profile and a poor prognosis. Circulating tumour DNA (ctDNA) analysis may be useful for NEC management. This study aimed at describing ctDNA mutations, to assess their predictive value for response to chemotherapies, and their change according to disease progression.

Methods: The CIRCAN-NEC study included patients with GEPNEC or NEC from an unknown primary, scheduled to begin first or second-line chemotherapy. Blood samples were collected prior to chemotherapy initiation, at first evaluation, and during disease progression. ctDNA were sequenced by next-generation sequencing (NGS). Molecular response was defined as a decrease of at least 30% of the mutant allele fraction (MAF).

Results: All 24 patients included received platinum-etoposide first-line chemotherapy; 19 received a FOLFIRI-based post first-line regimen. Twenty-two patients had at least one driver mutation: TP53 (n=21), RB1 (n=2), KRAS (n=4), BRAF (n=3). Ten (42%) had a "adenocarcinoma-like" profile. Five of six patients with matching ctDNA/tissue NGS harboured at least one concordant mutation (44% concordance at the gene level). The concordance rate between ctDNA-mutation/immunohistochemistry-profile was 64% (7/11) for TP53/p53+ and 14% (1/7) for RB1/pRb-. In this pilot study including few patients by subgroups, patients with KRAS (HR=3.60, 95%CI [1.06-12.04]) and BRAF (HR=4.25, 95%CI [1.11-16.40]) mutations had shorter progression-free survival (PFS) under platinum-etoposide, while the two patients with RB1 mutations had shorter PFS under FOLFIRI-based chemotherapy. Twenty-eight periods of treatment were assessed: 10 patients had a molecular response (7/10 had a morphological response), which was associated with longer PFS (HR=0.37, 95%CI [0.15; 0.91]).

Conclusion: This pilot study shows a high sensitivity of ctDNA assessment, which is encouraging for the future management of GEPNEC (tumour molecular diagnosis and evaluation of disease progression).
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http://dx.doi.org/10.1159/000512502DOI Listing
October 2020

Deciphering heterogeneity of septic shock patients using immune functional assays: a proof of concept study.

Sci Rep 2020 09 30;10(1):16136. Epub 2020 Sep 30.

Laboratoire Commun de Recherche Hospices Civils de Lyon-bioMérieux, Joint Research Unit Hospices Civils de Lyon-bioMérieux, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Bâtiment 3F, Pierre-Bénite, 69495, Lyon, France.

The complexity of sepsis pathophysiology hinders patient management and therapeutic decisions. In this proof-of-concept study we characterised the underlying host immune response alterations using a standardised immune functional assay (IFA) in order to stratify a sepsis population. In septic shock patients, ex vivo LPS and SEB stimulations modulated, respectively, 5.3% (1/19) and 57.1% (12/21) of the pathways modulated in healthy volunteers (HV), highlighting deeper alterations induced by LPS than by SEB. SEB-based clustering, identified 3 severity-based groups of septic patients significantly different regarding mHLA-DR expression and TNFα level post-LPS, as well as 28-day mortality, and nosocomial infections. Combining the results from two independent cohorts gathering 20 HV and 60 patients, 1 cluster grouped all HV with 12% of patients. The second cluster grouped 42% of patients and contained all non-survivors. The third cluster grouped 46% of patients, including 78% of those with nosocomial infections. The molecular features of these clusters indicated a distinctive contribution of previously described genes defining a "healthy-immune response" and a "sepsis-related host response". The third cluster was characterised by potential immune recovery that underlines the possible added value of SEB-based IFA to capture the sepsis immune response and contribute to personalised management.
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http://dx.doi.org/10.1038/s41598-020-73014-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7527338PMC
September 2020

Front-Line Maintenance Therapy in Advanced Ovarian Cancer-Current Advances and Perspectives.

Cancers (Basel) 2020 Aug 25;12(9). Epub 2020 Aug 25.

Oncology Department, Hôpital Lyon Sud, Institut de Cancérologie des Hospices Civils de Lyon (IC-HCL) and Université de Lyon, 69310 Lyon, France.

Ovarian tumor is the gynecological cancer associated with the highest mortality. Most diseases are diagnosed at an advanced stage, which impairs the chances of prolonged complete remission. The standard front-line treatment of advanced stages combines surgery in an expert center with platinum-based chemotherapy. Most patients experience a relapse in the years following the initial treatment. During the last decade, anti-angiogenic agents used in the maintenance setting improved progression free survival (PFS) over chemotherapy alone. More recently, PARP inhibitors demonstrated substantial efficacy, mainly in patients with germinal or somatic mutations or other homologous recombination deficiencies (HRD), all involved in double strand DNA Damage Repair (DDR). Other therapeutic paradigms are currently being explored, including combinations of immune-checkpoints inhibitors, chemotherapy, bevacizumab and PARP inhibitors. In addition to these clinical advances, molecular characterization of the tumors and their correlations with drugs efficacy are needed to better understand which patient will benefit the most from the various treatments available to date.
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http://dx.doi.org/10.3390/cancers12092414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7564452PMC
August 2020

Apparent False Lateralization of Seizure Onset by Scalp EEG in Temporal Lobe Epilepsy Associated with Cerebral Cavernous Malformation: A Case Report and Overview.

Brain Sci 2020 Aug 24;10(9). Epub 2020 Aug 24.

Escuela de Medicina y Ciencias de la Salud, GI en Neurociencias-NeURos, Universidad del Rosario, Bogotá 111221, Colombia.

False lateralization of ictal onset by scalp electroencephalogram (EEG) is an infrequent entity that has been reported in patients with mesial temporal lobe epilepsy associated with hippocampal sclerosis (HS). In these cases, a tendency for rapid seizures that spread through the frontal-limbic system and hippocampal commissural pathways to the contralateral hemisphere has been proposed. Cerebral cavernous malformations (CCMs), which constitute a collection of abnormally configured small blood vessels with irregular structures, is a well-defined epilepsy-associated pathology. Their primary association with seizures might be explained either as a result of physiological changes affecting the cerebral cortex immediately surrounding the CCM (an epileptogenic mechanism that is relevant for both, temporal and extratemporal lesions) or as a result of promoting epileptogenicity in remote but anatomo-functionally connected brain regions, a mechanism that is particularly relevant for temporal lobe lesions. To date, there have been only two publications on falsely lateralizing ictal onsets by EEG in temporal cavernoma, but not in other regions. Here, we report a rare case of apparent false lateralization of ictal onset by scalp EEG in a patient with a left medial frontal gyrus cavernoma (supplementary motor area), and discuss some relevant pathophysiological mechanisms of false lateralization.
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http://dx.doi.org/10.3390/brainsci10090584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7565586PMC
August 2020

Cytological features and nuclear scores: Diagnostic tools in preoperative fine needle aspiration of indeterminate thyroid nodules with RAS or BRAF K601E mutations?

Cytopathology 2021 01 12;32(1):37-44. Epub 2020 Oct 12.

Centre de Biologie et Pathologie Sud, Centre Hospitalier Lyon Sud, Pierre Bénite, France.

Introduction: The cytological diagnosis of follicular-patterned thyroid lesions is challenging, especially since the World Health Organisation classification has recognised non-invasive follicular thyroid neoplasm with papillary-like features. These entities are often classified as indeterminate on cytology. Molecular testing has been proposed to help classify indeterminate nodules. RAS and K601E BRAF mutations are mostly encountered in follicular-patterned lesions, but their diagnostic value is not well established. Nuclear scores have also been proposed to help classify indeterminate lesions.

Objective: To investigate the correlation between cytological features and histology and to assess nuclear scores in a series of indeterminate RAS or BRAF K601E positive thyroid nodules.

Methods: The cytological parameters of 69 indeterminate RAS or BRAF K601E-positive thyroid nodules were evaluated. The Strickland and Maletta scores and a new nuclear score were assessed. Diagnosis of malignant, benign or indolent neoplasms was confirmed in each case by histology. Malignant and indolent nodules were considered surgical nodules, and adenomas non-surgical nodule.

Results: Surgical nodules were associated with the presence of ground glass nuclei (P = .001), grooves (P < .001) or irregular nuclear membranes (P = .01) on cytology. Nuclear scores were more often ≥2 in surgical nodules compared to benign ones (P < .001), with high sensitivity, but a low negative predictive value.

Conclusions: Analysis of nuclear features is useful to distinguish non-surgical from surgical nodules in indeterminate FNAs. Although nuclear scores are not ideal rule-out tests for indeterminate RAS or BRAF K601E positive nodules, they seem useful to screen non-molecular tested or non-mutated indeterminate FNAs. This work shows that meticulous analysis of nuclear features on cytological specimens can be useful to distinguish non-surgical nodules (adenoma) from surgical nodules in indeterminate FNAs. Although nuclear scores are not rule-out tests for indeterminate RAS or BRAF K601E positive nodules, they are useful in screening non-molecular tested or non-mutated indeterminate FNAs for surgery.
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http://dx.doi.org/10.1111/cyt.12904DOI Listing
January 2021

Lipofibromatosis-Like Neural Tumor: A Case Report and Review of the Literature.

Am J Dermatopathol 2020 Nov;42(11):881-884

Hospices Civils de Lyon, Hôpital Lyon Sud, Service d'anatomie et de cytologie pathologiques, Pierre Bénite, France.

Lipofibromatosis-like neural tumors (LPF-NT) are soft tissue tumors characterized by a lipofibromatosis-like pattern, CD34/PS100 positivity, and recurrent NTRK1 gene rearrangement. It occurs mainly in pediatric patients or young adults. We report here, the first case of LPF-NT in a middle-aged adult initially misdiagnosed as a myoepithelial tumor. LPF-NT may have a locally aggressive course but no recurrence was seen after complete surgeries, whereas metastatic diseases remain exceptional.
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http://dx.doi.org/10.1097/DAD.0000000000001734DOI Listing
November 2020

Animal aggregations promote emergent aquatic plant production at the aquatic-terrestrial interface.

Ecology 2020 10 19;101(10):e03126. Epub 2020 Aug 19.

Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019, USA.

The roles mobile animals and abiotic processes play as vectors for resource transfers between ecosystems ("subsidies") are well studied, but the idea that resources from animals with limited mobility may be transported across boundaries through intermediate taxa remains unexplored. Aquatic plants ("macrophytes") are globally distributed and may mediate transfers of aquatic-derived nutrients from aggregations of aquatic animals to terrestrial ecosystems when consumed by terrestrial herbivores. We used mesocosms (94 × 44 cm) to test whether aquatic animal-generated biogeochemical hotspots increase growth and nutrient content in macrophytes using the macrophyte Justicia americana and freshwater mussels. Justicia americana biomass production increased and belowground biomass allocation changed with increasing mussel density. At high mussel density, water-column phosphorus increased and carbon:phosphorus ratios in J. americana tissues decreased. We deployed motion-sensing cameras to explore herbivory on J. americana growing along the margins of the Kiamichi River, Oklahoma, and documented feeding by large mammals (Odocoileus virginianus, Sus scrofa, and Bos taurus). Thus, biogeochemical hotspots generated by aquatic animal aggregations can promote macrophyte production that subsequently is transferred to terrestrial animals. More broadly, this suggests that reductions in aquatic animal biomass may have bottom-up impacts that indirectly affect terrestrial ecosystems via plant-animal interactions bridging ecosystem boundaries.
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http://dx.doi.org/10.1002/ecy.3126DOI Listing
October 2020

Transcriptomic and immunohistochemical approaches identify HLA-G as a predictive biomarker of gestational choriocarcinoma resistance to monochemotherapy.

Gynecol Oncol 2020 09 5;158(3):785-793. Epub 2020 Jun 5.

Joint Research Unit Hospices Civils de Lyon-bioMérieux, Hospices Civils de Lyon, Lyon Sud Hospital, 165 chemin du grand Revoyet, 69495 Pierre Bénite, France; Medical Diagnostic Discovery Department (MD3), bioMérieux S.A., Marcy l'Etoile, France; Joint Research Unit Hospices Civils de Lyon-bioMérieux, EA 7426 Pathophysiology of Injury-Induced Immunosuppression, PI3, Claude Bernard Lyon 1 University, Edouard Herriot Hospital, Lyon, France.

Objective: Using a transcriptional approach on tissue samples, we sought to identify predictive biomarkers of post molar malignant transformation, and of choriocarcinoma chemosensitivity to mono- (methotrexate or actinomycin D) or polychemotherapy [EMA(Etoposide, Methotrexate, Actinomycin D)-CO(Cyclophosphamide, Vincristine) and EMA-EP(Etoposide, Cisplatine)] regimens.

Methods: We studied the expression of a 760-gene panel (PanCancer Pathway) related to oncogenesis and immune tolerance in tissue samples of complete hydatidiform moles and gestational choriocarcinoma.

Results: We did not identify any differentially expressed gene between moles with post molar malignant transformation in choriocarcinoma (n = 14) and moles with remission (n = 20). In monochemoresistant choriocarcinoma (n = 34), four genes (HLA-G, COL27A1, IL1R2 and GLI3) had a significantly reduced expression and one (THEM4) had an increased expression [FDR (false discovery rate) adjusted p-value ≤ 0.05] when compared to monochemosensitive choriocarcinoma (n = 9). The proportion of trophoblast cells and the intensity of immunohistochemical HLA-G expression were reduced in monochemoresistant choriocarcinoma (p < 0.05). In polychemoresistant choriocarcinoma (n = 20) we did not identify differentially expressed genes with an FDR adjusted p-value ≤ 0.05 when compared to polychemosensitive choriocarcinoma (n = 15). Gene pathway analysis revealed a predicted activation of IFN ᵞ in monochemoresistant choriocarcinoma and inhibited IL2 and TNF in polychemoresistant choriocarcinoma. The main biological functions predicted to be altered in chemoresistant choriocarcinoma were related to immunological homeostasis and leukopoiesis.

Conclusion: HLA-G is a strong candidate gene to predict choriocarcinoma resistance to monochemotherapy and that further studies are required to implement its routine quantification in the decision process for the management of gestational choriocarcinoma.
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http://dx.doi.org/10.1016/j.ygyno.2020.05.042DOI Listing
September 2020

Transcriptome profiling of gastric-type endocervical adenocarcinomas identifies key signaling pathways for tumor progression.

Gynecol Oncol 2020 06 18;157(3):775-782. Epub 2020 Apr 18.

Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France; Cancer Research Center of Lyon. INSERMU1052, Lyon, France; Réseau INCa des tumeurs rares gynecologiques (TMRG) and GYNECO group (www.ovaire-rare.org/TMRG), France.

Objective: Gastric-type endocervical carcinoma is a rare entity of carcinoma of the cervix. In contrast to the intestinal type, the gastric type is not related to Human Papilloma Virus (HPV) infection and has been reported to be much more aggressive than the usual type. Oncogenic pathways involved in this poor-prognosis phenotype are largely unexplored.

Methods: We compared activation of the main signaling pathways involved in cancer progression between the intestinal- (n = 5), gastric- (n = 6) and usual-type (n = 6) adenocarcinomas of the cervix using a targeted transcriptomic approach (expression of 770 genes) on FFPE samples.

Results: We identified a gene-expression signature composed of 11 genes that allows the classification of these endocervical carcinoma as three distinct molecular entities. There were similarities between mucinous endocervical carcinomas (gastric and intestinal types) despite difference in pathogenesis related to HPV infection. Among HPV-related endocervical carcinoma, the intestinal type could be molecularly distinguished from the usual type by high expression of EIF2AK3 and low expression of PPFIBP2 genes, supporting its classification as a distinct entity. Overexpression of TAL1 and S1PR1 genes were characteristic of the gastric type. The usual type was characterized by high expression of occludin and VAV3 genes. Tight junction disruptions might play an essential role in the metastatic potential of mucinous endocervical carcinoma with concomitant loss of OCLN and claudin 4 proteins. An overexpression of NTRK1 transcript was observed in mucinous endocervical carcinomas when compared to the usual type.

Conclusions: This transcriptomic study identified a signature that supports the classification of endocervical carcinomas as three distinct entities: usual-, intestinal- and gastric-type. It also points out to disruption of tight junctions as a potential mechanism of metastatic dissemination of these rare tumors.
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http://dx.doi.org/10.1016/j.ygyno.2020.04.046DOI Listing
June 2020

Poorly differentiated thyroid carcinoma with pleomorphic giant cells-a case report.

Virchows Arch 2020 Oct 1;477(4):597-601. Epub 2020 Apr 1.

Pathology Department, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre-Bénite, France.

Poorly differentiated thyroid carcinoma (PDTC) refers to a malignant tumour that displays an intermediate prognosis between well-differentiated carcinomas and anaplastic thyroid carcinomas (ATC). In the thyroid, pleomorphic giant cells are observed in ATC or in some non-neoplastic thyroid diseases. We described the case of a 43-year-old woman with a 34-mm nodule in her thyroid right lobe. Microscopic examination revealed an encapsulated tumour with a main solid growth pattern and extensive capsular invasion. Multiple images of angioinvasion were observed. There was neither necrosis nor inflammation. Most of the tumour cells were medium-sized and intermingled with pleomorphic giant tumour cells with bizarre features. The immunoprofile (keratins +, TTF1+, Pax 8+) proved their thyroid origin. By NGS, no molecular alteration was identified. The patient was treated by surgery and radioiodine therapy and she has no recurrence after a follow-up of 24 months. Our case meets all the histological criteria of the Turin proposal for PDTC but with pleomorphic giant cells and is very different from ATC according to clinical, histological and immunohistochemical features. Pleomorphic tumour giant cells in thyroid carcinomas could be present in PDTC and do not always represent dedifferentiation and more aggressive carcinoma, thyroid neoplasm.
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http://dx.doi.org/10.1007/s00428-020-02807-7DOI Listing
October 2020

The apoptosis inhibitor Bcl-xL controls breast cancer cell migration through mitochondria-dependent reactive oxygen species production.

Oncogene 2020 04 17;39(15):3056-3074. Epub 2020 Feb 17.

Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008, Lyon, France.

The Bcl-xL apoptosis inhibitor plays a major role in vertebrate development. In addition to its effect on apoptosis, Bcl-xL is also involved in cell migration and mitochondrial metabolism. These effects may favour the onset and dissemination of metastasis. However, the underlying molecular mechanisms remain to be fully understood. Here we focus on the control of cell migration by Bcl-xL in the context of breast cancer cells. We show that Bcl-xL silencing led to migration defects in Hs578T and MDA-MB231 cells. These defects were rescued by re-expressing mitochondria-addressed, but not endoplasmic reticulum-addressed, Bcl-xL. The use of BH3 mimetics, such as ABT-737 and WEHI-539 confirmed that the effect of Bcl-xL on migration did not depend on interactions with BH3-containing death accelerators such as Bax or BH3-only proteins. In contrast, the use of a BH4 peptide that disrupts the Bcl-xL/VDAC1 complex supports that Bcl-xL by acting on VDAC1 permeability contributes to cell migration through the promotion of reactive oxygen species production by the electron transport chain. Collectively our data highlight the key role of Bcl-xL at the interface between cell metabolism, cell death, and cell migration, thus exposing the VDAC1/Bcl-xL interaction as a promising target for anti-tumour therapy in the context of metastatic breast cancer.
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http://dx.doi.org/10.1038/s41388-020-1212-9DOI Listing
April 2020

Towards standardization of immune functional assays.

Clin Immunol 2020 01 21;210:108312. Epub 2019 Nov 21.

Joint Research Unit Hospices Civils de Lyon-bioMérieux, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France; Virologie et Pathologie Humaine - Virpath Team, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS UMR5308, ENS Lyon, Claude Bernard Lyon 1 University, Lyon, France.

Recent advances in the immunotherapy field require evaluation of the immune function to adapt therapeutic decisions. Immune functional assays (IFA) are able to reveal the immune status and would be useful to further adapt and/or improve patient's care. However, standardized methods are needed to implement IFA in clinical settings. We carried out an independent validation of a published method used to characterize the underlying host response to infectious conditions using an IFA. We evaluated the reproducibility and robustness of this IFA and the associated readout using an independent healthy volunteers (HV) cohort. Expression of a 44-gene signature and IFNγ protein secretion was assessed after stimulation. We observed a strong host-response correlation between the two cohorts. We also highlight that standardized methods for immune function evaluation exist and could be implemented in larger-scale studies. This IFA could be a relevant tool to reveal innate and adaptive immune dysfunction in immune-related disorders patients.
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http://dx.doi.org/10.1016/j.clim.2019.108312DOI Listing
January 2020

mTORC1 Activation Requires DRAM-1 by Facilitating Lysosomal Amino Acid Efflux.

Mol Cell 2019 10 3;76(1):163-176.e8. Epub 2019 Sep 3.

Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK. Electronic address:

Sensing nutrient availability is essential for appropriate cellular growth, and mTORC1 is a major regulator of this process. Mechanisms causing mTORC1 activation are, however, complex and diverse. We report here an additional important step in the activation of mTORC1, which regulates the efflux of amino acids from lysosomes into the cytoplasm. This process requires DRAM-1, which binds the membrane carrier protein SCAMP3 and the amino acid transporters SLC1A5 and LAT1, directing them to lysosomes and permitting efficient mTORC1 activation. Consequently, we show that loss of DRAM-1 also impacts pathways regulated by mTORC1, including insulin signaling, glycemic balance, and adipocyte differentiation. Interestingly, although DRAM-1 can promote autophagy, this effect on mTORC1 is autophagy independent, and autophagy only becomes important for mTORC1 activation when DRAM-1 is deleted. These findings provide important insights into mTORC1 activation and highlight the importance of DRAM-1 in growth control, metabolic homeostasis, and differentiation.
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http://dx.doi.org/10.1016/j.molcel.2019.07.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892261PMC
October 2019

Clinical efficacy of the optimal biological dose in early-phase trials of anti-cancer targeted therapies.

Eur J Cancer 2019 10 31;120:40-46. Epub 2019 Aug 31.

Faculty of Medicine Lyon-Sud, Claude Bernard University Lyon 1, EMR UCBL/HCL 3738, University of Lyon, Lyon, France; Department of Medical Oncology, Cancerology Institute of Hospices Civils de Lyon (IC-HCL), CITOHL, Lyon-Sud Hospital, Lyon, France. Electronic address:

Background: Determining the optimal biological dose (OBD) has been described as an alternative strategy to the maximum tolerated doses (MTDs) for identifying the recommended phase II trial doses (RP2Ds) of phase I anti-cancer therapies. However, the clinical relevance is still unknown. An extensive review was performed to assess if the OBDs defined in early-phase trials were useful for subsequent drug development and approvals.

Methods: All the molecular targeted therapies approved by the Food and Drug Administration (FDA) in solid oncology or in haematological malignancies before July 2018 were listed through the National Cancer Institute Database. The early-phase trial publications investigating these drugs as single agents were retrieved and analysed to identify the drugs for which OBDs were reported. The publications of subsequent pivotal efficacy clinical trials leading to the approvals were retrieved, and OBDs compared with the final labelled doses and dosing schedules.

Results: A total of 87 early-phase trial publications were analysed, corresponding to 81 FDA-approved targeted therapies. OBDs were reported for 40% (32/81) of these drugs (19 small molecules, 13 monoclonal antibodies). MTDs were not identified for 59% (19/32) of molecules. When the OBDs were selected as the RP2Ds (18/32 molecules), the final FDA-approved doses were consistent with the OBDs for 83% of the drugs, which is much higher than the previously reported 58% rate when MTDs were chosen as the RP2Ds.

Conclusion: Although still poorly investigated, the OBD may be a relevant and complementary end-point for early-phase trials of targeted therapies.
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http://dx.doi.org/10.1016/j.ejca.2019.08.002DOI Listing
October 2019

TERT promoter mutations identify a high-risk group in metastasis-free advanced thyroid carcinoma.

Eur J Cancer 2019 02 12;108:41-49. Epub 2019 Jan 12.

Hospices Civils de Lyon, Fédération D'Endocrinologie, Bron Cedex, F-69677, France; Université Lyon 1, HESPER EA 7425, Lyon, F-69008, France.

Background: TERT promoter mutations are associated with adverse clinicopathological characteristics in thyroid carcinomas and considered as a major indicator of poor outcomes. Nevertheless, most studies have pooled heterogeneous types of thyroid carcinomas and have been conducted retrospectively. We investigated the association between TERT promoter mutations and recurrence in a prospective series of 173 intermediate- to high-risk patients with thyroid cancer.

Patients: Patients referred for radioiodine treatment after thyroidectomy for intermediate- to high-risk differentiated thyroid carcinoma were included in a prospective observational study and tested for TERT promoter, BRAF, and RAS mutations of their primary tumours. We analysed the relationship between TERT promoter mutations and outcomes.

Results: The prevalence of TERT promoter mutations was 20.2% (35/173) in the total population. It was significantly higher in tumours harbouring aggressive histological features (poorly differentiated carcinoma, tall cell variant of papillary cancer or widely invasive follicular cancer) than in non-aggressive tumours: 32.7% (16/49) versus 15.3% (19/124; p = 0.020). TERT promoter mutations were also strongly associated with age ≥45 years (p = 0.005), pT4 stage (p = 0.015), metastatic disease (p = 0.014), and extrathyroidal extension (p = 0.002). TERT promoter mutations were associated with poor outcomes in the total population (p < 0.001) but not in the subgroup of non-metastatic patients (p = 0.051). However, they were associated with a worse outcome in patients both free of metastases and devoid of aggressive histological features. Neither BRAF nor RAS mutations were associated with event-free survival in non-metastatic patients.

Conclusion: Although their prognostic value does not seem to overcome that of histology, TERT promoter mutations may help to better define the prognosis of localized thyroid cancer patients without aggressive histology.
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http://dx.doi.org/10.1016/j.ejca.2018.12.003DOI Listing
February 2019

Application of Mito-Priming to Generate BCL-2 Addicted Cells.

Methods Mol Biol 2019 ;1877:45-60

Cancer Research UK Beatson Institute, Glasgow, UK.

The majority of apoptotic stimuli trigger cell death through the mitochondrial pathway of apoptosis. Invariably, mitochondrial apoptosis requires engagement of mitochondrial outer membrane permeabilization or MOMP to initiate cell death. We have developed a new method, called mito-priming, that allows for rapid and synchronous induction of mitochondrial apoptosis in an on-target manner. Mito-priming uses coexpression of pro- and antiapoptotic Bcl-2 proteins to render cells sensitive to the addition of Bcl-2 targeting BH3-mimetic drugs. This chapter describes how to design mito-priming constructs and apply them to generate mito-primed lines. Second, we describe how to validate cell death sensitivity of mito-primed lines using different methods. Finally, we describe how to generate MOMP-resistant cell lines, using CRISPR-Cas9 mediated deletion of BAX and BAK. Facilitating the investigation of mitochondrial apoptosis, mito-priming provides a clean, robust way to induce mitochondrial apoptosis both in vitro and in vivo.
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http://dx.doi.org/10.1007/978-1-4939-8861-7_3DOI Listing
May 2019

Comparison of RT-qPCR and Nanostring in the measurement of blood interferon response for the diagnosis of type I interferonopathies.

Cytokine 2019 01 7;113:446-452. Epub 2018 Nov 7.

CIRI, Centre International de Recherche en Infectiologie - International Center for Infectiology Research, Lyon, France; Inserm, U1111 Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; Université Lyon 1, Lyon, France; CNRS, UMR5308, Lyon, France; Service d'Immunologie biologique, Hospices Civils de Lyon and Université Claude-Bernard Lyon 1, Lyon, France; Centre de référence des rhumatismes inflammatoires et maladies auto-immunes systémiques rares de l'enfant RAISE, Hôpital Femme Mère Enfant, Bron, France.

Type I interferonopathies are characterized by an increase of circulating type I interferon (IFN) concentration. Type I interferonopathies refer to rare Mendelian genetic disorders such as Aicardi-Goutières Syndrome (AGS) as well as more frequent and polygenic auto-immune diseases like systemic lupus erythematosus (SLE). Yet, detection of type I IFN in these patients remains challenging as its amount is usually very low in patients' sera. Thus, the detection of interferon-stimulating genes has been proposed as an alternative for the detection of this cytokine but sensitivy, specificity and predictive values of the assay have not been reported so far. In this study, we propose two different methods based on Nanostring or RT-qPCR to measure in the clinical routine the IFN response, defined as a set of transcripts that are systemically induced by IFNs. The IFN signature is composed of 6 IFN stimulated genes (ISGs) and has a strong predictive value for the diagnosis of type I interferonopathies. The use of this simple test might represent a gold standard for the evaluation of various autoimmune diseases. Moreover, this test could also be used to monitor patients treated with drugs targeting type I IFN pathway. When comparing both methods - Nanostring and qPCR - in terms of analytical performance, they provided similar results but Nanostring was quicker, easier to multiplex, and almost fully-automated, which represent a more reliable assay for the daily clinical practice.
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http://dx.doi.org/10.1016/j.cyto.2018.10.023DOI Listing
January 2019

Opioid prescribing for acute postoperative pain after cutaneous surgery.

J Am Acad Dermatol 2019 Mar 2;80(3):743-748. Epub 2018 Oct 2.

Division of Dermatologic Surgery, Mayo Clinic, Rochester, Minnesota. Electronic address:

Background: Little information is available to predict which patients require opioid analgesia following cutaneous surgery. When opioids are indicated, information regarding the optimal opioid agent selection and dosage is lacking.

Objective: To make recommendations for opioid prescription after cutaneous surgery.

Methods: A PubMed literature search was conducted to review the available literature. Recommendations are presented on the basis of available evidence and the opinion of the authors.

Results: Most patients undergoing cutaneous surgery do not require opioid analgesia. For those who do, the duration of pain warranting opioid analgesia is generally less than 36 hours. Opioid refill requests warrant a follow-up visit to ascertain the cause of ongoing pain after excisional procedures.

Limitations: The recommendations are not based on prospective randomized trials.

Conclusions: The presented recommendations for opioid prescription practice are derived from available evidence, recommendations, and expert opinion.
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http://dx.doi.org/10.1016/j.jaad.2018.09.032DOI Listing
March 2019

Effect of Buparlisib, a Pan-Class I PI3K Inhibitor, in Refractory Follicular and Poorly Differentiated Thyroid Cancer.

Thyroid 2018 09;28(9):1174-1179

8 Service de Médecine Nucléaire et de Cancérologie Endocrinienne, Institut Gustave Roussy , Villejuif et Université Paris Saclay, France .

Background: Dysregulation of the phosphatidylinositol 3-kinase (PI3K) pathway is frequent in advanced follicular (FTC) and poorly differentiated thyroid (PDTC) carcinomas and has been implicated in oncogenesis and tumor progression. This study investigated the efficacy and safety of buparlisib, a pan-PI3K inhibitor in radioiodine refractory FTC and PDTC.

Methods: The primary endpoint of this open-label, multicenter, phase 2 pilot study was progression-free survival (PFS) at 6 months. The sample size was determined considering that a PFS ≤50% at 6 months would denote an absence of benefits (null hypothesis). Secondary endpoints were objective response rate, PFS at 12 months, overall survival at 6 and 12 months, and safety based on the frequency and severity of adverse events (AEs).

Results: Forty-three patients (19M/24 F; median age: 67 years) with metastatic, radioiodine refractory, progressive disease received buparlisib, 100 mg, daily. Histology was PDTC in 25 (58%), FTC in 17 (40%), and Hürthle cell carcinoma in 1 (2%). RAS mutation was found in 44% (12/27) and activation of the PI3K pathway in 35% (8/23) of tested tumors. The probability of PFS was 41.7% [95% confidence interval (CI) 7.7-55.5] at 6 months and 20.9% [CI 0-35.7] at 12 months, lower than the 50% expected PFS. At 6 months, 25.6% patients had stable disease, 48.8% were progressive and 25.6% had stopped treatment due to AE. The response to therapy was not influenced by age, sex, histology, or genetic alterations. The overall survivals at 6 and 12 months were 85.9% [CI 76-97] and 78.7 % [CI 67-92], respectively. The mean tumor growth rate decreased from 3.78 mm/month [CI 2.61-4.95] before treatment to 0.8 mm/month [CI -0.2-1.88] during treatment (p < 0.02). Severe grade 3-4 AEs occurred in 27 patients (63%), including hepatitis (25%), hyperglycemia (21%), mood disorders (12%), and skin toxicity (12%), with favorable outcome after temporary or permanent treatment discontinuation or dose reduction.

Conclusions: Buparlisib did not result in significant efficacy in advanced FTC and PDTC. However, the decrease in tumor growth rate may suggest incomplete inhibition of oncogenic pathways and/or escape mechanisms. This should lead to evaluate combined therapy associating inhibitors of both the PI3K and mitogen-activated protein kinase pathways.
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http://dx.doi.org/10.1089/thy.2017.0663DOI Listing
September 2018

Reply to Dr Ozden et al.

Cytopathology 2018 12 11;29(6):599. Epub 2018 Sep 11.

Service de Biochimie et Biologie moléculaire, Hospices Civils de Lyon, Pierre-Bénite, France.

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http://dx.doi.org/10.1111/cyt.12620DOI Listing
December 2018

Mitochondrial inner membrane permeabilisation enables mtDNA release during apoptosis.

EMBO J 2018 09 26;37(17). Epub 2018 Jul 26.

Cancer Research UK Beatson Institute, Glasgow, UK

During apoptosis, pro-apoptotic BAX and BAK are activated, causing mitochondrial outer membrane permeabilisation (MOMP), caspase activation and cell death. However, even in the absence of caspase activity, cells usually die following MOMP Such caspase-independent cell death is accompanied by inflammation that requires mitochondrial DNA (mtDNA) activation of cGAS-STING signalling. Because the mitochondrial inner membrane is thought to remain intact during apoptosis, we sought to address how matrix mtDNA could activate the cytosolic cGAS-STING signalling pathway. Using super-resolution imaging, we show that mtDNA is efficiently released from mitochondria following MOMP In a temporal manner, we find that following MOMP, BAX/BAK-mediated mitochondrial outer membrane pores gradually widen. This allows extrusion of the mitochondrial inner membrane into the cytosol whereupon it permeablises allowing mtDNA release. Our data demonstrate that mitochondrial inner membrane permeabilisation (MIMP) can occur during cell death following BAX/BAK-dependent MOMP Importantly, by enabling the cytosolic release of mtDNA, inner membrane permeabilisation underpins the immunogenic effects of caspase-independent cell death.
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http://dx.doi.org/10.15252/embj.201899238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120664PMC
September 2018

[DICER1 mutated, solid/trabecular thyroid papillary carcinoma in an 11-year-old child].

Ann Pathol 2018 Oct 5;38(5):316-320. Epub 2018 Jun 5.

Service d'anatomie et cytologie pathologique, centre hospitalier Lyon Sud, hospices civils de Lyon, 165, chemin du Grand-Revoyet, 69310 Pierre-Bénite, France.

We report the case of an 11-year-old patient diagnosed with a solid variant of papillary thyroid carcinoma. Papillary thyroid carcinoma (PTC) is the most common thyroid cancer, representing 80-90% of all newly diagnosed thyroid cancers. Among the many variants described, solid/trabecular variant of papillary thyroid carcinoma is a rare entity and account for 3% of thyroid cancers. It is more common in children and young adults, and it is seen in higher proportion in post radiation papillary thyroid carcinoma cases. Histologically, solid variant papillary carcinoma is characterized by a predominantly solid, trabecular or insular growth pattern, and the presence of cytological features typical of PTC. Its main differential diagnosis is poorly differentiated thyroid carcinoma. It has a less favorable prognosis than the classical papillary type, with a higher risk of distant metastasis, extrathyroidal extension and lympho-vascular invasion. It is associated with a slightly lower long-term survival in adult cases, but not in children. The management of solid variant PTC includes surgery, associated or not with postoperative radioiodine ablation, according to the aggressiveness criteria. Our patient had a DICER1 somatic mutation. Carriers of germline DICER1 mutations are predisposed to a rare cancer syndrome, the DICER1 syndrome, with a higher risk of numerous tumors and infrequently differentiated thyroid carcinomas.
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http://dx.doi.org/10.1016/j.annpat.2018.04.003DOI Listing
October 2018

Decoding Allosteric Communication Pathways in Cyclophilin A with a Comparative Analysis of Perturbed Conformational Ensembles.

J Phys Chem B 2018 06 13;122(25):6528-6535. Epub 2018 Jun 13.

Department of Chemistry , Georgia State University , Atlanta , Georgia 30302-3965 , United States.

Conformational dynamics plays the key role in allosteric regulation of enzymes. Despite numerous experimental and computational efforts, the mechanism of how dynamics couple enzymatic function is poorly understood. Here, we introduce a new approach to exploring the dynamics-function relationship combining computational mutagenesis, microsecond-long molecular dynamics simulations, and side-chain torsion angle analyses. We apply our approach to elucidate the allosteric mechanism in cyclophilin A (CypA), a peptidyl-prolyl cis-trans isomerase known to participate in diverse biological processes and be associated with many diseases including cancer. Multiple single mutations are performed in CypA at previously discovered hotspot residues distal from the active site, and residues displaying significant dynamical changes upon mutations are then identified. The mutation-responsive residues delineate three distinct pathways potentially mediating allosteric communications between distal sites: two pathways resemble the allosteric networks identified in a recent experimental study, whereas the third represents a novel pathway. A residue-residue contact analysis is also performed to complement the findings. Furthermore, a recently developed difference contact network analysis is employed to explain mutation-specific allosteric effects. Our results suggest that comparing multiple conformational ensembles generated under various mutational conditions is a powerful tool to gain novel insights into enzymatic functions that are difficult to obtain through examining a single system such as the wild-type. Our approach is easy to extend for other systems. The results can also be utilized to facilitate the design of potent therapeutics targeting CypA.
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http://dx.doi.org/10.1021/acs.jpcb.8b03824DOI Listing
June 2018