Genetic diversity, population structure and origin of the native goats in Central Laos

Abstract

Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (F ST: 0.011–0.043) and negligible inbreeding coefficients (F IS: −0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92–6.85 Mb, with short ROH segments (1–5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20–40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.

Switching from combination therapy with entecavir hydrate plus tenofovir alafenamide fumarate to tenofovir alafenamide fumarate monotherapy in patients with chronic hepatitis B based on nucleotide sequences of hepatitis B virus pregenome RNA

Switching from combination therapy with entecavir hydrate plus tenofovir alafenamide fumarate to tenofovir alafenamide fumarate monotherapy in patients with chronic hepatitis B based on nucleotide sequences of hepatitis B virus pregenome RNA

We devised a method to analyze drug resistance profile of hepatitis B virus pregenome RNA even when serum hepatitis B virus DNA is undetectable during antiviral therapy. By using this approach, we verified that patients receiving combination therapy with entecavir hydrate plus tenofovir alafenamide fumarate for chronic hepatitis B virus infection due to experiencing viral breakthrough or partial response during initial lamivudine or entecavir hydrate administration were able to safely transition to tenofovir alafenamide fumarate monotherapy.


Abstract

Aim

Patients with chronic hepatitis B virus (HBV) infection experiencing viral breakthrough (BTH) or partial response (PR) during lamivudine (LAM) or entecavir hydrate (ETV) administration often took ETV plus tenofovir alafenamide fumarate (TAF) due to the emergence of a drug-resistance mutation. However, in patients lacking drug-resistance mutation against TAF, sufficient antiviral effects may be achievable with TAF monotherapy. We assessed the drug-resistance profile through nucleotide sequences of HBV pregenome RNA, and subsequently changed to TAF monotherapy from ETV plus TAF.

Methods

This prospective study included 25 patients with serum HBV-DNA below 20 IU/mL under ETV plus TAF administration. Pregenome RNA nucleotide sequences of HBV in the sera were analyzed using direct sequencing and deep sequencing. ETV was discontinued in patients without rtA194T and rtS106C + rtH126Y + rtD134E + rtL269I quadruple mutations in direct sequencing.

Results

LAM-PR, LAM-BTH, ETV-PR, and ETV-BTH were observed in 1, 16, 7, and 1 patient(s), respectively. Pregenome RNA nucleotide sequences were analyzable in 20 patients. Among the 12 patients classified as LAM-BTH, six patients showed rtL180M + rtM204V/I in direct sequencing, and one patient showed minor clones containing rtL180M + rtM204V + A194T in deep sequencing at a frequency of 0.3%. In the six patients classified as ETV-PR, one patient harbored rtM204I. No clones showing rtS106C + rtH126Y + rtD134E + rtL269I quadruple mutation were detected in deep sequencing. Subsequently, ETV was discontinued, and serum HBV-DNA remained undetectable up to 48 weeks in all patients.

Conclusion

Patients receiving ETV plus TAF due to partial response or BTH during initial LAM or ETV administration were able to safely transition to TAF monotherapy based on nucleotide sequences of HBV pregenome RNA in the sera.

Natural history and clinical features of hepatitis C virus infection during childhood: A nationwide, observational survey in Japan

Natural history and clinical features of hepatitis C virus infection during childhood: A nationwide, observational survey in Japan

In the present study, 10.4% of Japanese children infected with hepatitis C virus transmitted from mother to child cleared the infection 3.1 years after birth. We also showed that direct-acting antiviral agent therapy is a safe and highly effective treatment. Direct-acting antiviral agent treatment should be provided to prevent transmission from mother to child.


Abstract

Aim

Few data on spontaneous clearance rates of cases of mother-to-child transmission of hepatitis C viral (HCV) infection are available in Japan. Furthermore, the treatment courses of interferon-based and direct-acting antiviral agent (DAA) therapies for children are also unclear. Our aim was thus to clarify the long-term natural progression of HCV infection and the treatment outcomes of children in Japan.

Methods

We conducted a combined multicenter, observational survey involving 65 pediatric institutions in Japan. Pediatric HCV infection cases with patients born between 1973 and 2021 were collected over the 11-year period from 2012 to 2022. A total of 563 patients were enrolled, with 190 excluded for having insufficient laboratory data or treatment information, resulting in 373 eligible cases.

Results

Of 328 cases of mother-to-child infection, 34 (10.4%) had spontaneous clearance, with a median time to spontaneous clearance of 3.1 years (range 0.9–7.2 years). Of the total 373 eligible cases, 190 received antiviral therapy (interferon-based therapy, 158; DAA therapy, 32). Sustained virologic response rates after first-line treatment were 75.3% (119/158) and 100% (32/32) for interferon-based therapy and DAA therapy, respectively, with the DAA group showing a shorter time from therapy initiation to viral negativity (2.7 vs. 1.0 months; p = 0.0031).

Conclusions

Approximately 10% of Japanese children infected by mother-to-child transmission achieve spontaneous resolution of HCV infection. Our findings indicate that DAA therapy is safe and highly effective in Japanese children, achieving higher sustained virologic response rates and shorter time to clearance of the virus compared with interferon-based therapy.

Optimal treatment strategy and prognostic analysis of salvage liver transplantation for patients with early hepatocellular carcinoma recurrence after hepatectomy

Abstract

Aim

We aimed to investigate the prognostic factors for salvage liver transplant in patients with early hepatocellular carcinoma recurrence after hepatectomy.

Methods

This retrospective analysis included 53 patients who underwent salvage living-donor liver transplantation between January 2007 and January 2018. There were 24 and 29 patients in the early (recurrence ≤24 months after primary liver resection) and the late recurrence groups, respectively.

Results

In the multivariate Cox regression model, pre-liver transplant downstaging therapy, early recurrence (ER) after primary liver resection , and recurrence-to-liver-transplant ≥12 months were independent risks to predict recurrent hepatocellular carcinoma recurrence after salvage living-donor liver transplantation. Compared with the late recurrence group, the ER group showed lower disease-free survival rates (p < 0.001); however, the overall survival rates did not differ between the two groups (p = 0.355). The 1-, 3-, and 5-year disease-free survival rates were 83.3%, 70.6%, and 66.2%, and 96.0%, 91.6%, and 91.6% in the early and late recurrence groups, respectively. When stratified by recurrence-to-liver transplant time and pre-liver transplant downstaging therapy in the ER group, disease-free survival and overall survival rates were significantly different.

Conclusion

ER after primary liver resection with advanced tumor status and a longer period of recurrence-to-liver-transplant (≥12 months) have a negative impact on salvage liver transplant. Our findings provide novel recommendations for treatment strategies and eligibility for salvage liver transplant candidates.

Genomic dissection of brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae) resistance in Indica rice genotypes

Genomic dissection of brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae) resistance in Indica rice genotypes

New Nilaparvata lugens resistant genotypes were reported. Six BPH resistance genes showed significant association and these genes either alone or in combination could be introgressed into elite varieties with genomic approach to develop robust resistant rice varieties against N. lugens biotype 4. The identified genotypes could be useful for novel R genes identification, host–insect interaction and genomic studies.


Abstract

The population growth and the regular breakout of Nilaparvata lugens pose a significant risk to rice cultivation. Four different N. lugens biotypes have been identified worldwide, with biotype 4 being the most destructive and prevalent throughout Asia, particularly in India. Therefore, a rice variety with multiple resistance genes/alleles is required for effective management of N. lugens. Hence, 191 rice genotypes collected from various parts of India were evaluated for resistance to N. lugens. Further, SSR markers representing 23 different N. lugens resistant (R) genes were assayed to identify genomic regions associated with resistance. The results of the genetic analysis showed that the average genetic diversity value of all markers was 0.165 and polymorphic information content of 0.145 for all the markers used. The population structure and cluster analysis divided the studied genotypes into three distinct groups, with resistant genotypes grouped separately. These findings were confirmed by the principal coordinate analysis, which categorized resistant genotypes, moderately resistant genotypes, and susceptible genotypes into distinct components. Additionally, 90% of the genetic variation was between individuals of populations and 10% between the populations. Marker-trait association study through mixed linear model and generalized linear model identified six SSR markers such as RM6732 (Bph15), RM314 (Bph6), RM16999 (Bph6), RM7 (QBph3), RM401 (bph4), and RM7102 (Bph1), which were significantly associated with various phenotypic parameters, such as feeding mark, honeydew excretion, percent damage and nymphal survival. The resistant genes identified in these genotypes could help in the marker-assisted rice variety development with durable resistance against N. lugens.

High expression of autotaxin is associated with poor recurrence‐free survival in cholangiocarcinoma

Abstract

Background and Aim

Autotaxin (ATX) is an extracellular lysophospholipase D that catalyzes the hydrolysis of lysophosphatidylcholine into lysophosphatidic acid (LPA). Recent accumulating evidence indicates the biological roles of ATX in malignant tumors. However, the expression and clinical implications of ATX in human cholangiocarcinoma (CCA) remain elusive.

Methods

In this study, the expression of ATX in 97 human CCA tissues was evaluated by immunohistochemistry. Serum ATX levels were determined in CCA patients (n = 26) and healthy subjects (n = 8). Autotaxin expression in cell types within the tumor microenvironment was characterized by immunofluorescence staining.

Results

High ATX expression in CCA tissue was significantly associated with a higher frequency of lymph node metastasis (p = 0.050). High ATX expression was correlated with shorter overall survival (p = 0.032) and recurrence-free survival (RFS) (p = 0.001) than low ATX expression. In multivariate Cox analysis, high ATX expression (p = 0.019) was an independent factor for shorter RFS. Compared with low ATX expression, high ATX expression was significantly associated with higher Ki-67-positive cell counts (p < 0.001). Serum ATX levels were significantly higher in male CCA patients than in healthy male subjects (p = 0.030). In the tumor microenvironment of CCA, ATX protein was predominantly expressed in tumor cells, cancer-associated fibroblasts, plasma cells, and biliary epithelial cells.

Conclusions

Our study highlights the clinical evidence and independent prognostic value of ATX in human CCA.

Risk of colorectal cancer in patients with primary sclerosing cholangitis and concomitant inflammatory bowel disease compared with primary sclerosing cholangitis only

Risk of colorectal cancer in patients with primary sclerosing cholangitis and concomitant inflammatory bowel disease compared with primary sclerosing cholangitis only

Although primary sclerosing cholangitis (PSC) is frequently linked to inflammatory bowel disease, a known risk factor for colorectal cancer, it remains uncertain whether PSC alone poses an independent risk for colorectal cancer. Our retrospective cohort study conducted at a tertiary medical center reveals that individuals with PSC have an increased risk of colorectal cancer compared with the general population. Our findings suggest that PSC patients may benefit from more frequent colonoscopy screening when compared with individuals without PSC.


Abstract

Aim

Primary sclerosing cholangitis (PSC) increases the risk of colorectal cancer (CRC) in inflammatory bowel disease (IBD) patients; however, there is a paucity of literature to suggest PSC alone as an independent risk factor for CRC. We aimed to determine if PSC is an independent risk factor for CRC in a large tertiary care medical center. Optimizing screening intervals is of great importance, given the burden and risks associated with a lifetime of colonoscopy screening.

Methods

This retrospective cohort study consists of patients diagnosed with PSC preceding IBD (PSC–IBD) and PSC-only before January 6, 2023 from a large, tertiary, academic medical center. Patients diagnosed with IBD concurrently or before PSC were excluded to reduce IBD's impact on CRC risk. Demographic data and colonoscopy findings were collected and assessed.

Results

Overall, 140 patients from all NYU Langone Health clinical settings were included. Patients with PSC–IBD were more likely to be diagnosed with CRC (23.3% vs. 1.8%, p < 0.01) and either low-grade or uncharacterized dysplasia (16.7% vs. 0.0%, p < 0.01) compared with those with PSC-only. Among PSC-only patients, the estimated CRC risk was significantly elevated compared with that expected of the standard NYU Langone population (SIR 9.2, 95% CI 1.1, 33.2).

Conclusions

Our study revealed a significantly heightened CRC risk in PSC–IBD patients compared with those with PSC-only. Importantly, individuals with PSC-only also face a greater CRC risk compared with the general population. Individuals with PSC-alone may require extended screening and surveillance colonoscopy intervals compared with those with PSC–IBD, yet still require more frequent monitoring than screening guidelines recommend for the general population.

Impact of electrical muscle stimulation on serum myostatin level and maintenance of skeletal muscle mass in patients undergoing living‐donor liver transplantation: Single‐center controlled trial

Abstract

Aim

Sarcopenia is reportedly associated with a poor prognosis in patients who undergo living-donor liver transplantation (LDLT), most of whom are not able to tolerate muscle strengthening exercise training. Myostatin is one of the myokines and a negative regulator of skeletal muscle growth. The clinical feasibility of an electrical muscle stimulation (EMS) system, which exercises muscle automatically by direct electrical stimulation, has been reported. In this study, we aimed to determine the effect of perioperative application of SIXPAD, which is a type of EMS system, with reference to the serum myostatin and sarcopenia in LDLT patients.

Method

Thirty patients scheduled for LDLT were divided into a SIXPAD group (n = 16) and a control group (n = 14). In the SIXPAD group, EMS was applied to the thighs twice daily. The serum myostatin was measured in samples obtained before use of SIXPAD and immediately before LDLT. The psoas muscle index (PMI) at the level of the third lumbar vertebra and the quadriceps muscle area were compared on computed tomography images before use of SIXPAD and 1 month after LDLT.

Results

The preoperative serum myostatin was found to be higher in LDLT patients than in healthy volunteers and EMS significantly reduced the serum myostatin. Electrical muscle stimulation prevented a postoperative reduction not only in the area of the quadriceps muscles but also in the PMI despite direct stimulation of the thigh muscles.

Conclusion

Stimulation of muscles by EMS decreases the serum myostatin and helps to maintain skeletal muscle in patients who have undergone LDLT.

Genetic parameters for different types of medullated fibre in Alpacas

Abstract

The quality of alpaca textile fibre has great potential, especially if objectionable fibres (coarse and medullated fibres) that cause itching are reduced, considering that objectionable fibres can be identified by diameter and medullation types. The objective of this study was to estimate genetic parameters for medullar types and their respective diameters to evaluate the possibility of incorporating them as selection criteria in alpaca breeding programmes. The research used 3149 alpaca fibre samples collected from 2020 to 2022, from a population of 1626 Huacaya type alpacas. The heritability and correlations of the percentages of non-medullated (NM), fragmented medulle (FM), uncontinuous medullated (UM), continuous medullated (CM), and strongly medullated (SM) fibres were analysed, also the fibre diameter (FD) for each of the medullation types. The heritability estimated for medullation types were 0.25 ± 0.01, 0.18 ± 0.01, 0.10 ± 0.01, 0.20 ± 0.01 and 0.11 ± 0.01 for NM, FM, UM, CM and SM, respectively. The genetic correlations for medullation categories ranged from 0.15 ± 0.03 to 0.66 ± 0.02 (in absolute values). The heritabilility estimated for fibre diameter (FD) of each of the medullation types were 0.29 ± 0.03, 0.27 ± 0.02, 0.35 ± 0.02, 0.30 ± 0.02, 0.25 ± 0.02 and 0.10 ± 0.02 for FD, FD_NM, FD_FM, FD_UM, FD_CM and FD_SM, respectively. The genetic correlations for fibre diameter of the medullation types ranged from 0.04 ± 0.04 to 0.97 ± 0.01. FD, NM and FM are the main traits to be used as selection criteria under a genetic index, since they would reduce fibre diameter, and also increase NM and FM, and, in addition reducing indirectly CM, SM, and SM_FD. Therefore, the quality of alpaca fibre could be improved.

Glycemic control target for liver and cardiovascular events risk in metabolic dysfunction‐associated steatotic liver disease

Glycemic control target for liver and cardiovascular events risk in metabolic dysfunction-associated steatotic liver disease

The risk of liver-related events as well as major adverse cardiovascular events increased in a dose-dependent fashion with an increase in hemoglobin A1c (HbA1c) levels, except for patients with HbA1c <5.0% for liver-related events. An HbA1c level of 7% was the optimal threshold associated with a lower risk of complications and may be utilized as a target for glycemic control in patients with MASLD.


Abstract

Aims

Optimizing glycemic control may prevent liver-related events and major adverse cardiovascular events (MACE) in patients with metabolic dysfunction-associated steatotic liver disease (MASLD). However, the optimal hemoglobin A1c (HbA1c) threshold associated with a lower risk of complications, particularly liver-related events as well as MACE is unknown.

Methods

We investigated a nationwide population-based cohort and identified 633 279 patients with MASLD, with a mean follow-up of 4.2 years. Hemoglobin A1c levels were measured annually. The primary endpoint was the risk of liver-related events and MACE and to determine the optimal HbA1c level associated with the risk of complications.

Results

Mean HbA1c (per 1%) was associated with liver-related events (subdistribution hazard ratio [sHR] 1.26; 95% confidence interval [CI], 1.12–1.42) as well as MACE (sHR 1.36; 95% CI, 1.32–1.41) after adjustment for confounders. Multivariable sHR (95% CI) for HbA1c of <5.0%, 6.0%–6.9%, 7.0%–7.9%, 8.0%–8.9%, and ≥9.0% (reference, 5.0%–5.9%) were 14 (9.1–22), 1.70 (1.2–2.3), 3.32 (2.3–4.8), 3.81 (2.1–6.8), and 4.83 (2.4–9.6) for liver-related events, and 1.24 (0.8–1.8), 1.27 (1.2–1.4), 1.70 (1.5–2.0), 2.36 (1.9–2.9), and 4.17 (3.5–5.0) for MACE. An HbA1c level of 7% was selected as the optimal threshold for predicting complications (sHR 2.40 [1.8–3.2] for liver-related events and 1.98 [1.8–2.2] for MACE).

Conclusion

The risk of liver-related events as well as MACE increased in a dose-dependent fashion with an increase in HbA1c levels, except for patients with HbA1c <5.0% for liver-related events. An HbA1c level of 7% was the optimal threshold associated with a lower risk of complications and may be utilized as a target for glycemic control in patients with MASLD.