{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T15:41:05Z","timestamp":1776872465712,"version":"3.51.2"},"update-to":[{"DOI":"10.12688\/wellcomeopenres.15419.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,11,11]],"date-time":"2022-11-11T00:00:00Z","timestamp":1668124800000}}],"reference-count":53,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2022,11,11]],"date-time":"2022-11-11T00:00:00Z","timestamp":1668124800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["098481"],"award-info":[{"award-number":["098481"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns4:p>\n                    <ns4:bold>Background<\/ns4:bold>\n                    : Surgery to correct trichiasis is a key component of the World Health Organisation trachoma control strategy, however unfavourable outcomes such as eyelid contour abnormalities (ECA) following surgery are relatively common. This study aimed to understand the transcriptional changes associated with the early development of ECA and the impact of doxycycline, which has anti-inflammatory and anti-fibrotic properties, upon these transcription patterns.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Methods<\/ns4:bold>\n                    : One thousand Ethiopians undergoing trichiasis surgery were enrolled in a randomised controlled trial following informed consent. Equal groups of randomly assigned individuals were orally administered with 100mg\/day of doxycycline (n=499) or placebo (n=501) for 28 days. Conjunctival swabs were collected immediately prior to surgery and at one- and six-months post-surgery. 3\u2019 mRNA sequencing was performed on paired baseline and one-month samples from 48 individuals; 12 in each treatment\/outcome group (Placebo-Good outcome, Placebo-Poor outcome, Doxycycline-Good outcome, Doxycycline-Poor outcome). qPCR validation was then performed for 46 genes of interest in 145 individuals who developed ECA at one month and 145 matched controls, using samples from baseline, one and six months.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Results<\/ns4:bold>\n                    : All treatment\/outcome groups upregulated genes associated with wound healing pathways at one month relative to baseline, however no individual differences were detected between groups. The summed expression of a highly coexpressed cluster of pro-fibrotic genes was higher in patients that developed ECA in the placebo group relative to controls. qPCR validation revealed that all genes in this cluster and a number of other pro-inflammatory genes were strongly associated with ECA, however these associations were not modulated by trial arm.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Conclusions<\/ns4:bold>\n                    : The development of post-operative ECA is associated with overexpression of pro-inflammatory and pro-fibrotic genes including growth factors, matrix metalloproteinases, collagens and extracellular matrix proteins. There was no evidence that doxycycline modulated the association between gene expression and ECA.\n                  <\/ns4:p>","DOI":"10.12688\/wellcomeopenres.15419.2","type":"journal-article","created":{"date-parts":[[2022,11,11]],"date-time":"2022-11-11T08:30:14Z","timestamp":1668155414000},"page":"130","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["The conjunctival transcriptome in Ethiopians after trichiasis surgery: associations with the development of eyelid contour abnormalities and the effect of oral doxycycline treatment"],"prefix":"10.12688","volume":"4","author":[{"given":"Tamsyn","family":"Derrick","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6161-8427","authenticated-orcid":false,"given":"Esmael","family":"Habtamu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zerihun","family":"Tadesse","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"E. 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.16862.r36397, Emily W. Gower, Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 04 Oct 2019, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-130\/v1#referee-response-36397","order":0,"name":"referee-response-36397","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Tamsyn Derrick<\/b>; \n<i>Posted: 07 Sep 2022<\/i>; \n<b>&nbsp;The introduction has been updated as suggested.<\/b>  \n<b>&nbsp;We agree that it would be interesting to look at post-operative appearance and ECA development in this group and at the transcriptomic level. This study was not designed to look at this question and we think that it is not in scope for this paper. We did not take photos immediately after surgery or day-one postop. This gap has now been highlighted in the discussion as potentially requiring further work.<\/b>  \n<b>We have clarified that the FPC system was used in grading <\/b> &nbsp; \n<b>We have added that the samples that failed QC did not differ from those that passed QC by age, sex, or group. A sentence has been added on lines 247-250 to clarify this and the numbers in each group are shown below. <\/b>  \n<b>Doxy_good<\/b> \n<b>Doxy_poor<\/b> \n<b>Placebo_good<\/b> \n<b>Placebo_poor<\/b>  \n<b>Excluded samples<\/b> \n<b>37 (39.4%)<\/b> \n<b>7 (7.5%)<\/b> \n<b>40 (42.6%)<\/b> \n<b>10 (10.6%)<\/b>  \n<b>Included samples<\/b> \n<b>300 (38.8%)<\/b> \n<b>92 (11.9%)<\/b> \n<b>295 (38.1%)<\/b> \n<b>87 (11.2%)<\/b>  \n<b>We removed the repeated paragraph from the results. <\/b>  \n<b>We added the suggested Merbs et al citation to the discussion <\/b>  \n<b>All instances of \u2018recurrence\u2019 in the paper have been changed to \u2018post-operative trichiasis\u2019.<\/b> &nbsp; \n<b>We agree there is a wider range of reported outcomes. This has been adjusted to reflect this. We believe the most suitable references for this is the review conducted by Rajak et al (Trachomatous Trichiasis and its management in endemic countries) and Cochrane review &nbsp;by Burton et al (Interventions for trachomatous trichiasis). We have revised the sentence and added these two references. <\/b>  \n<b>We have removed the incorrect citation in the introduction and corrected patients<\/b>  \n<b>We have added figures&nbsp; regarding ECAs as requested. <\/b>","URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-130\/v2#referee-comment-5104","order":1,"name":"referee-comment-5104","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.16862.r41831, Hon Shing Ong, Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, 01 Feb 2021, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-130\/v1#referee-response-41831","order":2,"name":"referee-response-41831","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Tamsyn Derrick<\/b>; \n<i>Posted: 07 Sep 2022<\/i>; Abstract: \u201812 in each treatment\/ECA outcome group\u2019 requires more description. From the abstract, it is unclear to the reader, what these groups are. It is only available in the methods section of the main manuscript.  \n<b>This has been clarified<\/b>  Methods: The nurse-surgeons have been described as \u2018experienced\u2019. Perhaps a quantification of the number of years of experience (e.g. median or range) of the nurses should be included. Also, how many nurse-surgeons were involved in this study?  \n<b>We have added additional information of the prior experience of surgeons to lines 139-142&nbsp;<\/b>  Methods: As this is within an RCT, the method of randomisation should be described.  \n<b>Full trial details are published elsewhere and this statement has been added to the methods. <\/b>  Methods: Were there specific exclusion criteria (e.g. patients already on specific anti-inflammatory drugs)?&nbsp;  \n<b>As above, full trial details including exclusion criteria are published elsewhere and this statement has been added to the methods. <\/b>  Methods: Of the 98 samples that failed QC, which groups were the samples from? Was the number of failed samples relatively equal in the moderate\/severe ECA group compared to samples taken from individuals without\/mild ECA?  \n<b>As described above, the samples that failed did not differ from those that passed QC by age, sex, or group. A sentence has been added to clarify this and the numbers in each group are shown to reviewer 1<\/b>  Methods: Details of the power calculation for both analyses should be included. Were the sample sizes adequate to detect differences between the groups for the RNA seq experiments? Also, the power of the study is relevant as the study reported results showing no evidence of doxycycline treatment affecting gene expression and ECA development.  \n<b>RNAseq experiments were conceived to be hypothesis generating for TLDA target selection. The number of samples selected was limited by RNA quality and sufficiency for RNAseq and the total budget available. The a priori design of this nested study within a clinical trial, was the assessment of gene expression profiles in all people developing ECA (and a matched control group).&nbsp; As the numbers that would go on to develop ECA were not known beforehand a separate sample size calculation for this outcome was not performed and a post-hoc power calculation is not a recommended practice.\u201d &nbsp;<\/b>  The first paragraph of the results have been described in the Methods section and can probably be left out.  \n<b>This has been removed<\/b>  For table 1, were there significant differences in the baseline characteristics between the groups?  \n<b>Samples were selected for RNA-seq based upon trachomatous scarring and eyelid distortion characteristics at baseline, one and six months, as described on line 183. There was no difference in sex between groups (Chi2 P value 0.763), however age distribution differed slightly between groups (ANOVA P value 0.0143). <\/b>  For table 2, it appears that more genes were up-regulated in poor outcome groups compared to control groups. Also, there were a higher number of differentially expressed genes in the \u2018doxycycline-good\u2019 group compared to \u2018placebo-good\u2019 group. Were these statistically significant  \n<b>This observation is described in the first paragraph of the results section; As this was a descriptive testing for differences between total numbers of differentially expressed genes was not performed.<\/b>  For table 5, were there significant differences in the baseline clinical and demographic characteristics between the groups?  \n<b>Groups with no or mild ECA at one month were matched to those with moderate\/severe ECA by age, sex and trial arm. There was no difference between groups in baseline conjunctival scarring (Chi2 P value 0.192), age (ANOVA P value 0.0737) or sex (Chi2 P value 0.162). <i>C. trachomatis<\/i> was detected in only 8 samples therefore differences between groups were not tested.<\/b>  The authors could perhaps include a short paragraph on the relevance of their transcriptome findings on understanding the pathophysiology of ECA development and how this is important in the future development of targeted anti-inflammatory or anti-fibrotic therapies.  \n<b>The final paragraph of the discussion has been updated to address this point. &nbsp;<\/b>","URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-130\/v2#referee-comment-5105","order":3,"name":"referee-comment-5105","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.20379.r61396, Swati Singh, Ophthalmic Plastic Surgery, Orbit and Ocular Oncology Services, Centre for Ocular Regeneration, L V Prasad Eye Institute, Hyderabad, Telangana, 05 Jul 2023, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/4-130\/v2#referee-response-61396","order":4,"name":"referee-response-61396","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was funded by Wellcome [098481]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":5,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}