Publications by authors named "Elaine Lim"

70 Publications

Cost-effectiveness of pertuzumab and trastuzumab biosimilar combination therapy as initial treatment for HER2-positive metastatic breast cancer in Singapore.

Authors:
Li-Jen Cheng Lydia Loke Elaine Hsuen Lim Fiona Pearce Mohamed Ismail Abdul Aziz Kwong Ng

Expert Rev Pharmacoecon Outcomes Res 2021 Feb 17:1-8. Epub 2021 Feb 17.

Agency for Care Effectiveness (ACE), Ministry of Health , Singapore.

Background: This study evaluates the cost-effectiveness of pertuzumab with trastuzumab biosimilar and docetaxel as initial treatment for HER2-positive metastatic breast cancer (MBC) in Singapore.

Methods: A partitioned survival model with three health states was developed to evaluate the cost-effectiveness of trastuzumab biosimilar and docetaxel with or without pertuzumab from a healthcare system perspective over a 15-year time horizon for patients with HER2-positive MBC. Key clinical inputs were derived from the CLEOPATRA trial. Health state utilities were derived from the literature and direct medical costs were obtained from local public healthcare institutions.

Results: The base-case resulted in an incremental cost-effectiveness ratio (ICER) of SGD366,658 (USD272,244) per quality-adjusted life-year (QALY) gained. One-way sensitivity analyses showed that the ICER was sensitive to utilities in the progression-free state, price of pertuzumab and time horizon. When the price for trastuzumab reference biologic (branded) was applied, the ICER was even higher (SGD426,996 [USD317,045]/QALY).

Conclusion: Although trastuzumab biosimilar reduced the cost of the pertuzumab combination regimen, the ICER remained high and was not cost effective in Singapore's context. As pertuzumab contributed 80% of the overall combination treatment cost, price reductions for pertuzumab will be required to improve the cost-effectiveness of combination treatment to an acceptable level.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1080/14737167.2021.1880323DOI Listing
February 2021

Whole exome sequencing uncovered highly penetrant recessive mutations for a spectrum of rare genetic pediatric diseases in Bangladesh.

Authors:
Hosneara Akter Mohammad Shahnoor Hossain Nushrat Jahan Dity Md Atikur Rahaman K M Furkan Uddin Nasna Nassir Ghausia Begum Reem Abdel Hameid Muhammad Sougatul Islam Tahrima Arman Tusty Mohammad Basiruzzaman Shaoli Sarkar Mazharul Islam Sharmin Jahan Elaine T Lim Marc Woodbury-Smith Dimitri James Stavropoulos Darren D O'Rielly Bakhrom K Berdeiv A H M Nurun Nabi Mohammed Nazmul Ahsan Stephen W Scherer Mohammed Uddin

NPJ Genom Med 2021 Feb 16;6(1):14. Epub 2021 Feb 16.

College of Medicine, Mohammed Bin Rashid University of Medicine and Health Science, Dubai, UAE.

Collectively, rare genetic diseases affect a significant number of individuals worldwide. In this study, we have conducted whole-exome sequencing (WES) and identified underlying pathogenic or likely pathogenic variants in five children with rare genetic diseases. We present evidence for disease-causing autosomal recessive variants in a range of disease-associated genes such as DHH-associated 46,XY gonadal dysgenesis (GD) or 46,XY sex reversal 7, GNPTAB-associated mucolipidosis II alpha/beta (ML II), BBS1-associated Bardet-Biedl Syndrome (BBS), SURF1-associated Leigh Syndrome (LS) and AP4B1-associated spastic paraplegia-47 (SPG47) in unrelated affected members from Bangladesh. Our analysis pipeline detected three homozygous mutations, including a novel c. 863 G > C (p.Pro288Arg) variant in DHH, and two compound heterozygous variants, including two novel variants: c.2972dupT (p.Met991Ilefs*) in GNPTAB and c.229 G > C (p.Gly77Arg) in SURF1. All mutations were validated by Sanger sequencing. Collectively, this study adds to the genetic heterogeneity of rare genetic diseases and is the first report elucidating the genetic profile of (consanguineous and nonconsanguineous) rare genetic diseases in the Bangladesh population.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41525-021-00173-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7887195PMC
February 2021

Engineering adeno-associated viral vectors to evade innate immune and inflammatory responses.

Authors:
Ying Kai Chan Sean K Wang Colin J Chu David A Copland Alexander J Letizia Helena Costa Verdera Jessica J Chiang Meher Sethi May K Wang William J Neidermyer Yingleong Chan Elaine T Lim Amanda R Graveline Melinda Sanchez Ryan F Boyd Thomas S Vihtelic Rolando Gian Carlo O Inciong Jared M Slain Priscilla J Alphonse Yunlu Xue Lindsey R Robinson-McCarthy Jenny M Tam Maha H Jabbar Bhubanananda Sahu Janelle F Adeniran Manish Muhuri Phillip W L Tai Jun Xie Tyler B Krause Andyna Vernet Matthew Pezone Ru Xiao Tina Liu Wei Wang Henry J Kaplan Guangping Gao Andrew D Dick Federico Mingozzi Maureen A McCall Constance L Cepko George M Church

Sci Transl Med 2021 Feb;13(580)

Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.

Nucleic acids are used in many therapeutic modalities, including gene therapy, but their ability to trigger host immune responses in vivo can lead to decreased safety and efficacy. In the case of adeno-associated viral (AAV) vectors, studies have shown that the genome of the vector activates Toll-like receptor 9 (TLR9), a pattern recognition receptor that senses foreign DNA. Here, we engineered AAV vectors to be intrinsically less immunogenic by incorporating short DNA oligonucleotides that antagonize TLR9 activation directly into the vector genome. The engineered vectors elicited markedly reduced innate immune and T cell responses and enhanced gene expression in clinically relevant mouse and pig models across different tissues, including liver, muscle, and retina. Subretinal administration of higher-dose AAV in pigs resulted in photoreceptor pathology with microglia and T cell infiltration. These adverse findings were avoided in the contralateral eyes of the same animals that were injected with the engineered vectors. However, intravitreal injection of higher-dose AAV in macaques, a more immunogenic route of administration, showed that the engineered vector delayed but did not prevent clinical uveitis, suggesting that other immune factors in addition to TLR9 may contribute to intraocular inflammation in this model. Our results demonstrate that linking specific immunomodulatory noncoding sequences to much longer therapeutic nucleic acids can "cloak" the vector from inducing unwanted immune responses in multiple, but not all, models. This "coupled immunomodulation" strategy may widen the therapeutic window for AAV therapies as well as other DNA-based gene transfer methods.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1126/scitranslmed.abd3438DOI Listing
February 2021

Electrocardiographic predictors of successful resynchronization of left bundle branch block by His bundle pacing.

Authors:
Ahran D Arnold Matthew J Shun-Shin Daniel Keene James P Howard Ji-Jian Chow Elaine Lim Smaragda Lampridou Alejandra A Miyazawa Amal Muthumala Mark Tanner Norman A Qureshi David C Lefroy Michael Koa-Wing Nick W F Linton Phang Boon Lim Nicholas S Peters Prapa Kanagaratnam Angelo Auricchio Darrel P Francis Zachary I Whinnett

J Cardiovasc Electrophysiol 2021 Feb 4;32(2):428-438. Epub 2021 Jan 4.

National Heart and Lung Institute, Imperial College London, Hammersmith Hospital, London, UK.

Background: His bundle pacing (HBP) is an alternative to biventricular pacing (BVP) for delivering cardiac resynchronization therapy (CRT) in patients with heart failure and left bundle branch block (LBBB). It is not known whether ventricular activation times and patterns achieved by HBP are equivalent to intact conduction systems and not all patients with LBBB are resynchronized by HBP.

Objective: To compare activation times and patterns of His-CRT with BVP-CRT, LBBB and intact conduction systems.

Methods: In patients with LBBB, noninvasive epicardial mapping (ECG imaging) was performed during BVP and temporary HBP. Intrinsic activation was mapped in all subjects. Left ventricular activation times (LVAT) were measured and epicardial propagation mapping (EPM) was performed, to visualize epicardial wavefronts. Normal activation pattern and a normal LVAT range were determined from normal subjects.

Results: Forty-five patients were included, 24 with LBBB and LV impairment, and 21 with normal 12-lead ECG and LV function. In 87.5% of patients with LBBB, His-CRT successfully shortened LVAT by ≥10 ms. In 33.3%, His-CRT resulted in complete ventricular resynchronization, with activation times and patterns indistinguishable from normal subjects. EPM identified propagation discontinuity artifacts in 83% of patients with LBBB. This was the best predictor of whether successful resynchronization was achieved by HBP (logarithmic odds ratio, 2.19; 95% confidence interval, 0.07-4.31; p = .04).

Conclusion: Noninvasive electrocardiographic mapping appears to identify patients whose LBBB can be resynchronized by HBP. In contrast to BVP, His-CRT may deliver the maximum potential ventricular resynchronization, returning activation times, and patterns to those seen in normal hearts.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1111/jce.14845DOI Listing
February 2021

The ectopy-triggering ganglionated plexuses in atrial fibrillation.

Authors:
Min-Young Kim Belinda Sandler Markus B Sikkel Christopher D Cantwell Kevin M Leong Vishal Luther Louisa Malcolme-Lawes Michael Koa-Wing Fu Siong Ng Norman Qureshi Afzal Sohaib Zachary I Whinnett Michael Fudge Elaine Lim Michelle Todd Ian Wright Nicholas S Peters Phang Boon Lim Nicholas W F Linton Prapa Kanagaratnam

Auton Neurosci 2020 11 21;228:102699. Epub 2020 Jul 21.

Myocardial Function Section, NHLI, Imperial College London, UK; Department of Cardiology, Imperial College Healthcare NHS Trust, London, UK; Imperial Centre for Cardiac Engineering, Imperial College London, London, UK. Electronic address:

Background: Epicardial ganglionated plexuses (GP) have an important role in the pathogenesis of atrial fibrillation (AF). The relationship between anatomical, histological and functional effects of GP is not well known. We previously described atrioventricular (AV) dissociating GP (AVD-GP) locations. In this study, we hypothesised that ectopy triggering GP (ET-GP) are upstream triggers of atrial ectopy/AF and have different anatomical distribution to AVD-GP.

Objectives: We mapped and characterised ET-GP to understand their neural mechanism in AF and anatomical distribution in the left atrium (LA).

Methods: 26 patients with paroxysmal AF were recruited. All were paced in the LA with an ablation catheter. High frequency stimulation (HFS) was synchronised to each paced stimulus for delivery within the local atrial refractory period. HFS responses were tagged onto CARTO™ 3D LA geometry. All geometries were transformed onto one reference LA shell. A probability distribution atlas of ET-GP was created. This identified high/low ET-GP probability regions.

Results: 2302 sites were tested with HFS, identifying 579 (25%) ET-GP. 464 ET-GP were characterised, where 74 (16%) triggered ≥30s AF/AT. Median 97 (IQR 55) sites were tested, identifying 19 (20%) ET-GP per patient. >30% of ET-GP were in the roof, mid-anterior wall, around all PV ostia except in the right inferior PV (RIPV) in the posterior wall.

Conclusion: ET-GP can be identified by endocardial stimulation and their anatomical distribution, in contrast to AVD-GP, would be more likely to be affected by wide antral circumferential ablation. This may contribute to AF ablation outcomes.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.autneu.2020.102699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7511599PMC
November 2020

Anatomical Distribution of Ectopy-Triggering Plexuses in Patients With Atrial Fibrillation.

Authors:
Min-Young Kim Belinda C Sandler Markus B Sikkel Christopher D Cantwell Kevin M Leong Vishal Luther Louisa Malcolme-Lawes Michael Koa-Wing Fu Siong Ng Norman Qureshi Afzal Sohaib Zachary I Whinnett Michael Fudge Elaine Lim Michelle Todd Ian Wright Nicholas S Peters Phang Boon Lim Nicholas W F Linton Prapa Kanagaratnam

Circ Arrhythm Electrophysiol 2020 09 27;13(9):e008715. Epub 2020 Jul 27.

Myocardial Function Section, Imperial Centre for Translational and Experimental Medicine (M.-Y.K., B.C.S., M.B.S., C.D.C., F.S.N., N.S.P., P.B.L., N.W.F.L., P.K.), Imperial College London, United Kingdom.

View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1161/CIRCEP.120.008715DOI Listing
September 2020

Publisher Correction: Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder.

Authors:
Elaine T Lim Mohammed Uddin Silvia De Rubeis Yingleong Chan Anne S Kamumbu Xiaochang Zhang Alissa M D'Gama Sonia N Kim Robert Sean Hill Arthur P Goldberg Christopher Poultney Nancy J Minshew Itaru Kushima Branko Aleksic Norio Ozaki Mara Parellada Celso Arango Maria J Penzol Angel Carracedo Alexander Kolevzon Christina M Hultman Lauren A Weiss Menachem Fromer Andreas G Chiocchetti Christine M Freitag George M Church Stephen W Scherer Joseph D Buxbaum Christopher A Walsh

Nat Neurosci 2020 Sep;23(9):1176

Division of Genetics and Genomics, Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41593-020-0681-zDOI Listing
September 2020

Efficacy, patterns of use and cost of Pertuzumab in the treatment of HER2+ metastatic breast cancer in Singapore: The National Cancer Centre Singapore experience.

Authors:
Sylwan Rahardja Ryan Ying Cong Tan Rehena Sultana Fun Loon Leong Elaine Hsuen Lim

World J Clin Oncol 2020 Mar;11(3):143-151

National Cancer Centre Singapore, Singapore 169610, Singapore.

Background: Pertuzumab is a humanized anti-human epidermal growth factor receptor 2 (HER2) monoclonal antibody found in a Phase III clinical trial to significantly improve median survival in HER2 positive metastatic breast cancer (MBC) when used in combination with a taxane and Trastuzumab, and its clinical efficacy has transformed the therapeutic landscape of HER2-positive breast cancer. There are currently few reports on the pattern of use and value of Pertuzumab in real world settings. Our study describes the clinical efficacy and treatment costs of Pertuzumab in HER2-positive MBC treated in a tertiary cancer centre in Singapore in a predominantly Asian population.

Aim: To investigate the clinical efficacy and treatment costs of Pertuzumab in HER2-positive MBC in an Asian population in Singapore.

Methods: A retrospective study of 304 HER2-positive MBC patients seen at National Cancer Centre Singapore between 2011-2017 was conducted. Demographic and clinical data were extracted from electronic medical records. Clinical characteristics and billing data of patients who received Pertuzumab were compared with those who did not.

Results: Thirty-one (62.0%) of the fifty (16.4%) patients who received Pertuzumab as first-line therapy. With a median follow-up of 21.5 mo, there was a statistically significant difference in the median overall survival between Pertuzumab and non-Pertuzumab groups [51.5 (95%CI: 35.8-60.0) 32.9 (95%CI: 28.1-37.5) mo; 0.0128]. Two (4.88%) patients in the Pertuzumab group experienced grade 3 (G3) cardiotoxicity. The median treatment cost incurred for total chemotherapy for the Pertuzumab group was 130456 Singapore Dollars compared to 34523 Singapore Dollars for the non-Pertuzumab group. The median percentage of total chemotherapy costs per patient in the Pertuzumab group spent on Pertuzumab was 50.3%.

Conclusion: This study shows that Pertuzumab use in the treatment of metastatic breast cancer is associated with a significantly better survival and a low incidence of serious cardiotoxicity. However, the proportionate cost of Pertuzumab therapy remains high and further cost-effectiveness studies should be conducted.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.5306/wjco.v11.i3.143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103528PMC
March 2020

Multiplex immunohistochemistry/immunofluorescence (mIHC/IF) for PD-L1 testing in triple-negative breast cancer: a translational assay compared with conventional IHC.

Authors:
Joe Yeong Tira Tan Zi Long Chow Qing Cheng Bernett Lee Amanda Seet Johnathan Xiande Lim Jeffrey Chun Tatt Lim Clara Chong Hui Ong Aye Aye Thike Sahil Saraf Benjamin Yong Cheng Tan Yong Cheng Poh Sidney Yee Jin Liu Elaine Lim Jabed Iqbal Rebecca Dent Puay Hoon Tan

J Clin Pathol 2020 Sep 22;73(9):557-562. Epub 2020 Jan 22.

Division of Pathology, Singapore General Hospital, Singapore

Background: Programmed death-ligand 1 (PD-L1) monoclonal antibody therapy has recently gained approval for treating metastatic triple-negative breast cancer (TNBC) -, in particular in the PD-L1 patient subgroup of the recent IMpassion130 trial. The SP142 PD-L1 antibody clone was used as a predictive assay in this trial, but this clone was found to be an outlier in previous harmonisation studies in lung cancer.

Aims: To address the comparability of PD-L1 clones in TNBC, we evaluated the concordance between conventional immunohistochemistry (IHC) and multiplex immunohistochemistry/immunofluorescence (mIHC/IF) that allowed simultaneous quantification of three different PD-L1 antibodies (22C3, SP142 and SP263).

Methods: Our cohort comprised 25 TNBC cases, 12 non-small-cell lung carcinomas and 8 other cancers. EpCAM labelling was used to distinguish tumour cells from immune cells.

Results: Moderate-to-strong correlations in PD-L1 positivity were found between results obtained through mIHC/IF and IHC. Individual concordance rates in the study ranged from 67% to 100%, with Spearman's rank correlation coefficient values up to 0.88.

Conclusions: mIHC/IF represents a promising tool in the era of cancer immunotherapy, as it can simultaneously detect and quantify PD-L1 labelling with multiple antibody clones, and allow accurate evaluation of tumour and immune cells. Clinicians and pathologists require this information to predict patient response to anti-PD-1/PD-L1 therapy. The adoption of this assay may represent a significant advance in the management of therapeutically challenging cancers. Further analysis and assay harmonisation are essential for translation to a routine diagnostic setting.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1136/jclinpath-2019-206252DOI Listing
September 2020

Detection and prognostic relevance of circulating tumour cells (CTCs) in Asian breast cancers using a label-free microfluidic platform.

Authors:
Yoon-Sim Yap Man Chun Leong Yong Wei Chua Kiley Wei Jen Loh Guek Eng Lee Elaine Hsuen Lim Rebecca Dent Raymond Chee Hui Ng John Heng-Chi Lim Garima Singh Angela Tan Guofeng Guan Andrew Wu Yi Fang Lee Ali Asgar S Bhagat Darren Wan-Teck Lim

PLoS One 2019 25;14(9):e0221305. Epub 2019 Sep 25.

Division of Medical Oncology, National Cancer Centre Singapore, Singapore.

Objectives: We aimed to study the prevalence of CTCs in breast cancer (BC) patients undergoing neoadjuvant or palliative therapy with a label-free microfluidic platform (ClearCell FX), and its prognostic relevance in metastatic BC (mBC).

Materials And Methods: Peripheral blood samples were collected from 108 BC patients before starting a new line of treatment ("baseline"), majority of whom had mBC (76/108; 70.4%). CTCs were retrieved by dean flow fractionation that enriched for larger cells, and enumerated using immunofluorescence-based staining. Progression-free survival (PFS) in mBC patients was analysed using Kaplan-Meier method; cox proportional hazard models were used for univariable and multivariable analyses.

Results: The detection rate of CTCs before starting a new line of treatment was 75.9% (n = 108; median: 8 CTCs/7.5 ml blood) at a cut off of ≥2 CTCs. PFS was inferior for mBC patients with baseline CTC count ≥5 CTCs/7.5 ml blood vs. those with < 5 CTCs/7.5 ml blood (median PFS: 4.3 vs. 7.0 months; p-value: 0.037). The prognostic relevance of CTCs was most significant in patients with HER2- mBC (median PFS: 4.1 vs. 8.3 months; p-value: 0.032), luminal (HR+HER2-) subtype (median PFS: 4.2 vs. 8.3 months; p-value: 0.048), and patients who had one or more prior treatments (median PFS: 4.2 vs. 7.0 months; p-value: 0.02). On multivariable analysis, baseline CTC level (hazard ratio (HR): 1.84, p-value: 0.02) and pre-treatment status (HR: 1.87, p-value: 0.05) were independent predictors of PFS.

Conclusions: This work demonstrates the prognostic significance of CTCs in mBC detected using a label-free size-based enrichment platform.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0221305PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6760773PMC
March 2020

Evaluation of phospho-histone H3 in Asian triple-negative breast cancer using multiplex immunofluorescence.

Authors:
Chi Peng Timothy Lai Joe Poh Sheng Yeong An Sen Tan Chong Hui Clara Ong Bernett Lee Jeffrey Chun Tatt Lim Aye Aye Thike Jabed Iqbal Rebecca Alexandra Dent Elaine Hsuen Lim Puay Hoon Tan

Breast Cancer Res Treat 2019 Nov 13;178(2):295-305. Epub 2019 Aug 13.

Division of Pathology, Singapore General Hospital, 20 College Road, Singapore, 169856, Singapore.

Purpose: We used multiplex immunofluorescence (mIF) to determine whether mitotic rate represents an independent prognostic marker in triple-negative breast cancer (TNBC). Secondary aims were to confirm the prognostic significance of immune cells in TNBC, and to investigate the relationship between immune cells and proliferating tumour cells.

Methods: A retrospective Asian cohort of 298 patients with TNBC diagnosed from 2003 to 2015 at the Singapore General Hospital was used in the present study. Formalin-fixed, paraffin-embedded breast cancer samples were analysed on tissue microarrays using mIF, which combined phospho-histone H3 (pHH3) expression with cytokeratin (CK) and leukocyte common antigen (CD45) expression to identify tumour and immune cells, respectively.

Results: Multivariate analysis showed that a high pHH3 index was associated with significantly improved overall survival (OS; p = 0.004), but this was not significantly associated with disease-free survival (DFS; p = 0.22). Similarly, multivariate analysis also revealed that a pHH3 positive count of > 1 cell per high-power field in the malignant epithelial compartment was an independent favourable prognostic marker for OS (p = 0.033) but not for DFS (p = 0.250). Furthermore, a high CD45 index was an independent favourable prognostic marker for DFS (p = 0.018), and there was a significant positive correlation between CD45 and pHH3 index (Spearman rank correlation coefficient, 0.250; p < 0.001).

Conclusions: Mitotic rates as determined by pHH3 expression in epithelial cells are significantly associated with improved survival in TNBC. mIF analysis of pHH3 in combination with CK and CD45 could help clinicians in prognosticating patients with TNBC.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1007/s10549-019-05396-5DOI Listing
November 2019

The role of Ki-67 in Asian triple negative breast cancers: a novel combinatory panel approach.

Authors:
An Sen Tan Joe Poe Sheng Yeong Chi Peng Timothy Lai Chong Hui Clara Ong Bernett Lee Jeffrey Chun Tatt Lim Aye Aye Thike Jabed Iqbal Rebecca Alexandra Dent Elaine Hsuen Lim Puay Hoon Tan

Virchows Arch 2019 Dec 12;475(6):709-725. Epub 2019 Aug 12.

Division of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Diagnostics Tower, Singapore, 169856, Singapore.

The proliferation marker Ki-67 is frequently used to assess aggressiveness in the pathological evaluation of cancer, but its role remains uncertain in triple-negative breast cancer (TNBC). We aimed to quantify and localize Ki-67 expression in both epithelial and immune compartments in TNBC and investigate its association with clinicopathological parameters and survival outcomes. A total of 406 TNBC cases diagnosed between 2003 and 2015 at Singapore General Hospital were recruited. Using state-of-the-art, 7-colour multiplex immunofluorescence (mIF) tissue microarrays (TMAs) were stained to assess the abundance, density and spatial distribution of Ki-67-positive tumour cells and immune cells co-decorated with cytokeratin (CK) and leukocyte common antigen (CD45) respectively. Furthermore, MKI67 mRNA profiles were analysed using NanoString technology. In multivariate analysis adjusted for tumour size, histologic grade, age at diagnosis, and lymph node stage, a high Ki-67 labelling index (LI) > 0.3% was associated with improved disease-free survival (DFS; HR = 0.727; p = 0.027). High Ki-67-positive immune cell count per TMA was a favourable prognostic marker for both DFS (HR = 0.379; p = 0.00153) and overall survival (OS; HR = 0.473; p = 0.0482). The combination of high Ki-67 LI and high MKI67 expression was associated with improved DFS (HR = 0.239; p = 0.00639) and OS (HR = 0.213; p = 0.034). This study is among the first to highlight that Ki-67 is associated with favourable prognosis in an adjuvant setting in TNBC, and the mIF-based evaluation of Ki-67 expression on both tumour and immune cells represents a novel prognostic approach.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1007/s00428-019-02635-4DOI Listing
December 2019

Recessive gene disruptions in autism spectrum disorder.

Authors:
Ryan N Doan Elaine T Lim Silvia De Rubeis Catalina Betancur David J Cutler Andreas G Chiocchetti Lynne M Overman Aubrie Soucy Susanne Goetze Christine M Freitag Mark J Daly Christopher A Walsh Joseph D Buxbaum Timothy W Yu

Nat Genet 2019 07 17;51(7):1092-1098. Epub 2019 Jun 17.

Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.

Autism spectrum disorder (ASD) affects up to 1 in 59 individuals. Genome-wide association and large-scale sequencing studies strongly implicate both common variants and rare de novo variants in ASD. Recessive mutations have also been implicated but their contribution remains less well defined. Here we demonstrate an excess of biallelic loss-of-function and damaging missense mutations in a large ASD cohort, corresponding to approximately 5% of total cases, including 10% of females, consistent with a female protective effect. We document biallelic disruption of known or emerging recessive neurodevelopmental genes (CA2, DDHD1, NSUN2, PAH, RARB, ROGDI, SLC1A1, USH2A) as well as other genes not previously implicated in ASD including FEV (FEV transcription factor, ETS family member), which encodes a key regulator of the serotonergic circuitry. Our data refine estimates of the contribution of recessive mutation to ASD and suggest new paths for illuminating previously unknown biological pathways responsible for this condition.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41588-019-0433-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629034PMC
July 2019

Voltage during atrial fibrillation is superior to voltage during sinus rhythm in localizing areas of delayed enhancement on magnetic resonance imaging: An assessment of the posterior left atrium in patients with persistent atrial fibrillation.

Authors:
Norman A Qureshi Steven J Kim Chris D Cantwell Valtino X Afonso Wenjia Bai Rheeda L Ali Matt J Shun-Shin Louisa C Malcolme-Lawes Vishal Luther Kevin M W Leong Elaine Lim Ian Wright Szabi Nagy Sajad Hayat Fu Siong Ng Michael Koa Wing Nick W F Linton David C Lefroy Zachary I Whinnett D Wyn Davies Prapa Kanagaratnam Nicholas S Peters Phang Boon Lim

Heart Rhythm 2019 09 3;16(9):1357-1367. Epub 2019 Jun 3.

Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom. Electronic address:

Background: Bipolar electrogram voltage during sinus rhythm (V) has been used as a surrogate for atrial fibrosis in guiding catheter ablation of persistent atrial fibrillation (AF), but the fixed rate and wavefront characteristics present during sinus rhythm may not accurately reflect underlying functional vulnerabilities responsible for AF maintenance.

Objective: The purpose of this study was determine whether, given adequate temporal sampling, the spatial distribution of mean AF voltage (V) better correlates with delayed-enhancement magnetic resonance imaging (MRI-DE)-detected atrial fibrosis than V.

Methods: AF was mapped (8 seconds) during index ablation for persistent AF (20 patients) using a 20-pole catheter (660 ± 28 points/map). After cardioversion, V was mapped (557 ± 326 points/map). Electroanatomic and MRI-DE maps were co-registered in 14 patients.

Results: The time course of V was assessed from 1-40 AF cycles (∼8 seconds) at 1113 locations. V stabilized with sampling >4 seconds (mean voltage error 0.05 mV). Paired point analysis of V from segments acquired 30 seconds apart (3667 sites; 15 patients) showed strong correlation (r = 0.95; P <.001). Delayed enhancement (DE) was assessed across the posterior left atrial (LA) wall, occupying 33% ± 13%. V distributions were (median [IQR]) 0.21 [0.14-0.35] mV in DE vs 0.52 [0.34-0.77] mV in non-DE regions. V distributions were 1.34 [0.65-2.48] mV in DE vs 2.37 [1.27-3.97] mV in non-DE. V threshold of 0.35 mV yielded sensitivity of 75% and specificity of 79% in detecting MRI-DE compared with 63% and 67%, respectively, for V (1.8-mV threshold) CONCLUSION: The correlation between low-voltage and posterior LA MRI-DE is significantly improved when acquired during AF vs sinus rhythm. With adequate sampling, mean AF voltage is a reproducible marker reflecting the functional response to the underlying persistent AF substrate.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.hrthm.2019.05.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6722483PMC
September 2019

The Genetic Landscape of Diamond-Blackfan Anemia.

Authors:
Jacob C Ulirsch Jeffrey M Verboon Shideh Kazerounian Michael H Guo Daniel Yuan Leif S Ludwig Robert E Handsaker Nour J Abdulhay Claudia Fiorini Giulio Genovese Elaine T Lim Aaron Cheng Beryl B Cummings Katherine R Chao Alan H Beggs Casie A Genetti Colin A Sieff Peter E Newburger Edyta Niewiadomska Michal Matysiak Adrianna Vlachos Jeffrey M Lipton Eva Atsidaftos Bertil Glader Anupama Narla Pierre-Emmanuel Gleizes Marie-Françoise O'Donohue Nathalie Montel-Lehry David J Amor Steven A McCarroll Anne H O'Donnell-Luria Namrata Gupta Stacey B Gabriel Daniel G MacArthur Eric S Lander Monkol Lek Lydie Da Costa David G Nathan Andrei A Korostelev Ron Do Vijay G Sankaran Hanna T Gazda

Am J Hum Genet 2019 Feb;104(2):356

View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.ajhg.2018.12.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372259PMC
February 2019

Prognostic value of CD8 + PD-1+ immune infiltrates and PDCD1 gene expression in triple negative breast cancer.

Authors:
Joe Yeong Jeffrey Chun Tatt Lim Bernett Lee Huihua Li Clara Chong Hui Ong Aye Aye Thike Wei Hseun Yeap Yi Yang Ansel Yi Herh Lim Timothy Kwang Yong Tay Jin Liu Siew-Cheng Wong Jinmiao Chen Elaine Hsuen Lim Jabed Iqbal Rebecca Dent Evan W Newell Puay Hoon Tan

J Immunother Cancer 2019 02 6;7(1):34. Epub 2019 Feb 6.

Division of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Singapore, 169856, Singapore.

The role of programmed cell death protein-1 (PD-1)/programmed cell death ligand 1 (PD-L1) in triple negative breast cancer (TNBC) remains to be fully understood. In this study, we investigated the role of PD-1 as a prognostic marker for TNBC in an Asian cohort (n = 269). Samples from patients with TNBC were labeled with antibodies against PD-L1 and PD-1, and subjected to NanoString assays to measure the expression of immune-related genes. Associations between disease-free survival (DFS), overall survival (OS) and biomarker expression were investigated. Multivariate analysis showed that tumors with high PD-1 immune infiltrates harbored significantly increased DFS, and this increase was significant even after controlling for clinicopathological parameters (HR 0.95; P = 0.030). In addition, the density of cells expressing both CD8 and PD-1, but not the density of CD8PD-1 immune infiltrates, was associated with improved DFS. Notably, this prognostic significance was independent of clinicopathological parameters and the densities of total CD8 cell (HR 0.43, P = 0.011). At the transcriptional level, high expression of PDCD1 within the tumor was significantly associated with improved DFS (HR 0.38; P = 0.027). In line with these findings, high expression of IFNG (HR 0.38; P = 0.001) and IFN signaling genes (HR 0.46; p = 0.027) was also associated with favorable DFS. Inclusion of PD-1 immune infiltrates and PDCD1 gene expression added significant prognostic value for DFS (ΔLRχ = 6.35; P = 0.041) and OS (ΔLRχ = 9.53; P = 0.008), beyond that provided by classical clinicopathological variables. Thus, PD-1 mRNA and protein expression status represent a promising, independent indicator of prognosis in TNBC.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1186/s40425-019-0499-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366051PMC
February 2019

REST and Neural Gene Network Dysregulation in iPSC Models of Alzheimer's Disease.

Authors:
Katharina Meyer Heather M Feldman Tao Lu Derek Drake Elaine T Lim King-Hwa Ling Nicholas A Bishop Ying Pan Jinsoo Seo Yuan-Ta Lin Susan C Su George M Church Li-Huei Tsai Bruce A Yankner

Cell Rep 2019 01;26(5):1112-1127.e9

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

The molecular basis of the earliest neuronal changes that lead to Alzheimer's disease (AD) is unclear. Here, we analyze neural cells derived from sporadic AD (SAD), APOE4 gene-edited and control induced pluripotent stem cells (iPSCs). We observe major differences in iPSC-derived neural progenitor (NP) cells and neurons in gene networks related to neuronal differentiation, neurogenesis, and synaptic transmission. The iPSC-derived neural cells from SAD patients exhibit accelerated neural differentiation and reduced progenitor cell renewal. Moreover, a similar phenotype appears in NP cells and cerebral organoids derived from APOE4 iPSCs. Impaired function of the transcriptional repressor REST is strongly implicated in the altered transcriptome and differentiation state. SAD and APOE4 expression result in reduced REST nuclear translocation and chromatin binding, and disruption of the nuclear lamina. Thus, dysregulation of neural gene networks may set in motion the pathologic cascade that leads to AD.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.celrep.2019.01.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386196PMC
January 2019

The Genetic Landscape of Diamond-Blackfan Anemia.

Authors:
Jacob C Ulirsch Jeffrey M Verboon Shideh Kazerounian Michael H Guo Daniel Yuan Leif S Ludwig Robert E Handsaker Nour J Abdulhay Claudia Fiorini Giulio Genovese Elaine T Lim Aaron Cheng Beryl B Cummings Katherine R Chao Alan H Beggs Casie A Genetti Colin A Sieff Peter E Newburger Edyta Niewiadomska Michal Matysiak Adrianna Vlachos Jeffrey M Lipton Eva Atsidaftos Bertil Glader Anupama Narla Pierre-Emmanuel Gleizes Marie-Françoise O'Donohue Nathalie Montel-Lehry David J Amor Steven A McCarroll Anne H O'Donnell-Luria Namrata Gupta Stacey B Gabriel Daniel G MacArthur Eric S Lander Monkol Lek Lydie Da Costa David G Nathan Andrei A Korostelev Ron Do Vijay G Sankaran Hanna T Gazda

Am J Hum Genet 2018 12 29;103(6):930-947. Epub 2018 Nov 29.

Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

Diamond-Blackfan anemia (DBA) is a rare bone marrow failure disorder that affects 7 out of 1,000,000 live births and has been associated with mutations in components of the ribosome. In order to characterize the genetic landscape of this heterogeneous disorder, we recruited a cohort of 472 individuals with a clinical diagnosis of DBA and performed whole-exome sequencing (WES). We identified relevant rare and predicted damaging mutations for 78% of individuals. The majority of mutations were singletons, absent from population databases, predicted to cause loss of function, and located in 1 of 19 previously reported ribosomal protein (RP)-encoding genes. Using exon coverage estimates, we identified and validated 31 deletions in RP genes. We also observed an enrichment for extended splice site mutations and validated their diverse effects using RNA sequencing in cell lines obtained from individuals with DBA. Leveraging the size of our cohort, we observed robust genotype-phenotype associations with congenital abnormalities and treatment outcomes. We further identified rare mutations in seven previously unreported RP genes that may cause DBA, as well as several distinct disorders that appear to phenocopy DBA, including nine individuals with biallelic CECR1 mutations that result in deficiency of ADA2. However, no new genes were identified at exome-wide significance, suggesting that there are no unidentified genes containing mutations readily identified by WES that explain >5% of DBA-affected case subjects. Overall, this report should inform not only clinical practice for DBA-affected individuals, but also the design and analysis of rare variant studies for heterogeneous Mendelian disorders.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.ajhg.2018.10.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288280PMC
December 2018

Replication and Meta-analysis of the Association between BDNF Val66Met Polymorphism and Cognitive Impairment in Patients Receiving Chemotherapy.

Authors:
Chia Jie Tan Sheree Wan Ting Lim Yi Long Toh Terence Ng Angie Yeo Maung Shwe Koon Mian Foo Pat Chu Amit Jain Si-Lin Koo Rebecca A Dent Raymond Chee Hui Ng Yoon Sim Yap Elaine H Lim Kiley Wei-Jen Loh Wen Yee Chay Guek Eng Lee Tira Jing Ying Tan Sok Yuen Beh Mabel Wong Jack Junjie Chan Chiea Chuen Khor Han Kiat Ho Alexandre Chan

Mol Neurobiol 2019 Jul 31;56(7):4741-4750. Epub 2018 Oct 31.

Department of Pharmacy, Faculty of Science, National University of Singapore, Block S4, 18 Science Drive 4, Singapore, 117543, Singapore.

Cancer-related cognitive impairment (CRCI) adversely affects cancer patients. We had previously demonstrated that the BDNF Val66Met genetic polymorphism is associated with lower odds of subjective CRCI in the multitasking and verbal ability domains among breast cancer patients receiving chemotherapy. To further assess our previous findings, we evaluated the association of BDNF Val66Met polymorphism with subjective and objective CRCI in a temporally separate cohort of patients and pooled findings from both the original (n = 145) and current (n = 193) cohorts in a meta-analysis. Subjective CRCI was assessed using FACT-Cog. Objective CRCI was evaluated using computerized neuropsychological tests. Genotyping was carried out using Sanger sequencing. The association of BDNF Val66Met genotypes and CRCI was examined with logistic regression. A fixed-effect meta-analysis was conducted using the inverse variance method. In the meta-analysis (n = 338), significantly lower odds of CRCI were associated with Met allele carriers based on the global FACT-Cog score (OR = 0.52, 95% CI 0.29-0.94). Furthermore, Met allele carriers were at lower odds of developing impairment in the domains of memory (OR = 0.34, 95% CI: 0.17-0.70), multitasking (OR = 0.33, 95% CI: 0.18-0.59), and verbal ability (OR = 0.46, 95% CI: 0.24-0.88). Consistent with the previous study, lower odds of subjective CRCI among patients with the BDNF Met allele was observed after adjusting for potential confounders in the multitasking (OR = 0.30, 95% CI: 0.14-0.67) domain. In conclusion, carriers of the BDNF Met allele were protected against global subjective CRCI, particularly in the domains of memory, multitasking, and verbal ability. Our findings further contribute to the understanding of CRCI pathophysiology.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1007/s12035-018-1410-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6647505PMC
July 2019

A novel approach to mapping the atrial ganglionated plexus network by generating a distribution probability atlas.

Authors:
Min-Young Kim Markus B Sikkel Ross J Hunter Guy A Haywood David R Tomlinson Muzahir H Tayebjee Rheeda L Ali Chris D Cantwell Hanney Gonna Belinda C Sandler Elaine Lim Guy Furniss Dimitrios Panagopoulos Gordon Begg Gurpreet Dhillon Nicola J Hill James O'Neill Darrel P Francis Phang Boon Lim Nicholas S Peters Nick W F Linton Prapa Kanagaratnam

J Cardiovasc Electrophysiol 2018 12 5;29(12):1624-1634. Epub 2018 Oct 5.

Myocardial Function Section, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK.

Introduction: The ganglionated plexuses (GPs) of the intrinsic cardiac autonomic system are implicated in arrhythmogenesis. GP localization by stimulation of the epicardial fat pads to produce atrioventricular dissociating (AVD) effects is well described. We determined the anatomical distribution of the left atrial GPs that influence atrioventricular (AV) dissociation.

Methods And Results: High frequency stimulation was delivered through a Smart-Touch catheter in the left atrium of patients undergoing atrial fibrillation (AF) ablation. Three dimensional locations of points tested throughout the entire chamber were recorded on the CARTO™ system. Impact on the AV conduction was categorized as ventricular asystole, bradycardia, or no effect. CARTO maps were exported, registered, and transformed onto a reference left atrial geometry using a custom software, enabling data from multiple patients to be overlaid. In 28 patients, 2108 locations were tested and 283 sites (13%) demonstrated (AVD-GP) effects. There were 10 AVD-GPs (interquartile range, 11.5) per patient. Eighty percent (226) produced asystole and 20% (57) showed bradycardia. The distribution of the two groups was very similar. Highest probability of AVD-GPs (>20%) was identified in: inferoseptal portion (41%) and right inferior pulmonary vein base (30%) of the posterior wall, right superior pulmonary vein antrum (31%).

Conclusion: It is feasible to map the entire left atrium for AVD-GPs before AF ablation. Aggregated data from multiple patients, producing a distribution probability atlas of AVD-GPs, identified three regions with a higher likelihood for finding AVD-GPs and these matched the histological descriptions. This approach could be used to better characterize the autonomic network.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1111/jce.13723DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369684PMC
December 2018

Chromosomal instability-induced senescence potentiates cell non-autonomous tumourigenic effects.

Authors:
Qianqian He Bijin Au Madhura Kulkarni Yang Shen Kah J Lim Jiamila Maimaiti Cheng Kit Wong Monique N H Luijten Han C Chong Elaine H Lim Giulia Rancati Indrajit Sinha Zhiyan Fu Xiaomeng Wang John E Connolly Karen C Crasta

Oncogenesis 2018 Aug 15;7(8):62. Epub 2018 Aug 15.

Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.

Chromosomal instability (CIN), a high rate of chromosome loss or gain, is often associated with poor prognosis and drug resistance in cancers. Aneuploid, including near-polyploid, cells contain an abnormal number of chromosomes and exhibit CIN. The post-mitotic cell fates following generation of different degrees of chromosome mis-segregation and aneuploidy are unclear. Here we used aneuploidy inducers, nocodazole and reversine, to create different levels of aneuploidy. A higher extent of aneuploid and near-polyploid cells in a given population led to senescence. This was in contrast to cells with relatively lower levels of abnormal ploidy that continued to proliferate. Our findings revealed that senescence was accompanied by DNA damage and robust p53 activation. These senescent cells acquired the senescence-associated secretory phenotype (SASP). Depletion of p53 reduced the number of senescent cells with concomitant increase in cells undergoing DNA replication. Characterisation of these SASP factors demonstrated that they conferred paracrine pro-tumourigenic effects such as invasion, migration and angiogenesis both in vitro and in vivo. Finally, a correlation between increased aneuploidy and senescence was observed at the invasive front in breast carcinomas. Our findings demonstrate functional non-equivalence of discernable aneuploidies on tumourigenesis and suggest a cell non-autonomous mechanism by which aneuploidy-induced senescent cells and SASP can affect the tumour microenvironment to promote tumour progression.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41389-018-0072-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092349PMC
August 2018

The ESCRT-III Protein CHMP1A Mediates Secretion of Sonic Hedgehog on a Distinctive Subtype of Extracellular Vesicles.

Authors:
Michael E Coulter Cristina M Dorobantu Gerrald A Lodewijk François Delalande Sarah Cianferani Vijay S Ganesh Richard S Smith Elaine T Lim C Shan Xu Song Pang Eric T Wong Hart G W Lidov Monica L Calicchio Edward Yang Dilenny M Gonzalez Thorsten M Schlaeger Ganeshwaran H Mochida Harald Hess Wei-Chung Allen Lee Maria K Lehtinen Tomas Kirchhausen David Haussler Frank M J Jacobs Raphael Gaudin Christopher A Walsh

Cell Rep 2018 07;24(4):973-986.e8

Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

Endosomal sorting complex required for transport (ESCRT) complex proteins regulate biogenesis and release of extracellular vesicles (EVs), which enable cell-to-cell communication in the nervous system essential for development and adult function. We recently showed human loss-of-function (LOF) mutations in ESCRT-III member CHMP1A cause autosomal recessive microcephaly with pontocerebellar hypoplasia, but its mechanism was unclear. Here, we show Chmp1a is required for progenitor proliferation in mouse cortex and cerebellum and progenitor maintenance in human cerebral organoids. In Chmp1a null mice, this defect is associated with impaired sonic hedgehog (Shh) secretion and intraluminal vesicle (ILV) formation in multivesicular bodies (MVBs). Furthermore, we show CHMP1A is important for release of an EV subtype that contains AXL, RAB18, and TMED10 (ART) and SHH. Our findings show CHMP1A loss impairs secretion of SHH on ART-EVs, providing molecular mechanistic insights into the role of ESCRT proteins and EVs in the brain.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1016/j.celrep.2018.06.100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178983PMC
July 2018

Autophagy Governs Protumorigenic Effects of Mitotic Slippage-induced Senescence.

Authors:
Rekha Jakhar Monique N H Luijten Alex X F Wong Bing Cheng Ke Guo Suat P Neo Bijin Au Madhura Kulkarni Kah J Lim Jiamila Maimaiti Han C Chong Elaine H Lim Tee B K Tan Kong W Ong Yirong Sim Jill S L Wong James B K Khoo Juliana T S Ho Boon T Chua Indrajit Sinha Xiaomeng Wang John E Connolly Jayantha Gunaratne Karen C Crasta

Mol Cancer Res 2018 11 23;16(11):1625-1640. Epub 2018 Jul 23.

Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.

The most commonly utilized class of chemotherapeutic agents administered as a first-line therapy are antimitotic drugs; however, their clinical success is often impeded by chemoresistance and disease relapse. Hence, a better understanding of the cellular pathways underlying escape from cell death is critical. Mitotic slippage describes the cellular process where cells exit antimitotic drug-enforced mitotic arrest and "slip" into interphase without proper chromosome segregation and cytokinesis. The current report explores the cell fate consequence following mitotic slippage and assesses a major outcome following treatment with many chemotherapies, therapy-induced senescence. It was found that cells postslippage entered senescence and could impart the senescence-associated secretory phenotype (SASP). SASP factor production elicited paracrine protumorigenic effects, such as migration, invasion, and vascularization. Both senescence and SASP factor development were found to be dependent on autophagy. Autophagy induction during mitotic slippage involved the autophagy activator AMPK and endoplasmic reticulum stress response protein PERK. Pharmacologic inhibition of autophagy or silencing of autophagy-related ATG5 led to a bypass of G arrest senescence, reduced SASP-associated paracrine tumorigenic effects, and increased DNA damage after S-phase entry with a concomitant increase in apoptosis. Consistent with this, the autophagy inhibitor chloroquine and microtubule-stabilizing drug paclitaxel synergistically inhibited tumor growth in mice. Sensitivity to this combinatorial treatment was dependent on p53 status, an important factor to consider before treatment. Clinical regimens targeting senescence and SASP could provide a potential effective combinatorial strategy with antimitotic drugs. .
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1158/1541-7786.MCR-18-0024DOI Listing
November 2018

An enhanced CRISPR repressor for targeted mammalian gene regulation.

Authors:
Nan Cher Yeo Alejandro Chavez Alissa Lance-Byrne Yingleong Chan David Menn Denitsa Milanova Chih-Chung Kuo Xiaoge Guo Sumana Sharma Angela Tung Ryan J Cecchi Marcelle Tuttle Swechchha Pradhan Elaine T Lim Noah Davidsohn Mo R Ebrahimkhani James J Collins Nathan E Lewis Samira Kiani George M Church

Nat Methods 2018 08 16;15(8):611-616. Epub 2018 Jul 16.

Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA.

The RNA-guided endonuclease Cas9 can be converted into a programmable transcriptional repressor, but inefficiencies in target-gene silencing have limited its utility. Here we describe an improved Cas9 repressor based on the C-terminal fusion of a rationally designed bipartite repressor domain, KRAB-MeCP2, to nuclease-dead Cas9. We demonstrate the system's superiority in silencing coding and noncoding genes, simultaneously repressing a series of target genes, improving the results of single and dual guide RNA library screens, and enabling new architectures of synthetic genetic circuits.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1038/s41592-018-0048-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129399PMC
August 2018

High Densities of Tumor-Associated Plasma Cells Predict Improved Prognosis in Triple Negative Breast Cancer.

Authors:
Joe Yeong Jeffrey Chun Tatt Lim Bernett Lee Huihua Li Noel Chia Clara Chong Hui Ong Weng Kit Lye Thomas Choudary Putti Rebecca Dent Elaine Lim Aye Aye Thike Puay Hoon Tan Jabed Iqbal

Front Immunol 2018 30;9:1209. Epub 2018 May 30.

Division of Pathology, Singapore General Hospital, Singapore, Singapore.

Breast cancer is the most common malignancy affecting women, but the heterogeneity of the condition is a significant obstacle to effective treatment. Triple negative breast cancers (TNBCs) do not express HER2 or the receptors for estrogen or progesterone, and so often have a poor prognosis. Tumor-infiltrating T cells have been well-characterized in TNBC, and increased numbers are associated with better outcomes; however, the potential roles of B cells and plasma cells have been large. Here, we conducted a retrospective correlative study on the expression of B cell/plasma cell-related genes, and the abundance and localization of B cells and plasma cells within TNBCs, and clinical outcome. We analyzed 269 TNBC samples and used immunohistochemistry to quantify tumor-infiltrating B cells and plasma cells, coupled with NanoString measurement of expression of immunoglobulin metagenes. Multivariate analysis revealed that patients bearing TNBCs with above-median densities of CD38 plasma cells had significantly better disease-free survival (DFS) (HR = 0.44; 95% CI 0.26-0.77;  = 0.004) but not overall survival (OS), after adjusting for the effects of known prognostic factors. In contrast, TNBCs with higher immunoglobulin gene expression exhibited improved prognosis (OS  = 0.029 and DFS  = 0.005). The presence of B cells and plasma cells was positively correlated ( < 0.0001,  = 0.558), while immunoglobulin gene IGKC, IGHM, and IGHG1 mRNA expression correlated specifically with the density of CD38 plasma cells (IGKC  < 0.0001,  = 0.647; IGHM  < 0.0001,  = 0.580; IGHG1  < 0.0001,  = 0.655). Interestingly, after adjusting the multivariate analysis for the effect of intratumoral CD38 plasma cell density, the expression levels of all three genes lost significant prognostic value, suggesting a biologically important role of plasma cells. Last but not least, the addition of intratumoral CD38 plasma cell density to clinicopathological features significantly increased the prognostic value for both DFS (ΔLRχ = 17.28,  = 1.71E-08) and OS (ΔLRχ = 10.03,  = 6.32E-08), compared to clinicopathological features alone. The best combination was achieved by integrating intratumoral CD38 plasma cell density and IGHG1 which conferred the best added prognostic value for DFS (ΔLRχ = 27.38,  = 5.22E-10) and OS (ΔLRχ = 21.29,  = 1.03E-08). Our results demonstrate that the role of plasma cells in TNBC warrants further study to elucidate the relationship between their infiltration of tumors and disease recurrence.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.3389/fimmu.2018.01209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988856PMC
August 2019

Enabling multiplexed testing of pooled donor cells through whole-genome sequencing.

Authors:
Yingleong Chan Ying Kai Chan Daniel B Goodman Xiaoge Guo Alejandro Chavez Elaine T Lim George M Church

Genome Med 2018 04 19;10(1):31. Epub 2018 Apr 19.

Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.

We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DNA barcodes as markers of donor identity. Instead, we take advantage of common single nucleotide polymorphisms, whole-genome sequencing, and an algorithm to calculate the proportions from the sequencing data. By testing using simulated and real data, we showed that our method robustly predicts the individual proportions from a mixed-pool of numerous donors, thus enabling the multiplexed testing of diverse donor cells en masse.More information is available at https://pgpresearch.med.harvard.edu/poolseq/.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1186/s13073-018-0541-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909281PMC
April 2018

Association of mitochondrial DNA content in peripheral blood with cancer-related fatigue and chemotherapy-related cognitive impairment in early-stage breast cancer patients: a prospective cohort study.

Authors:
Jung-Woo Chae Peh Siang Chua Terence Ng Angie Hui Ling Yeo Maung Shwe Yan Xiang Gan Sreemanee Dorajoo Koon Mian Foo Kiley Wei-Jen Loh Si-Lin Koo Wen Yee Chay Tira Jing Ying Tan Sok Yuen Beh Elaine Hsuen Lim Guek Eng Lee Rebecca Dent Yoon Sim Yap Raymond Ng Han Kiat Ho Alexandre Chan

Breast Cancer Res Treat 2018 Apr 8;168(3):713-721. Epub 2018 Jan 8.

Department of Pharmacy, National University of Singapore, Blk S4A Level 3, 18 Science Drive 4, Singapore, 117543, Singapore.

Purpose: Cancer-related fatigue (CRF) and chemotherapy-related cognitive impairment (CRCI) are reported to be associated with mitochondrial dysfunction. Hence, mitochondrial DNA (mtDNA) content, a biomarker of mitochondrial dysfunction, is hypothesized to correlate with the onset of CRF and CRCI. This study aims to evaluate the association between peripheral blood mtDNA content reduction and severity of CRF and CRCI in patients receiving chemotherapy.

Methods: This was a prospective cohort study. Early-stage breast cancer patients receiving anthracycline- or taxane-based chemotherapy were recruited. CRF was assessed using MFSI-SF, and CRCI was assessed using FACT-Cog and CANTAB at two timepoints: baseline (T1; prior to treatment) and 6 weeks after initiation of treatment (T2). mtDNA content was measured at both timepoints using real-time quantitative polymerase chain reaction. Multiple logistic regression was utilized to evaluate the association between mtDNA reduction and worsening of CRF and CRCI, adjusting for age, anxiety, insomnia, plasma cytokines concentrations, and other clinically important covariates.

Results: A total of 108 patients (age 52.0 ± 9.2 years; 82.4% Chinese; 64.8% receiving anthracycline-based chemotherapy) were recruited. Proportions of patients with worsening of CRF increased from the lower to the upper quartiles of mtDNA reduction (22.2, 33.3, 55.6, and 63.0% in quartiles 1, 2, 3, and 4, respectively, p = 0.001 for trend). Reduction of mtDNA content was significantly greater among those with worsening of CRF and CRCI compared to those without CRF [mean reduction (± SD): 36.5 (46.1) vs. 9.4 (34.5), p < 0.001]. After adjusting for covariates, every 1-unit reduction of the mtDNA content was associated with a 4% increased risk for worsening of CRF (95% CI, 1-6%; p = 0.009).

Conclusions: This is the first study to show that the reduction of mtDNA content in peripheral blood is associated with the onset of CRF in patients receiving chemotherapy. Further validation studies are required to confirm the findings.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1007/s10549-017-4640-7DOI Listing
April 2018

Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder.

Authors:
Elaine T Lim Mohammed Uddin Silvia De Rubeis Yingleong Chan Anne S Kamumbu Xiaochang Zhang Alissa M D'Gama Sonia N Kim Robert Sean Hill Arthur P Goldberg Christopher Poultney Nancy J Minshew Itaru Kushima Branko Aleksic Norio Ozaki Mara Parellada Celso Arango Maria J Penzol Angel Carracedo Alexander Kolevzon Christina M Hultman Lauren A Weiss Menachem Fromer Andreas G Chiocchetti Christine M Freitag George M Church Stephen W Scherer Joseph D Buxbaum Christopher A Walsh

Nat Neurosci 2017 09 17;20(9):1217-1224. Epub 2017 Jul 17.

Division of Genetics and Genomics, Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA.

We systematically analyzed postzygotic mutations (PZMs) in whole-exome sequences from the largest collection of trios (5,947) with autism spectrum disorder (ASD) available, including 282 unpublished trios, and performed resequencing using multiple independent technologies. We identified 7.5% of de novo mutations as PZMs, 83.3% of which were not described in previous studies. Damaging, nonsynonymous PZMs within critical exons of prenatally expressed genes were more common in ASD probands than controls (P < 1 × 10), and genes carrying these PZMs were enriched for expression in the amygdala (P = 5.4 × 10). Two genes (KLF16 and MSANTD2) were significantly enriched for PZMs genome-wide, and other PZMs involved genes (SCN2A, HNRNPU and SMARCA4) whose mutation is known to cause ASD or other neurodevelopmental disorders. PZMs constitute a significant proportion of de novo mutations and contribute importantly to ASD risk.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1038/nn.4598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672813PMC
September 2017

An unbiased index to quantify participant's phenotypic contribution to an open-access cohort.

Authors:
Yingleong Chan Michael Tung Alexander S Garruss Sarah W Zaranek Ying Kai Chan Jeantine E Lunshof Alexander W Zaranek Madeleine P Ball Michael F Chou Elaine T Lim George M Church

Sci Rep 2017 04 7;7:46148. Epub 2017 Apr 7.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

The Personal Genome Project (PGP) is an effort to enroll many participants to create an open-access repository of genome, health and trait data for research. However, PGP participants are not enrolled for studying any specific traits and participants choose the phenotypes to disclose. To measure the extent and willingness and to encourage and guide participants to contribute phenotypes, we developed an algorithm to score and rank the phenotypes and participants of the PGP. The scoring algorithm calculates the participation index (P-index) for every participant, where 0 indicates no reported phenotypes and 100 indicate complete phenotype reporting. We calculated the P-index for all 5,015 participants in the PGP and they ranged from 0 to 96.7. We found that participants mainly have either high scores (P-index > 90, 29.5%) or low scores (P-index < 10, 57.8%). While, there are significantly more males than female participants (1,793 versus 1,271), females tend to have on average higher P-indexes (P = 0.015). We also reported the P-indexes of participants based on demographics and states like Missouri and Massachusetts have better P-indexes than states like Utah and Minnesota. The P-index can therefore be used as an unbiased way to measure and rank participant's phenotypic contribution towards the PGP.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1038/srep46148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384003PMC
April 2017

Visualizing Localized Reentry With Ultra-High Density Mapping in Iatrogenic Atrial Tachycardia: Beware Pseudo-Reentry.

Authors:
Vishal Luther Markus Sikkel Nathan Bennett Fernando Guerrero Kevin Leong Norman Qureshi Fu Siong Ng Sajad A Hayat S M Afzal Sohaib Louisa Malcolme-Lawes Elaine Lim Ian Wright Michael Koa-Wing David C Lefroy Nick W F Linton Zachary Whinnett Prapa Kanagaratnam D Wyn Davies Nicholas S Peters Phang Boon Lim

Circ Arrhythm Electrophysiol 2017 Apr;10(4)

From the Department of Cardiology, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom (V.L., M.S., K.L., N.Q., F.S.N., S.A.H., S.M.A.S., L.M.-L., E.L., I.W., M.K.-W., D.C.L., N.W.F.L., Z.W., P.K., D.W.D., N.S.P., P.B.L.); and Boston Scientific Ltd, Marlborough, MA (N.B., F.G.).

Background: The activation pattern of localized reentry (LR) in atrial tachycardia remains incompletely understood. We used the ultra-high density Rhythmia mapping system to study activation patterns in LR.

Methods And Results: LR was suggested by small rotatory activations (carousels) containing the full spectrum of the color-coded map. Twenty-three left-sided atrial tachycardias were mapped in 15 patients (age: 64±11 years). 16 253±9192 points were displayed per map, collected over 26±14 minutes. A total of 50 carousels were identified (median 2; quartiles 1-3 per map), although this represented LR in only n=7 out of 50 (14%): here, rotation occurred around a small area of scar (<0.03 mV; 12±6 mm diameter). In LR, electrograms along the carousel encompassed the full tachycardia cycle length, and surrounding activation moved away from the carousel in all directions. Ablating fractionated electrograms (117±18 ms; 44±13% of tachycardia cycle length) within the carousel interrupted the tachycardia in every LR case. All remaining carousels were pseudo-reentrant (n=43/50 [86%]) occurring in areas of wavefront collision (n=21; median 0.5; quartiles 0-2 per map) or as artifact because of annotation of noise or interpolation in areas of incomplete mapping (n=22; median 1, quartiles 0-2 per map). Pseudo-reentrant carousels were incorrectly ablated in 5 cases having been misinterpreted as LR.

Conclusions: The activation pattern of LR is of small stable rotational activations (carousels), and this drove 30% (7/23) of our postablation atrial tachycardias. However, this appearance is most often pseudo-reentrant and must be differentiated by interpretation of electrograms in the candidate circuit and activation in the wider surrounding region.
View Article and Find Full Text PDF

Download full-text PDF

 Source
http://dx.doi.org/10.1161/CIRCEP.116.004724DOI Listing
April 2017