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Insertion/deletion polymorphisms (InDels) have been treated as a prospective and helpful genetic marker in the fields of forensic human identification, anthropology and population genetics for the past few years. In this study, we developed a six-dye multiplex typing system consisting of 34 autosomal InDels and Amelogenin for forensic application. The contained InDels were specifically selected for Chinese population with the MAF ≥ 0.25 in East Asia, which do not overlap with the markers of Investigator® DIPplex kit. The typing system was named as GoldeneyeTM DNA ID System 35InDel Kit, and a series of developmental validation studies including repeatability/reproducibility, concordance, accuracy, sensitivity, stability, species specificity and population genetics were conducted on this kit. We confirmed that the 35InDel kit is precise, sensitive, species specific and robust for forensic practice. Moreover, the 35InDel kit is capable of typing DNA extracted from forensic routine case-type samples as well as degraded samples and mixture samples. All markers are proved to be highly polymorphic with an average observed heterozygosity (He) of 0.4582. The combined power of discrimination (CPD) is 0.999 999 999 999 978 and the combined power of exclusion in duos (CPED) and trios (CPET) are 0.978 837 and 0.999573, respectively, which are higher than those of the Investigator® DIPplex kit. Thus, the GoldeneyeTM DNA ID System 35InDel kit is suitable for forensic human identification and could serve as a supplementary typing system for paternity testing. Supplemental data for this article is available online at https://doi.org/10.1080/20961790.2021.1945723 .

Personal identification using the tumor DNA not only plays an important role in postoperative tissue management but also might be the only accessible source of biological material in forensic identification. Short tandem repeat (STR) is the worldwide accepted forensic marker; however, widespread loss of heterozygosity (L) in tumor tissues challenges the personal identification using the conventional capillary electrophoresis (CE)-based STR typing system (CE-STR). Because the tumors are mixtures of tumor cells and basal cells, we inferred that every germline-originated allele should be detected if the detection method was sensitive enough. Next-generation sequencing (NGS) is known as a highly sensitive application, which might be a promising tool for tumor source identification. In the study, we genotyped and compared the STR results between the platforms, and we found that the concordance was only 91.43%. Higher sensitivity did help identify more germline-originated alleles as expected, and 93.89% of them could be captured by using an NGS-based STR system (NGS-STR). The identity-by-state (IBS) scoring system was applied to generate a new tumor source identification method based on NGS-STR, and the number of loci with 2 identical alleles (A2) proved to be an ideal criterion for the larger area under the receiver operating characteristic (ROC) curve (AUC). Both the sensitivity and specificity were above 98% in the cutoff of A2 to distinguish the paired carcinoma (PC) sample group from the unrelated individual (UI) group, the simulated full sibling (FS) group, and the simulated parent–offspring (PO) group.

Abstract Background Targeted therapy for triple‐negative breast cancer (TNBC) remains a challenge. N6‐methyladenosine (m6A) is the most abundant internal mRNA modification in eukaryotes, and it regulates the homeostasis and function of modified RNA transcripts in cancer. However, the role of leucine‐rich pentatricopeptide repeat containing protein (LRPPRC) as an m6A reader in TNBC remains poorly understood. Methods Western blotting, reverse transcription‐polymerase chain reaction (RT‐qPCR) and immunohistochemistry were used to investigate LRPPRC expression levels. Dot blotting and colorimetric enzyme linked immunosorbent assay (ELISA) were employed to detect m6A levels. In vitro functional assays and in vivo xenograft mouse model were utilised to examine the role of LRPPRC in TNBC progression. Liquid chromatography–mass spectrometry/mass spectrometry and Seahorse assays were conducted to verify the effect of LRPPRC on glycolysis. MeRIP‐sequencing, RNA‐sequencing, MeRIP assays, RNA immunoprecipitation assays, RNA pull‐down assays and RNA stability assays were used to identify the target genes of LRPPRC. Patient‐derived xenografts and organoids were employed to substantiate the synthetic lethality induced by LRPPRC knockdown plus glutaminase inhibition. Results The expressions of LRPPRC and m6A RNA were elevated in TNBC, and the m6A modification site could be recognised by LRPPRC. LRPPRC promoted the proliferation, metastasis and glycolysis of TNBC cells both in vivo and in vitro. We identified lactate dehydrogenase A (LDHA) as a novel direct target of LRPPRC, which recognised the m6A site of LDHA mRNA and enhanced the stability of LDHA mRNA to promote glycolysis. Furthermore, while LRPPRC knockdown reduced glycolysis, glutaminolysis was enhanced. Moreover, the effect of LRPPRC on WD40 repeat domain‐containing protein 76 (WDR76) mRNA stability was impaired in an m6A‐dependent manner. Then, LRPPRC knockdown plus a glutaminase inhibition led to synthetic lethality. Conclusions Our study demonstrated that LRPPRC promoted TNBC progression by regulating metabolic reprogramming via m6A modification. These characteristics shed light on the novel combination targeted therapy strategies to combat TNBC.

Background Short tandem repeats (STRs) are consecutive repetition of a repeat motif and widely used in forensic medicine and human genetics because of their high polymorphism. Subjects and methods In the current study, 23 autosomal STR loci were genotyped from 1263 unrelated healthy individuals living in Panjin City, Liaoning Province, Northeastern China using the VeriFilerTM Express PCR Amplification Kit. The population comparison was performed between the Panjin Han population and the other relevant groups to further explore the structure of Panjin Han and its relationship with the other groups. Results The results found 316 alleles across the 23 STRs and the corresponding allelic frequencies ranged from 0.5198 to 0.0004. Except for D3S1358, TPOX, TH01, and D3S1358, all STR loci were highly polymorphic (PIC > 0.7), with the Penta E locus having the highest degree of polymorphism (0.9147). For population comparison, the exact test of population differentiation found that no significant difference was observed between the Panjin Han and the other Han populations, except for Guangdong Han and Jiangxi Han. Conclusion The Panjin Han population showed significant differences with the other ethnic groups in China (Bouyei, Dong, Hui, Miao, Tibetan, and Uygur) and the foreign ethnic groups.

Abstract Background To rethink the clinical significance of standardized uptake values (SUVs) of nasopharyngeal carcinoma (NPC) on 18F-fluorodeoxyglucose (18F-FDG) positron-emission tomography (PET). Methods We retrospectively reviewed 369 NPC patients who underwent pretreatment 18F-FDG PET. The predictive value of the SUVmax of the primary tumor (SUVmax-t) and regional lymph nodes (SUVmax-n) was evaluated using probability density functions. Receiver operating characteristic curves were used to determine optimal cutoffs for the SUVmax-n/SUVmax-t ratio (NTR). Kaplan–Meier and Cox regression analyses were used to assess survival. Results The optimal SUVmax-t and SUVmax-n cutoffs were 7.5 and 6.9, respectively. High SUVmax-t and SUVmax-n were related to local and regional recurrence, respectively. Patients with low SUVmax had better 3-year overall survival (OS). To avoid cross-sensitization of cutoff points, we stratified patients with high SUVmax into the low and high NTR groups. The 3-year distant metastasis-free survival (DMFS; 92.3 vs. 80.6%, P = 0.009), progression-free survival (PFS; 84.0 vs. 67.7%, P = 0.011), and OS (95.9 vs. 89.2%, P = 0.002) significantly differed between the high vs. low NTR groups for patients with high SUVmax. Multivariable analysis showed that NTR was an independent prognostic factor for DMFS (hazard ratio [HR]: 2.037, 95% CI: 1.039–3.992, P = 0.038), PFS (HR: 1.636, 95% CI: 1.021–2.621, P = 0.041), and OS (HR: 2.543, 95% CI: 1.214–5.325, P = 0.013). Conclusion High SUVmax was associated with NPC recurrence. NTR is a potential prognosticator for DMFS, suggesting that heterogeneity in the pretreatment 18F-FDG uptake between the primary tumor and lymph nodes is associated with high invasion and metastatic potential.

Abstract Background The B3GNT6 protein is a member of the O-GlcNAc transferase (OGT) family and is responsible for the production of the core 3 structure of O-glycans. It is generally expressed in the gastrointestinal (GI) tract; however, its clinical significance in colorectal cancer remains largely unexplored. Methods We obtained mRNA transcriptomic sequencing data from 3 gene expression omnibus (GEO) datasets (GSE37182, GSE39582, GSE103512) and The Cancer Genome Atlas (TCGA) to compare the B3GNT6 mRNA levels between colorectal cancer and normal tissues and further evaluate its value as a prognostic marker in colorectal cancer. We further validated this at the protein level in our cohort using immunohistochemical staining of B3GNT6 as well as the Human Protein Atlas online database. Results B3GNT6 expression was downregulated in colorectal cancer tissues as compared to that in the normal tissues at both mRNA and protein levels. Downregulation of B3GNT6 expression was found to be associated with poor overall survival in patients with colorectal cancer as per the data in GSE39582 and TCGA databases. Low B3GNT6 mRNA levels were significantly associated with chromosome instability (CIN) and KRAS mutations in patients with colorectal cancer. Gene set enrichment analysis (GSEA) revealed that low B3GNT6 expression levels in colorectal cancer were associated with increased proteasome activity. Conclusions The results of this study demonstrate that low expression of B3GNT6 is a potential biomarker for poor outcomes in patients with CRC. Moreover, the low expression of B3GNT6 may indicate more frequent activation of the KRAS/ERK signaling pathway, high CIN, and increased proteasomal activity. These novel findings may prove helpful for molecular diagnosis and provide a new therapeutic target for colorectal cancer.

Abstract Introduction To identify the subset of patients with de novo nasopharyngeal carcinoma (NPC) for whom [18F] fluorodeoxyglucose positron emission tomography and computed tomography (18F-FDG PET/CT) should be recommended, and to determine whether PET/CT is a cost-effective decision for precise M staging in endemic areas. Materials and methods Retrospective analysis of data of 4469 patients diagnosed with de novo NPC between January 2014 and December 2019. The detection rate of distant metastasis was compared between different groups. Univariate and multiple logistic regression analysis was applied to identify the risk factors for distant metastasis. The cost-effectiveness of the diagnostic strategies was assessed. Results The detection rate of distant metastasis in the whole cohort was 5.46%. In multivariate analysis, male sex, T3-4 stage, N2-3 stage, and high plasma Epstein-Barr virus (EBV) DNA (≥ 14,650 copies/mL) were risk factors for distant metastases. NPC patients with T3-4 stage combined with N2-3 stage, high EBV DNA combined with male sex, or N2-3 stage combined with high EBV DNA were defined as recommended group with relatively higher tendency for metastasis. Distant metastasis incidence in recommended group and unrecommended group were 10.25% and 1.75%, respectively (P

Small open reading frames (sORFs) can encode functional polypeptides or act as cis-translational regulators in stress responses in eukaryotes. Their number and potential importance have only recently become clear in plants. In this study, we identified a novel sORF gene in sweet potato, IbEGF, which encoded the 83-amino acid polypeptide containing an EGF_CA domain. The expression of IbEGF was induced by PEG6000, H2O2, abscisic acid (ABA), methyl-jasmonate (MeJA) and brassinosteroid (BR). The IbEGF protein was localized to the nucleus and cell membrane. Under drought stress, overexpression of IbEGF enhanced drought tolerance, promoted the accumulation of ABA, MeJA, BR and proline and upregulated the genes encoding superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) in transgenic sweet potato. The IbEGF protein was found to interact with IbCOP9-5α, a regulator in the phytohormone signalling pathways. These results suggest that IbEGF interacting with IbCOP9-5α enhances drought tolerance by regulating phytohormone signalling pathways, increasing proline accumulation and further activating reactive oxygen species (ROS) scavenging system in transgenic sweet potato.

BTB-TAZ (BT)-domain proteins regulate plant development and pathogen defense. However, their roles in resistance to abiotic stresses remain largely unknown. In this study, we found that the sweetpotato BT protein-encoding gene IbBT4 significantly enhanced the drought tolerance of Arabidopsis. IbBT4 expression was induced by PEG6000, H2O2 and brassinosteroids (BRs). The IbBT4-overexpressing Arabidopsis seeds presented higher germination rates and longer roots in comparison with those of WT under 200 mM mannitol stress. Under drought stress the transgenic Arabidopsis plants exhibited significantly increased survival rates and BR and proline contents and decreased water loss rates, MDA content and reactive oxygen species (ROS) levels. IbBT4 overexpression upregulated the BR signaling pathway and proline biosynthesis genes and activated the ROS-scavenging system under drought stress. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays revealed that the IbBT4 protein interacts with BR-ENHANCED EXPRESSION 2 (BEE2). Taken together, these results indicate that the IbBT4 gene provides drought tolerance by enhancing both the BR signaling pathway and proline biosynthesis and further activating the ROS-scavenging system in transgenic Arabidopsis.

Several members of the MYB transcription factor family have been found to regulate growth, developmental processes, metabolism, and biotic and abiotic stress responses in plants. However, the role of MYB116 in plants is still unclear. In this study, a MYB transcription factor gene IbMYB116 was cloned and characterized from the sweetpotato [Ipomoea batatas (L.) Lam.] line Xushu55-2, a line that is considered to be drought resistant. We show here that IbMYB116 is a nuclear protein and that it possesses a transactivation domain at the C terminus. This gene exhibited a high expression level in the leaf tissues of Xushu55-2 and was strongly induced by PEG6000 and methyl-jasmonate (MeJA). The IbMYB116-overexpressing Arabidopsis plants showed significantly enhanced drought tolerance, increased MeJA content, and a decreased H2O2 level under drought stress. The overexpression of IbMYB116 in Arabidopsis systematically upregulated jasmonic acid (JA) biosynthesis genes and activated the JA signaling pathway as well as reactive oxygen species (ROS)-scavenging system genes under drought stress conditions. The overall results suggest that the IbMYB116 gene might enhance drought tolerance by activating a ROS-scavenging system through the JA signaling pathway in transgenic Arabidopsis. These findings reveal, for the first time, the crucial role of IbMYB116 in the drought tolerance of plants.