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Article ; Online: Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2

Chang, Jessie J-Y / Gleeson, Josie / Rawlinson, Daniel / De Paoli-Iseppi, Ricardo / Zhou, Chenxi / Mordant, Francesca L / Londrigan, Sarah L / Clark, Michael B / Subbarao, Kanta / Stinear, Timothy P / Coin, Lachlan J M / Pitt, Miranda E

Frontiers in immunology

2022 Volume 13, Page(s) 832223

Abstract: Better methods to interrogate host-pathogen interactions during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections are imperative to help understand and prevent this disease. Here we implemented RNA-sequencing (RNA-seq) using Oxford ... ...

Abstract	Better methods to interrogate host-pathogen interactions during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections are imperative to help understand and prevent this disease. Here we implemented RNA-sequencing (RNA-seq) using Oxford Nanopore Technologies (ONT) long-reads to measure differential host gene expression, transcript polyadenylation and isoform usage within various epithelial cell lines permissive and non-permissive for SARS-CoV-2 infection. SARS-CoV-2-infected and mock-infected Vero (African green monkey kidney epithelial cells), Calu-3 (human lung adenocarcinoma epithelial cells), Caco-2 (human colorectal adenocarcinoma epithelial cells) and A549 (human lung carcinoma epithelial cells) were analyzed over time (0, 2, 24, 48 hours). Differential polyadenylation was found to occur in both infected Calu-3 and Vero cells during a late time point (48 hpi), with Gene Ontology (GO) terms such as
MeSH term(s)	Animals ; COVID-19/genetics ; Caco-2 Cells ; Chlorocebus aethiops ; Humans ; Polyadenylation ; RNA, Messenger/metabolism ; Ribosomal Proteins/metabolism ; SARS-CoV-2 ; Sequence Analysis, RNA ; Vero Cells
Chemical Substances	RNA, Messenger ; Ribosomal Proteins
Language	English
Publishing date	2022-04-06
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.832223
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection.

Chang, Jessie J-Y / Rawlinson, Daniel / Pitt, Miranda E / Taiaroa, George / Gleeson, Josie / Zhou, Chenxi / Mordant, Francesca L / De Paoli-Iseppi, Ricardo / Caly, Leon / Purcell, Damian F J / Stinear, Timothy P / Londrigan, Sarah L / Clark, Michael B / Williamson, Deborah A / Subbarao, Kanta / Coin, Lachlan J M

Cell reports

2021 Volume 35, Issue 6, Page(s) 109108

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses subgenomic RNA (sgRNA) to produce viral proteins for replication and immune evasion. We apply long-read RNA and cDNA sequencing to in vitro human and primate infection models to study ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses subgenomic RNA (sgRNA) to produce viral proteins for replication and immune evasion. We apply long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA upregulates earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of open reading frame 1ab (ORF1ab) containing nsp1 joins to ORF10, and the 3' untranslated region (UTR) upregulates at 48 h post-infection in human cell lines. We identify double-junction sgRNA containing both TRS-dependent and -independent junctions. We find multiple sites at which the SARS-CoV-2 genome is consistently more modified than sgRNA and that sgRNA modifications are stable across transcript clusters, host cells, and time since infection. Our work highlights the dynamic nature of the SARS-CoV-2 transcriptome during its replication cycle.
MeSH term(s)	Animals ; COVID-19/genetics ; Caco-2 Cells ; Cell Line ; Chlorocebus aethiops ; Epigenesis, Genetic ; Genome, Viral/genetics ; Humans ; Immune Evasion ; Open Reading Frames ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Transcription, Genetic/genetics ; Transcriptome ; Vero Cells ; Viral Proteins/genetics
Chemical Substances	RNA, Viral ; Viral Proteins
Language	English
Publishing date	2021-04-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2021.109108
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Article: Arctic warming by abundant fine sea salt aerosols from blowing snow.

Gong, Xianda / Zhang, Jiaoshi / Croft, Betty / Yang, Xin / Frey, Markus M / Bergner, Nora / Chang, Rachel Y-W / Creamean, Jessie M / Kuang, Chongai / Martin, Randall V / Ranjithkumar, Ananth / Sedlacek, Arthur J / Uin, Janek / Willmes, Sascha / Zawadowicz, Maria A / Pierce, Jeffrey R / Shupe, Matthew D / Schmale, Julia / Wang, Jian

Nature geoscience

2023 Volume 16, Issue 9, Page(s) 768–774

Abstract: The Arctic warms nearly four times faster than the global average, and aerosols play an increasingly important role in Arctic climate change. In the Arctic, sea salt is a major aerosol component in terms of mass concentration during winter and spring. ... ...

Abstract	The Arctic warms nearly four times faster than the global average, and aerosols play an increasingly important role in Arctic climate change. In the Arctic, sea salt is a major aerosol component in terms of mass concentration during winter and spring. However, the mechanisms of sea salt aerosol production remain unclear. Sea salt aerosols are typically thought to be relatively large in size but low in number concentration, implying that their influence on cloud condensation nuclei population and cloud properties is generally minor. Here we present observational evidence of abundant sea salt aerosol production from blowing snow in the central Arctic. Blowing snow was observed more than 20% of the time from November to April. The sublimation of blowing snow generates high concentrations of fine-mode sea salt aerosol (diameter below 300 nm), enhancing cloud condensation nuclei concentrations up to tenfold above background levels. Using a global chemical transport model, we estimate that from November to April north of 70° N, sea salt aerosol produced from blowing snow accounts for about 27.6% of the total particle number, and the sea salt aerosol increases the longwave emissivity of clouds, leading to a calculated surface warming of +2.30 W m
Language	English
Publishing date	2023-09-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2396648-8
ISSN	1752-0908 ; 1752-0894
ISSN (online)	1752-0908
ISSN	1752-0894
DOI	10.1038/s41561-023-01254-8
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Article ; Online: Objective and subjective cognitive functioning in relation to psychopathology among women with early psychosis.

Tong, Alan C Y / Chang, Wing Chung / Chan, Angel N Y / Lin, Jessie J

Early intervention in psychiatry

2018 Volume 13, Issue 5, Page(s) 1227–1235

Abstract: Background: Subjective cognitive impairment (SCI) among early psychosis is under-recognized and under-studied. However, SCI is as important as objective impairment to be understood, since it assesses cognitive difficulties in real-life situations from a ...

Abstract	Background: Subjective cognitive impairment (SCI) among early psychosis is under-recognized and under-studied. However, SCI is as important as objective impairment to be understood, since it assesses cognitive difficulties in real-life situations from a personal perspective and is therefore an essence of individualized medicine. This study aims to explore the associations between the objective and subjective measures of cognitive impairments and to identify factors contributing to SCI among people with early psychosis. Methods: Participants were 60 females (mean age 24.57 ± 8.28) who had a diagnosis of psychotic-spectrum disorder within 5 years. They completed a battery of neuropsychological tests assessing a range of cognitive functions including verbal learning, memory, attention, and executive functions. The Subjective Cognitive Impairment Scale (SCIS) was used to assess their perceived cognitive decline. Psychotic symptoms and depression were also assessed. Results: SCIS was not correlated with any of the objective cognitive tests results. It was positively correlated with depression and positive symptoms. A hierarchical multiple regression model revealed that positive symptoms and depression together explained 31.9% of the total variance in SCIS and only depression significantly predicted SCI. Performances on the memory tests were correlated with, and predicted by negative symptoms. Conclusions: There was no correlation between SCI and objective cognitive performances in patients with early psychosis. Treatments should not only focus on symptomatic remission and performance of cognitive tests, but also place emphasis on improving moods and subjective cognitive functions of individuals with early psychosis.
MeSH term(s)	Adolescent ; Adult ; Attention ; Cognition ; Cognition Disorders/psychology ; Cognitive Dysfunction/psychology ; Depression/psychology ; Executive Function ; Female ; Humans ; Neuropsychological Tests ; Psychotic Disorders/psychology ; Verbal Learning ; Young Adult
Language	English
Publishing date	2018-11-28
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2272425-4
ISSN	1751-7893 ; 1751-7885
ISSN (online)	1751-7893
ISSN	1751-7885
DOI	10.1111/eip.12760
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Article ; Online: Long-read RNA sequencing identifies polyadenylation elongation and differential transcript usage of host transcripts during SARS-CoV-2 in vitro infection

Chang, Jessie J-Y / Gleeson, Josie / Rawlinson, Daniel / Pitt, Miranda E / De Paoli-Iseppi, Ricardo / Zhou, Chenxi / Mordant, Francesca L / Londrigan, Sarah L / Clark, Michael B / Subbarao, Kanta / Stinear, Timothy P / Coin, Lachlan J M

bioRxiv

Abstract	Better methods to interrogate host-pathogen interactions during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections are imperative to help understand and prevent this disease. Here we implemented RNA-sequencing (RNA-seq) combined with the Oxford Nanopore Technologies (ONT) long-reads to measure differential host gene expression, transcript polyadenylation and isoform usage within various epithelial cell lines permissive and non-permissive for SARS-CoV-2 infection. SARS-CoV-2-infected and mock-infected Vero (African green monkey kidney epithelial cells), Calu-3 (human lung adenocarcinoma epithelial cells), Caco-2 (human colorectal adenocarcinoma epithelial cells) and A549 (human lung carcinoma epithelial cells) were analysed over time (0, 2, 24, 48 hours). Differential polyadenylation was found to occur in both infected Calu-3 and Vero cells during a late time point (48 hpi), with Gene Ontology (GO) terms such as viral transcription and translation shown to be significantly enriched in Calu-3 data. Poly(A) tails showed increased lengths in the majority of the differentially polyadenylated transcripts in Calu-3 and Vero cell lines (up to ~136 nt in mean poly(A) length, padj = 0.029). Of these genes, ribosomal protein genes such as RPS4X and RPS6 also showed downregulation in expression levels, suggesting the importance of ribosomal protein genes during infection. Furthermore, differential transcript usage was identified in Caco-2, Calu-3 and Vero cells, including transcripts of genes such as GSDMB and KPNA2, which have previously been implicated in SARS-CoV-2 infections. Overall, these results highlight the potential role of differential polyadenylation and transcript usage in host immune response or viral manipulation of host mechanisms during infection, and therefore, showcase the value of long-read sequencing in identifying less-explored host responses to disease.
Keywords	covid19
Language	English
Publishing date	2021-12-15
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.12.14.472725
Database	COVID19

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Article ; Online: Efficacy of transcranial direct current stimulation (tDCS) as a treatment for persistent hallucinations in patients with schizophrenia: A systematic review and meta-analysis.

Lee, Edwin H M / Chan, Pik Ying / Law, Eunice Y L / Lin, Jessie J X / Hui, Christy L M / Chang, Wing Chung / Chan, Sherry K W / Chen, Eric Y H

Schizophrenia research

2018 Volume 202, Page(s) 423–425

MeSH term(s)	Hallucinations/etiology ; Hallucinations/therapy ; Humans ; Outcome Assessment (Health Care)/statistics & numerical data ; Schizophrenia/complications ; Schizophrenia/therapy ; Transcranial Direct Current Stimulation
Language	English
Publishing date	2018-08-24
Publishing country	Netherlands
Document type	Letter ; Meta-Analysis ; Systematic Review
ZDB-ID	639422-x
ISSN	1573-2509 ; 0920-9964
ISSN (online)	1573-2509
ISSN	0920-9964
DOI	10.1016/j.schres.2018.06.069
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Article ; Online: Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection

Chang, Jessie J.-Y. / Rawlinson, Daniel / Pitt, Miranda E. / Taiaroa, George / Gleeson, Josie / Zhou, Chenxi / Mordant, Francesca L. / De Paoli-Iseppi, Ricardo / Caly, Leon / Purcell, Damian F. J. / Stinear, Tim P. / Londrigan, Sarah L. / Clark, Michael B. / Williamson, Deborah A. / Subbarao, Kanta / Coin, Lachlan J M

bioRxiv

Abstract: SARS-CoV-2 uses subgenomic (sg)RNA to produce viral proteins for replication and immune evasion. We applied long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating ... ...

Abstract	SARS-CoV-2 uses subgenomic (sg)RNA to produce viral proteins for replication and immune evasion. We applied long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA was upregulated earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of ORF1ab containing nsp1 joined to ORF10 and 3prime UTR was upregulated at 48 hours post infection in human cell lines. We identified double-junction sgRNA containing both TRS-dependent and independent junctions. We found multiple sites at which the SARS-CoV-2 genome is consistently more modified than sgRNA, and that sgRNA modifications are stable across transcript clusters, host cells and time since infection. Our work highlights the dynamic nature of the SARS-CoV-2 transcriptome during its replication cycle. Our results are available via an interactive web-app at http://coinlab.mdhs.unimelb.edu.au/.
Keywords	covid19
Language	English
Publishing date	2020-12-22
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.12.22.423893
Database	COVID19

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Article ; Online: Health Care Utilization among Homeless-Experienced Adults Who Were Seen by a Mobile Addiction Health Clinic in Boston, Massachusetts: A Quasi-Experimental Study.

Fine, Danielle R / Joyce, Andrea / Chang, Yuchiao / Lewis, Elizabeth / Weinstock, Karen / Wright, Joseph / Gaeta, Jessie / Song, Zirui / Baggett, Travis P

Substance use & misuse

2023 Volume 58, Issue 9, Page(s) 1115–1120

Abstract: Background: ...

Abstract	Background:
MeSH term(s)	United States ; Adult ; Humans ; Female ; Male ; Boston/epidemiology ; Mobile Health Units ; Delivery of Health Care ; Patient Acceptance of Health Care ; Massachusetts ; Telemedicine ; Ill-Housed Persons ; Emergency Service, Hospital ; Retrospective Studies
Language	English
Publishing date	2023-05-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1310358-1
ISSN	1532-2491 ; 1082-6084
ISSN (online)	1532-2491
ISSN	1082-6084
DOI	10.1080/10826084.2023.2212279
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Article ; Online: Quality of life and functioning in first-episode psychosis Chinese patients with different antipsychotic medications.

Lee, Edwin H M / Hui, Christy L M / Lin, Jessie J X / Ching, Elaine Y N / Chang, W C / Chan, Sherry K W / Chen, Eric Y H

Early intervention in psychiatry

2016 Volume 10, Issue 6, Page(s) 535–539

Abstract: Aim: This study compared the quality of life and functioning of 285 first-episode psychosis Chinese patients with different antipsychotic medications in Hong Kong.: Method: Under the Jockey Club Early Psychosis project, a total of 285 patients were ... ...

Abstract	Aim: This study compared the quality of life and functioning of 285 first-episode psychosis Chinese patients with different antipsychotic medications in Hong Kong. Method: Under the Jockey Club Early Psychosis project, a total of 285 patients were recruited from all inpatient and outpatient psychiatric units in Hong Kong between 2009 and 2011. In addition to the medication information, patients were assessed with the Scale for the Assessment of Positive Symptoms, the Scale for the Assessment of Negative Symptoms, the Udvalg for Kliniske Undersøgelser (UKU), Barnes Akathisia Rating Scale (BARS), the Social and Occupational Functioning Assessment Scale (SOFAS), the Role Functioning Scale, and the Medical Outcomes Study Short Form 12-Item Health Survey (SF-12) after stabilization of mental condition. Differences between individual antipsychotic medications were compared using anova and multinomial regression model. Results: The results demonstrated significant differences between different antipsychotic medications in the mean of UKU neurological subscore, BARS total score, SOFAS score and SF-12 Mental Component Summary (MCS) score. Patients with haloperidol had higher mean UKU neurological subscore than patients with olanzapine or amisulpride. Risperidone was associated with higher mean BARS total score than olanzapine, amisulpride or sulpiride. Higher mean MCS was found in patients with amisulpride than patients with risperidone. Conclusions: The findings suggest that antipsychotics have differential associations with the quality of life and functioning in patients with first-episode psychosis. Future prospective study is warranted to investigate if patients with first-episode psychosis will benefit specific type of antipsychotics more than the others.
MeSH term(s)	Adult ; Antipsychotic Agents/adverse effects ; Antipsychotic Agents/therapeutic use ; Asian Continental Ancestry Group ; Female ; Humans ; Male ; Psychiatric Status Rating Scales ; Psychotic Disorders/drug therapy ; Quality of Life ; Treatment Outcome
Chemical Substances	Antipsychotic Agents
Language	English
Publishing date	2016
Publishing country	Australia
Document type	Journal Article ; Observational Study ; Research Support, Non-U.S. Gov't
ZDB-ID	2272425-4
ISSN	1751-7893 ; 1751-7885
ISSN (online)	1751-7893
ISSN	1751-7885
DOI	10.1111/eip.12246
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Article ; Online: Chinese label for people at risk for psychosis.

Lee, Edwin H M / Ching, Elaine Y N / Hui, Christy L M / Lin, Jessie J X / Chang, W C / Chan, Sherry K W / Chen, Eric Y H

Early intervention in psychiatry

2015 Volume 11, Issue 3, Page(s) 224–228

Abstract: Aim: With the movement of early detection and intervention for people at risk for psychosis, there is a growing need for a uniform terminology to describe the condition. A diagnostic label that can adapt into local culture and value may have positive ... ...

Abstract	Aim: With the movement of early detection and intervention for people at risk for psychosis, there is a growing need for a uniform terminology to describe the condition. A diagnostic label that can adapt into local culture and value may have positive effect in minimizing stigma. This study explored the preference of Chinese label for people at risk of psychosis and its associated stigma in Hong Kong. Methods: A total of 149 individuals from the general public and 51 health-care professionals were recruited between March 2013 and May 2014. The condition of at risk for psychosis was described in a vignette. Participants' preference of label and perceived stigma of the condition and their basic demographics were collected by self-administered questionnaires. Results: The most preferred Chinese label was 'yun-niang-qi' (developing period, 45%), followed by 'qian-qu-qi' (precursor period, 19%), 'feng-xian-qi' (risky period, 18%), 'zao-xian-qi' (early sign period, 16%) and 'gao-wei-qi' (high risk period, 4%). Gender, age, occupation and previous contact with mental health were not associated with preference of any Chinese label. Conclusions: The process in searching for this potential and locally accepted label for people at risk for psychosis has raised the awareness among the professionals. A proper label may help promote future clinical research and mental health services in Hong Kong.
MeSH term(s)	Asian Continental Ancestry Group ; Attitude of Health Personnel ; Humans ; Prodromal Symptoms ; Psychotic Disorders/diagnosis ; Public Opinion ; Social Stigma ; Terminology as Topic
Language	English
Publishing date	2015-02-26
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2272425-4
ISSN	1751-7893 ; 1751-7885
ISSN (online)	1751-7893
ISSN	1751-7885
DOI	10.1111/eip.12232
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