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INTRODUCTION: Caused by mutation or deletion of the CHM gene, choroideremia is a rare X-linked recessive chorioretinal dystrophy characterized by progressive degeneration of the retinal pigment epithelium, photoreceptors, and the choriocapillaris. There are few published reports of choroideremia associated with complex syndromic phenotypes due to large or contiguous gene deletions. METHODS: Case report and review of literature. RESULTS: We present a case of a 46-year-old male with a prior clinical diagnosis of syndromic retinitis pigmentosa, who was found to have syndromic choroideremia associated with a novel multi-gene deletion of 13.5 megabase pairs. This deletion encompassing 18 genes is one of the largest deletions reported in the literature. A total of 18 male cases of choroideremia associated with confirmed large or contiguous gene deletions have been published to date. Previously reported deletions range in size from 4 to 15 megabase pairs, and observed phenotypes include cleft lip and palate, ptosis, obesity, metabolic diseases, developmental delay, and hearing loss. DISCUSSION: The contribution of our case aims to expand our understanding of Xq21 deletions and prompts further investigation of genes found in this locus. Furthermore, it highlights the importance of including syndromic choroideremia on the differential diagnosis in the workup of other syndromic retinopathies, particularly those that feature obesity, hearing loss, or intellectual disability.

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Background: The pragmatism levels of randomized controlled trials (RCTs) mean how similar the interventions delivered in the trial setting match those in the setting where the results will be applied. We aimed to investigate the association between the consistency of pragmatism among the characteristics of RCT design and its effect size of results in Chinese herbal medicine (CHM) for irritable bowel syndrome (IBS). Methods: Eight English and Chinese language databases were searched for RCTs on CHM for IBS. Six reviewers independently assessed the pragmatism of trials using the pragmatic-explanatory continuum indicator summary 2 (PRECIS-2) tool. The consistency of pragmatism levels among the characteristics of RCT design was calculated using the coefficient of variation. Linear regression models were adopted to explore influence factors of the pragmatism of RCTs. Results: 78 RCTs were included. The level of consistency in the pragmatism for RCT's design was significantly correlated with the effect size of the results (binary outcome, r = -0.413; P = 0.005; continuous outcome, r = -0.779, P < 0.001). PRECIS-2 score was higher in trials with individualized interventions than fixed interventions (3.29 [0.32] vs 2.90 [0.32]; Cohen's d relative effect size, 0.52; P < 0.001) and in standard or usual-treatment-controlled trials than placebo-controlled (3.05 [0.37] vs 2.83 [0.28]; Cohen's d relative effect size, 0.32; P = 0.048). Conclusion: The consistency of pragmatism level across the 9 domains of the PRECIS-2 tool in CHM IBS RCTs was positively correlated with the effect size of the results.

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Background: A combination of standard biomedical treatment and traditional Chinese medicine (TCM) has been suggested as a therapeutic approach for rosacea that may significantly lower the recurrence rate and clinical symptom scores. We conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) to evaluate the impact of this combination treatment on clinical symptom and TCM syndrome scores, as well as on the scores of the Dermatology Life Quality Index (DLQI), erythema index (EI), and interleukin 37 (IL-37) levels in patients with rosacea. Methods: The PROSPERO registration number for the study is CRD42023472737. We systematically searched the PubMed, Embase, Web of Science, China National Knowledge Infrastructure Wanfang Database, China Biomedical Medicine database (CBM), and the VIP information resource integration service platform (cqvip) databases for RCTs (published from the beginning to September 2023, regardless of the language used) that compared the traditional Chinese medicine and standard biomedical treatment combination treatment to conventional anti-rosacea treatments. Our primary outcomes comprised the clinical symptom and TCM syndrome scores, and the scores of Dermatology Life Quality Index, erythema index, and IL-37 levels. We used a random-effects model to evaluate the pooled data. Results: We identified 260 studies. Of these, 13 eligible studies were employed for analysis (N = 1,348 participants). Compared with other anti-rosacea treatments, the TCM and standard biomedical treatment combination treatment yielded an improved mean reduction in the clinical symptom score -2.24% [95% CI (-3.02 to -1.46), p < 0.00001], TCM syndrome score -4.42 [95% CI (-5.33 to -3.50), p < 0.00001], and the score of DLQI of -2.55 [95% CI (-3.73 to -1.36), p < 0.00001], EI of -151.97 [95% CI (-276.59 to -27.36), p < 0.00001], and IL-37 level -4.23 [95% CI (-4.95 to -3.51), p = 0.854], as well as in the overall effective rate risk ratio (RR) = 1.25 [95%CI (1.18, 1.32), p = 0.994] and the recurrence rate = 0.27 [95%CI (0.15, 0.46), p = 0.297]. Conclusion: The TCM and standard biomedical treatment combination treatment can provide a better outcome, including a reduction in the TCM syndrome and clinical symptom scores, and in the scores of DLQI, EI, and IL-37. Hence, this combination is a viable and more effective therapeutic approach for rosacea. However, these results should be considered cautiously because of uncertain evidence and the low quality of the study reports considered in this meta-analysis. Systematic Review Registration: website, identifier CRD42023472737.

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BACKGROUND: Leber hereditary optic neuropathy (LHON) is an inherited progressive optic neuropathy usually caused by mitochondrial DNA mutations. Recently, autosomal recessive (arLHON), which is caused by biallelic mutations in the DNAJC30 gene (usually c.152A > G), has been described. The onset of LHON before the age of 12 is uncommon and it is typically associated with a more variable clinical course and a more favorable visual prognosis than adult-onset LHON. MATERIALS AND METHODS: Detailed clinical findings of a female child with vision loss due to arLHON together with choroideremia (CHM) carrier state are presented. RESULTS: Genetic testing for the three most common mitochondrial LHON pathogenic variants was negative. On suspicion of arLHON, genetic testing was continued with the next-generation sequencing (NGS) of the nuclear DNA, identifying a homozygous pathogenic variant in DNAJC3°c.152A > G, p.(Tyr51Cys), but no alterations in the CHM gene. Idebenone treatment was started 4.5 months after the first evaluation. Clinical diagnosis of the CHM carrier state was confirmed by multiplex ligation-dependent probe amplification (MLPA) assay, which revealed a heterozygous deletion of all exons of the CHM. CONCLUSIONS: In children with acute or subacute, simultaneous, or sequential vision loss that is unresponsive to immunomodulatory treatment, LHON should be considered as a possible diagnosis. Our case emphasizes the diagnostic advantage of sequencing DNAJC30 in parallel with the mitochondrial DNA, especially in Eastern European descent patients. Genomic rearrangement testing should be considered for patients with a CHM carrier phenotype who have negative results on sequencing tests.

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Unraveling the intricate centromere structure of human chromosomes holds profound implications, illuminating fundamental genetic mechanisms and potentially advancing our comprehension of genetic disorders and therapeutic interventions. This study rigorously identified and structurally analyzed alpha satellite higher-order repeats (HORs) within the centromere of human chromosome 15 in the complete T2T-CHM13 assembly using the high-precision GRM2023 algorithm. The most extensive alpha satellite HOR array in chromosome 15 reveals a novel cascading HOR, housing 429 15mer HOR copies, containing 4-, 7- and 11-monomer subfragments. Within each row of cascading HORs, all alpha satellite monomers are of distinct types, as in regular Willard's HORs. However, different HOR copies within the same cascading 15mer HOR contain more than one monomer of the same type. Each canonical 15mer HOR copy comprises 15 monomers belonging to only 9 different monomer types. Notably, 65% of the 429 15mer cascading HOR copies exhibit canonical structures, while 35% display variant configurations. Identified as the second most extensive alpha satellite HOR, another novel cascading HOR within human chromosome 15 encompasses 164 20mer HOR copies, each featuring two subfragments. Moreover, a distinct pattern emerges as interspersed 25mer/26mer structures differing from regular Willard's HORs and giving rise to a 34-monomer subfragment. Only a minor 18mer HOR array of 12 HOR copies is of the regular Willard's type. These revelations highlight the complexity within the chromosome 15 centromeric region, accentuating deviations from anticipated highly regular patterns and hinting at profound information encoding and functional potential within the human centromere.

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Background: The CONSORT Extension for Chinese Herbal Medicine Formula 2017 (CONSORT-CHM Formula 2017) has established a reporting standard for randomized controlled trials (RCTs) of Chinese Herbal Medicine Formula (CHMF) interventions; however, its adherence and implications for the design and execution of study design remain ambiguous. It is necessary to evaluate the level of compliance with the CONSORT-CHM Formula 2017 in RCTs conducted over the past 5 years, and to determine the reporting quality of clinical trials in this field. Methods: First, a systematic search is conducted for RCTs on CHMF in EBM Reviews, Allied and Complementary Medicine (AMED), Embase, Ovid-MEDLINE(R), Wanfang data, China National Knowledge Infrastructure (CNKI), VIP Chinese Medical Journal Database (VIP) and Chinese Biomedical Literature (CBM) database, that encompassed CHMF interventional RCTs published from 1 January 2018 to 8 June 2022, with language restriction to English or Chinese. Second, a descriptive analysis will be performed regarding the study design and general characteristics of the included trials. Third, for the quality assessment, we have subdivided the CONSORT-CHM Formula 2017 checklist (consisting of 22 extended items) into a total of 42 sub-questions to facilitate scoring, with a specific focus on the description, quality control, and safety assessment of CHMF interventions. Professional training and a pilot test on 100 randomly selected articles will be provided for all reviewers. Throughout this process, a standard operating procedure (SOP) for quality assessment will be developed to ensure consistency. Each item will be assessed by two reviewers in a paired back-to-back manner, and the compliance rate will be calculated to assess inter-rater agreement. Discussion: This review will identify the current reporting characteristics and quality of CHMF interventional studies and further evaluate the impact of CONSORT-CHM Formula 2017. The results may provide suggestions for future application or promotion of the guideline. Registration: The study has been registered on Open Science Framework (https://osf.io/xpn7f).

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BACKGROUND: Structural rearrangements in highly repetitive heterochromatin regions can result in miscarriage or foetal malformations; however, detecting and preventing the transmission of these rearrangements has been challenging. Recently, the completion of sequencing of the complete human genome (T2T-CHM13) has made it possible to accurately characterise structural rearrangements in these regions. We developed a method based on T2T-CHM13 and nanopore sequencing to detect and block structural rearrangements in highly repetitive heterochromatin sequences. METHODS: T2T-CHM13-based "Mapping Allele with Resolved Carrier Status" was performed for couples who carry structural rearrangements in heterochromatin regions. Using nanopore sequencing and the T2T-CHM13 reference genome, the precise breakpoints of inversions and translocations close to the centromere were detected and haplotypes were constructed using flanking single-nucleotide polymorphisms (SNPs). Haplotype linkage analysis was then performed by comparing consistent parental SNPs with embryonic SNPs to determine whether the embryos carried hereditary inversions or balanced translocations. Based on copy number variation and haplotype linkage analysis, we transplanted normal embryos, which were further verified by an amniotic fluid test. RESULTS: To validate this approach, we used nanopore sequencing of families with inversions and reciprocal translocations close to the centromere. Using the T2T-CHM13 reference genome, we accurately detected inversions and translocations in centromeres, constructed haplotypes and prevented the transmission of structural rearrangements in the offspring. CONCLUSIONS: This study represents the first successful application of T2T-CHM13 in human reproduction and provides a feasible protocol for detecting and preventing the transmission of structural rearrangements of heterochromatin in embryos.

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Background and Objective: The cancer-immunity cycle (CIC) is defined as a series of progressive events that cause an anticancer immune response leading to the killing of the cancer cell. The concept of CIC has important guiding significance for the clinical and basic tumor immunotherapy research. As one of the methods of traditional Chinese medicine (TCM), Chinese herbal medicine (CHM) has shown unique advantages in multitarget and multipathway immune regulation. However, the tumor immune circulation targeted by CHM is generally unclear at present. To provide reference for future clinical and basic research, we systematically reviewed the existing literature on CHM (including CHM monomers, CHM compounds, and CHM patent medicines) and the mechanisms related to its efficacy. Methods: We searched the PubMed and China National Knowledge Infrastructure (CNKI) databases for relevant Chinese-language and English-language literature published from January 1988 to October 2022. The literature was screened manually at three levels: title, abstract, and full text, to identify articles related to CHM and their mechanism of regulating tumor immunity. Key Content and Findings: By further classifying the CIC, it was confirmed that CHM can regulate the activation of dendritic cells (DCs) and macrophages and promote the presentation of tumor antigens. Meanwhile, CHM can also reverse tumor-immune escape by enhancing T-cell proliferation and infiltration. In addition, CHM can also enhance the antitumor ability of the body by regulating the killing process of tumor cells. Conclusions: The theory of a CIC is of guiding significance to regulating tumor immunity via CHM.

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Transposable elements have created the majority of the sequence in many genomes. In mammals, LINE-1 retrotransposons have been expanding for more than 100 million years as distinct, consecutive lineages; however, the drivers of this recurrent lineage emergence and disappearance are unknown. Most human genome assemblies provide a record of this ancient evolution, but fail to resolve ongoing LINE-1 retrotranspositions. Utilizing the human CHM1 long-read-based haploid assembly, we identified and cloned all full-length, intact LINE-1s, and found 29 LINE-1s with measurable in vitro retrotransposition activity. Among individuals, these LINE-1s varied in their presence, their allelic sequences, and their activity. We found that recently retrotransposed LINE-1s tend to be active in vitro and polymorphic in the population relative to more ancient LINE-1s. However, some rare allelic forms of old LINE-1s retain activity, suggesting older lineages can persist longer than expected. Finally, in LINE-1s with in vitro activity and in vivo fitness, we identified mutations that may have increased replication in ancient genomes and may prove promising candidates for mechanistic investigations of the drivers of LINE-1 evolution and which LINE-1 sequences contribute to human disease.

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BACKGROUND: Cancer-related fatigue (CRF) is an extremely common and long-term condition that affects the physical and mental health of oncology patients. While the treatment for CRF with western medicine and non-pharmacological therapy remains uncertain and challenging, traditional Chinese medicine (TCM) has become a trending option for the patients. Based on the findings from randomized controlled trials (RCTs), this study aims to identify and evaluate the evidence about the efficacy and safety of TCM for CRF. METHODS: A systematic literature search was conducted according to the PRISMA literature research guidelines. Seven electronic databases including PubMed, the Cochrane Library, Embase, Web of Science, Scopus, China National Knowledge Infrastructure (CNKI) and Wanfang database were searched to identify RCTs which investigated TCM in the treatment of CRF published since inception to December 2022. RCTs comparing TCM with no treatment, placebo, or pharmacological interventions were considered eligible for this review. The Consolidated Standards of Reporting Trials Statement extensions for Chinese herbal medicine Formulas (CONSORT-CHM) and the Cochrane Collaboration's Risk of Bias tool were used in this review to evaluate the quality and the risk of bias of all included trials. RESULTS: A total of 82 RCTs were included in this review, regardless of whether they were published in English or Chinese. After data extraction and results evaluation, 78 trials demonstrated overall efficacy in using TCM for CRF patients compared with the control group, in which 33 trials showed that the efficacy rate was statistically significant (p < 0.05 or p < 0.01). TCM was also shown to be beneficial in improving the scores of relevant scales (e.g., PFS, QoL, TCM syndrome score, other fatigue scales etc.) or physical tests indicators (e.g., cytokines, blood test etc.). The most common herbs found in Chinese medicine were Astragali Radix, Ginseng Radix and Codonopsis Radix. Some TCM products, such as Kangai Injection, Buzhong Yiqi Decoction and Shenqi Fuzheng Injection could provide a reference for medication in this review. A range of non-serious, reversible adverse effects associated with the use of TCM was also reported. However, the result of evaluation showed that none of the trials fully met all the CONSORT-CHM criteria, the quality of included trials was generally poor and the risk of bias was mostly uncertain. CONCLUSION: There is some evidence supporting the efficacy and safety of TCM in managing CRF in this systematic review. However, no clear conclusion can be made due to the inadequate reporting of efficacy and adverse reactions. In view of some concerns about the existing evidence after the evaluation, it is essential to standardize the comprehensive identification and efficacy measurement standards, improve the quality of RCTs and conduct more multicomponent therapies to provide an updated reference for CRF patients medication in the future. The protocol of this systematic review has been registered on PROSPERO (CRD42023413625). [ https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42023413625 ].

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Introduction: Chronic fatigue syndrome (CFS) is an increasingly common condition that is challenging to treat due to unclear etiology and a lack of consensus on clinical diagnosis and treatment guidance. Many affected people resorted to using traditional and complementary medicines (T&CMs). However, the evidence for T&CMs for CFS has been inconclusive and continues to evolve. The study aims to identify, summarize and assess the most recent evidence on the efficacy and safety of T&CMs for CFS. Methods: Randomized controlled trials (RCTs) investigating T&CMs for CFS published in English of Chinese between 1 January 2013 and 31 December 2022 were searched from 7 databases. RCTs comparing T&CMs with no treatment, placebo, or pharmacological medicine were included, irrespective of language or blinding. The Consolidated Standards of Reporting Trials Statement extensions for Chinese herbal medicine Formulas (CONSORT-CHM) and the Cochrane Collaboration's Risk of Bias tool were used to evaluate the quality and risk of bias of included studies. Results: A total of 62 RCTs investigating 43 types of T&CMs and involving 5,231 participants with CFS were included in this review. The primary outcome measures mainly included the scoring of fatigue symptoms using the validated tool Fatigue Scale-14 (FS-14) or the TCM syndrome score. The main interventions showing overall efficacy were Chaihu Guizhi Decoction and Buzhong Yiqi combined with Xiao Chaihu Decoction, and 148 ingredients were identified, including Astragali Radix, Glycyrrhizae Radix et Rhizoma, Atractylodis Macrocephalae Rhizoma, and Bupleuri Radix. The most significant effect was the improvement of fatigue, followed by TCM-diagnosed symptoms and other psychological conditions. No serious adverse effect had been reported. However, the quality of the RCTs included RCTs were found to be suboptimal, and the risk of bias remained uncertain. Conclusion: Some evidence from RCTs supported the efficacy and safety of T&CM in CFS. However, given the methodological and quality heterogenicity of the included studies, the recommendations of T&CMs in treating CFS remain inconclusive. To develop better quality evidence about T&CMs for CFS, future studies should employ more objective diagnosis standards and outcome measurements, larger sample size, and better bias control, and ensure the compliance with the corresponding reporting guidelines. Systematic Review Registration: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022362268, identifier CRD42022362268.

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Choroideremia is an X-linked retinal degeneration resulting from the progressive, centripetal loss of photoreceptors and choriocapillaris, secondary to the degeneration of the retinal pigment epithelium. Affected individuals present in late childhood or early teenage years with nyctalopia and progressive peripheral visual loss. Typically, by the fourth decade, the macula and fovea also degenerate, resulting in advanced sight loss. Currently, there are no approved treatments for this condition. Gene therapy offers the most promising therapeutic modality for halting or regressing functional loss. The aims of the current review are to highlight the lessons learnt from clinical trials in choroideremia, review endpoints, and propose a future strategy for clinical trials.

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Background: Allergic rhinitis is prevalent among children and can cause nasal itching, fatigue, and even hinder growth and development. The main discomfort symptom of allergic rhinitis is nasal itching. Clinical reports suggest that Chinese herbal medicine (CHM) is effective in allergy rhinitis treatment. Therefore, we evaluate the clinical efficacy of Chinese herbal medicine in treating nasal itching caused by allergic rhinitis in children. Methods: Nine databases, including PubMed, Embase, The Cochrane Library, Web of Science, China National Knowledge Infrastructure, Wan Fang Data, CQVIP, Chinese Biological Medicine, and ClinicalTrials.gov, were systematically searched from their inception until March 2023. Randomized controlled trials (RCTs) comparing the efficacy of Chinese herbal medicine, either alone or in combination with Western medicine, to Western medicine treatment or placebo intervention for treating allergic rhinitis in children were eligible for inclusion. The effectiveness of Chinese herbal medicines for nasal itching was mainly evaluated. The Risk of Bias tool 2.0 assessed the risk of bias. Statistical analysis using RevMan 5.3 and Stata/SE 12. The quality of evidence was evaluated by GRADEpro 3.6. Risk ratios (RR) with corresponding 95% confidence intervals (CI) were utilized to evaluate and present dichotomous data, while mean difference (MD) and standardized mean difference (SMD) were employed for continuous data. A fixed-effects model was applied in cases where the data exhibited homogeneity (p > 0.1, I2 < 50%), whereas a random-effects model was utilized for heterogeneous data. Statistical significance was determined by a p-value <0.05. This study was conducted by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, and its review protocol was registered on the International Platform for Registered Systematic Reviews and Meta-Analysis Programs (INPLASY202340076). Results: The review incorporated 23 studies. The meta-analysis indicated that herbal medicine was significantly related to the reduction of nasal itching (MD = -0.59, 95%CI: -0.94-0.24) and the increase of interleukin 10 level (SMD = 1.47, 95% CI: 0.90-2.05). Compared to Western medicine, the combining herbs and Western medicine showed better efficacy in relieving nasal itching, inhibiting immunoglobulin E, interleukin 4 and 33, enhancing interleukin 10, improving therapeutic efficiency, and reducing recurrent. Oral herbal medicine was more effective in treating nasal itching (MD = -0.45, 95% CI: -0.62-0.29). Combining oral and external herbal medicines was more efficient in treating nasal itching (MD = -0.44, 95% CI: -0.54-0.33), inhibiting immunoglobulin E, interleukin 4 (SMD = -0.87, 95% CI: -1.24-0.50) and 33 (SMD = -1.16, 95% CI: -1.54-0.77), and improving therapeutic efficiency. External herbal medicine did not show differences compared to Western medicines. Regarding safety, herbal medicine alone exhibited fewer adverse events than Western medicine; combining herbal and Western medicine showed no significant variation in adverse event incidence. Conclusion: Chinese herbal medicine (CHM) holds great potential in alleviating symptoms, modulating immune factors levels, and reducing relapse in pediatric rhinitis. Meanwhile, CHM is relatively safe. However, the efficacy and safety of CHM in treating pediatric rhinitis still need to be confirmed due to the inclusion of studies with low methodological quality, small sample sizes, and potential heterogeneity. More high-quality research is necessary to provide reliable evidence for the clinical application of CHM. Systematic Review Registration: INPLASY.com, identifier INPLASY202340076.

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Hydatidiform mole is the most common form of gestational trophoblastic disease. It is an abnormally formed placental tissue with characteristic changes in karyotype, arising in fertilization disorders. The presence of abundant paternal genetic information plays a key role in the pathogenesis of complete and partial hydatidiform moles. These lesions are characterized by a relatively wide spectrum of morphological changes that may not be fully expressed, especially in the early stages of pregnancy. In addition, some changes can be observed in non-molar gravidities, which, unlike hydatidiform moles, lack any risk of malignant transformation. Although conventional histological examination still plays a key role in the diagnosis, it should be supplemented by other methods that reliably differentiate individual lesions. Accurate diagnosis of molar gravidities is important not only for determining the correct therapeutic approach, but the obtained data may also contribute to further research of these pathological entities.

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The immunomodulatory roles of Chinese herbal Medicine (CHM) in aquatic animals have been well-recorded. However, how CHM impacts the intestinal microbiota and serum metabolism is not fully understood. In this study, the effects of different additive levels of CHM on the growth performance, immunity, intestinal flora and serum metabolism of hybrid grouper (♀Epinephelus fuscoguttatus × â™‚Epinephelus lanceolatu) were investigated. The addition of 0.5%, 1.0%, 1.5% and 2.0% Chinese herbal medicine compound to feed could significantly improve the weight gain rate (WGR), specific growth rate (SGR) and survival rate (SR) of grouper, reduced feed coefficient, while had no significant difference on morphometric parameter. The most significant improvement for the parameters above was observed in 1.5% group. Different addition levels of CHM could also significantly enhance the activities of ACP, AKP, SOD, CAT and LZM in serum. Accordingly, the supplementation of CHM significantly induced up-regulation of immune genes such as IL-8, IL-1ß, TNF-α, Nrf2, Lzm in the liver, spleen and head kidney of grouper, improved the resistance of grouper to V. harveyi as well. The intestinal flora analysis showed that at the phylum level, the main dominant species of intestinal microorganisms were Firmicutes, Proteobacteria, Bacteroidota, Actinobacteriota, Gemmatimonadota, Desulfobacterota, Fusobacteriota and Myxococcota. At the genus level, the high abundance was Lactobacillus, Streptococcus, Bacteroides, Escherichia, Romboutsia, Sphingomonas and Muribaculaceae. The abundance of probiotics (such as Lachnospiraceae, Lactobacillaceae, Streptococcaceae, etc) in CHM-supplement groups were higher (highest in 1.5% group) compared with control group. Moreover, a total of 11 common differential metabolic pathways were screened by LC-MS metabolism analysis of serum, they were Neuroactive ligand-receptor interaction, Purine metabolism, Linoleic acid, Glycerophospholipid metabolism, Taurine and hypotaurine metabolism, Arginine and proline metabolism, ABC transporters, Aminoacyl-tRNA biosynthesis, Arachidonic acid metabolism, Drug metabolism-cytochrome P450, alpha-Linolenic acid metabolism. Also, three common differential metabolites (PI(20:4(5Z,8Z,11Z,14Z)/18:1(11Z)), PC(20:3(8Z,11Z,14Z)/22:1(13Z)), PC(22:0/20:4(5Z,8Z,11Z,14Z)) associated with intestinal health, growth and disease resistance was found. These data will contributes to a comprehensive understand for the regulatory roles of CHM on fish, which is also beneficial for the disease control and sustainable development of aquaculture.

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BACKGROUND: The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental duplication, and other complex regions. The current human genome reference (GRCh38) has been widely used in various human genomic studies. However, the large-scale genomic differences between these two important genome assemblies are not characterized in detail yet. RESULTS: Here, in addition to the previously reported "non-syntenic" regions, we find 67 additional large-scale discrepant regions and precisely categorize them into four structural types with a newly developed website tool called SynPlotter. The discrepant regions (~ 21.6 Mbp) excluding telomeric and centromeric regions are highly structurally polymorphic in humans, where the deletions or duplications are likely associated with various human diseases, such as immune and neurodevelopmental disorders. The analyses of a newly identified discrepant region-the KLRC gene cluster-show that the depletion of KLRC2 by a single-deletion event is associated with natural killer cell differentiation in ~ 20% of humans. Meanwhile, the rapid amino acid replacements observed within KLRC3 are probably a result of natural selection in primate evolution. CONCLUSION: Our study provides a foundation for understanding the large-scale structural genomic differences between the two crucial human reference genomes, and is thereby important for future human genomics studies.

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Background: Hydatidiform moles (HM) are members of gestational trophoblastic diseases (GTD) and, in some cases, might progress to gestational trophoblastic neoplasia (GTN). HMs are either partial (PHM) or complete (CHM). Some HMs are challenging in arriving at a precise histopathological diagnosis. This study aims to investigate the expression of BCL-2 by immunohistochemistry (IHC) in HMs as well as in normal trophoblastic tissues "products of conception (POC) and placentas" using Tissue MicroArray (TMA) technique. Methods: TMAs were constructed using the archival material of 237 HMs (95 PHM and 142 CHM) and 202 control normal trophoblastic tissues; POC and unremarkable placentas. Sections were immunohistochemically stained using antibodies against BCL-2. The staining was assessed semi-quantatively (intensity and percentage of the positive cells) in different cellular components (trophoblasts and stromal cells). Results: BCL-2 showed cytoplasmic expression in more than 95% of trophoblasts of PHM, CHM and controls. The staining showed a significant reduction of the intensity from controls (73.7%), PHMs (76.3%) to CHM (26.9%). There was a statistically significant difference between PHM and CHM in the intensity (p-value 0.0005) and the overall scores (p-value 0.0005), but not the percentage score (p-value > 0.05). No significant difference was observed in the positivity of the villous stromal cells between the different groups. All cellular components were visible using the TMA model of two spots/case (3 mm diameter, each) in more than 90% of cases. Conclusions: Decreased BCL-2 expression in CHM compared to PHM and normal trophoblasts indicates increased apoptosis and uncontrolled trophoblastic proliferation. Construction of TMA in duplicates using cores of 3 mm diameter can overcome tissue heterogeneity of complex lesions.

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Pericentromeric tandemly repeated DNA of human satellites 1, 2, and 3 (HS1, HS2, and HS3) is actively transcribed in some cells. However, the functionality of the transcription remains obscure. Studies in this area have been hampered by the absence of a gapless genome assembly. The aim of our study was to map a transcript that we have previously described as HS2/HS3 on chromosomes using a newly published gapless genome assembly T2T-CHM13, and create a plasmid overexpressing the transcript to assess the influence of HS2/HS3 transcription on cancer cells. We report here that the sequence of the transcript is tandemly repeated on nine chromosomes (1, 2, 7, 9, 10, 16, 17, 22, and Y). A detailed analysis of its genomic localization and annotation in the T2T-CHM13 assembly revealed that the sequence belonged to HSAT2 (HS2) but not to the HS3 family of tandemly repeated DNA. The transcript was found on both strands of HSAT2 arrays. The overexpression of the HSAT2 transcript increased the transcription of the genes encoding the proteins involved in the epithelial-to-mesenchymal transition, EMT (SNAI1, ZEB1, and SNAI2), and the genes that mark cancer-associated fibroblasts (VIM, COL1A1, COL11A1, and ACTA2) in cancer cell lines A549 and HeLa. Co-transfection of the overexpression plasmid and antisense nucleotides eliminated the transcription of EMT genes observed after HSAT2 overexpression. Antisense oligonucleotides also decreased transcription of the EMT genes induced by tumor growth factor beta 1 (TGFß1). Thus, our study suggests HSAT2 lncRNA transcribed from the pericentromeric tandemly repeated DNA is involved in EMT regulation in cancer cells.

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The telomere-to-telomere (T2T) complete human reference has significantly improved our ability to characterize genome structural variation. To understand its impact on inversion polymorphisms, we remapped data from 41 genomes against the T2T reference genome and compared it to the GRCh38 reference. We find a ~ 21% increase in sensitivity improving mapping of 63 inversions on the T2T reference. We identify 26 misorientations within GRCh38 and show that the T2T reference is three times more likely to represent the correct orientation of the major human allele. Analysis of 10 additional samples reveals novel rare inversions at chromosomes 15q25.2, 16p11.2, 16q22.1-23.1, and 22q11.21.

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BACKGROUND: Immune checkpoint inhibitors (ICIs) have emerged as a revolutionary therapy in advanced squamous non-small cell lung cancer (sqNSCLC) and ushered a new era of immunotherapy. Despite of remarkable outcomes, a wide spectrum of immune-related adverse events (irAEs) was reported, among which cutaneous reactions were the most common. Cutaneous irAEs were mainly managed by glucocorticoids, whereas prolonged use of glucocorticoids may cuase kinds of side effects, especially in elderly paitients, and diminish the anti-tumor efficacy of ICIs, thus finding a safe and effective alternative approach to managing cutaneous irAEs is imperative. CASE SUMMARY: A 71-year-old man who was diagnosed with advanced sqNSCLC suffered from sporadic maculopapulars one week later after the fifth cycle of sintilimab treatment, and the skin lesions had been deteriorating rapidly. Skin biopsy revealed epidermal parakeratosis with a dense band-like lymphocytic infiltrate and acanthosis, indicating a diagnosis of immune-induced lichenoid dermatitis. Oral administration of traditional Chinese herbal formula modified Weiling decoction significantly alleviated the symptoms of the patient. The dosage of Weiling decoction were maintained for about three months without recurrence of cutaneous adverse reactions and any other side effects. The patient refused to receive further anti-tumor medication and stayed alive without disease progression at follow up. CONCLUSION: We present modified Weiling decoction successfully ameliorates immune-induced lichenoid dermatitis in a patient with sqNSCLC for the first time. This report indicates that Weiling decoction may be an effective and safe complementary or alternative approach for the treatment of cutaneous irAEs. Further investigation of the underling mechanism is required in the future.

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