Aggressive NK-cell leukemia （ANKL） is a rare form of NK cell neoplasm that is more prevalent among people from Asia and Central and South America. Patients usually die within days to months, even ...after receiving prompt therapeutic management. Here we performed the first comprehensive study of ANKL by integrating whole genome, transcriptome and targeted sequencing, cytokine array as well as functional assays. Mutations in the JAK-STAT pathway were identified in 48% （14/29） of ANKL patients, while the extracelinlar STAT3 stimulator IL10 was elevated by an average of 56-fold （P 〈 0.0001） in the plasma of all patients examined. Additional frequently mutated genes included TP53 （34%）, TET2 （28%）, CREBBP （21%） and MLL2 （21%）. Patient NK leukemia cells showed prominent activation of STAT3 phosphorylation, MYC expression and transcriptional activities in multiple metabolic path- ways. Functionally, STAT3 activation and MYC expression were critical for the proliferation and survival of ANKL cells. STAT signaling regulated the MYC transcription program, and both STAT signaling and MYC transcription were required to maintain the activation of nucleotide synthesis and glycolysis, Collectively, the JAK-STAT path- way represents a major target for genomic alterations and IL10 stimulation in ANKL. This newly discovered JAK/ STAT-MYC-biosynthesis axis may provide opportunities for the development of novel therapeutic strategies in treating this subtype of leukemia.
Background/Aims: Metabolic diseases are leading health concerns in today’s global society. In traditional Chinese medicine (TCM), one body type studied is the phlegm-dampness constitution (PC), which ...predisposes individuals to complex metabolic disorders. Genomic studies have revealed the potential metabolic disorders and the molecular features of PC. The role of epigenetics in the regulation of PC, however, is unknown. Methods: We analyzed a genome-wide DNA methylation in 12 volunteers using Illumina Infinium Human Methylation450 BeadChip on peripheral blood mononuclear cells (PBMCs). Eight volunteers had PC and 4 had balanced constitutions. Results: Methylation data indicated a genome-scale hyper-methylation pattern in PC. We located 288 differentially methylated probes (DMPs). A total of 256 genes were mapped, and some of these were metabolic-related. SQSTM1, DLGAP2 and DAB1 indicated diabetes mellitus; HOXC4 and SMPD3, obesity; and GRWD1 and ATP10A, insulin resistance. According to Ingenuity Pathway Analysis (IPA), differentially methylated genes were abundant in multiple metabolic pathways. Conclusion: Our results suggest the potential risk for metabolic disorders in individuals with PC. We also explain the clinical characteristics of PC with DNA methylation features.
N
-Methyladenosine (m
A) on mRNAs mediates different biological processes and its dysregulation contributes to tumorigenesis. How m
A dictates its diverse molecular and cellular effects in leukemias ...remains unknown. We found that YTHDC1 is the essential m
A reader in myeloid leukemia from a genome-wide CRISPR screen and that m
A is required for YTHDC1 to undergo liquid-liquid phase separation and form nuclear YTHDC1-m
A condensates (nYACs). The number of nYACs increases in acute myeloid leukemia (AML) cells compared with normal hematopoietic stem and progenitor cells. AML cells require the nYACs to maintain cell survival and the undifferentiated state that is critical for leukemia maintenance. Furthermore, nYACs enable YTHDC1 to protect m
A-mRNAs from the PAXT complex and exosome-associated RNA degradation. Collectively, m
A is required for the formation of a nuclear body mediated by phase separation that maintains mRNA stability and control cancer cell survival and differentiation.
Introduction FLT3 internal tandem duplication (ITD) is commonly detected in patients with acute myeloid leukemia (AML) and is known to confer poor prognosis. It has different insertion numbers, ...mutation burden, insertion sizes, insertion sites and insertion nucleotide sequences, showing complex diversity. However, the guideline of AML did not sufficiently consider the impact of the diversity of FLT3-ITD on treatment responses, and previous studies have not been consistent with the impact of FLT3-ITD diversity on clinical prognosis. In this study we examined the diversity of FLT3-ITD and correlated these parameters with clinical outcome in adult AML. In addition, we revealed the correlation between FLT3-ITD and drug resistance through evolutionary trajectories in primary resistant patients. Methods We included adult patients from 2016-2021 at Henan Cancer Hospital with newly diagnosed adult AML. next generation sequencing (NGS) was performed for all patients at diagnosis. The FLT3-ITD was also detected using conventional methods based on PCR, with a cut-off of 3% for positivity. The comparative analysis of NGS and PCR was done to validate the diversity of FLT3-ITD. Whole genome sequencing (WGS) data for multiple time points were used to analyze clonal evolution. Data were collected by chart review. The chi-squared or Fisher's exact test, Mann-Whitney U test, log-rank and Cox regression analyses were performed. Results Among 406 newly diagnosed adult AML patients, 24.4% (99/406) patients were detected with FLT3-ITD. The FLT3-ITD diversity was validated by NGS and PCR data from 90 FLT3-ITD positive patients. 61.1% (55/90) patients had single FLT3-ITD (sFLT3-ITD) (31M/24F, median age 46 at diagnosis, range 18-64), and 38.9% (35/90) patients carried multiple FLT3-ITDs (mFLT3-ITD) at the same time (23M/12F, median age 47 at diagnosis, range 19-64). A total of 161 FLT3-ITDs were detected, with a median mutation burden of 21.51% (0.71-93.21%) and a median insertion length of 36bp (9-189 bp). 80.20% of FLT3-ITD insertions were in the near-membrane region, and 45.54% of FLT3-ITD insertions contained exogenous nucleic acid sequences. Patients with mFLT3-ITD had a significantly lower CR rate than those with sFLT3-ITD (25.7% vs 60.0%, p=0.001), while the CR rate of patients with sFLT3-ITD was similar to patients without FLT3-ITD (60.0% vs 58.6%, p=0.521). In the setting of NPM1, the CR rate of patients with sFLT3-ITD+NPM1 mut improved significantly when compared to patients with sFLT3-ITD+NPM1 wild (76.9% vs 44.8%, p=0.015). Unfortunately, the state of NPM1 had no impact on the CR rate of patients with mFLT3-ITD. After a median follow-up of 38.9 months, the median overall survival (OS) has not been reached for patients with a single FLT3-ITD, and the median OS for patients with multiple FLT3-ITDs was only 12.4 months (95 CI, 3.8 to 20.9) ( p=0.028). Multivariate analysis confirmed its prognostic significance on CR rate (HR 2.13, 95% CI, 1.38-4.20, p=0.020) but not on OS. The mutation burden, insertion sizes, insertion sites and insertion nucleotide sequences of FLT3-ITD had no significant impact on the CR rate or OS. To explore the clonal architecture of mFLT3-ITD, single cell DNA sequencing on one patient showed that respective FLT3-ITD variants were detected in completely separated cell populations. This suggested that mFLT3-ITD independently occurred in different subclone. WGS data of persistent primary resistant patients at multiple time points were used to analyze the evolutionary trajectory under chemotherapy. We observed complete separation of evolving trajectory of different FLT3-ITD variants over the course of chemo-treatment. Importantly, FLT3-ITD subclone of diagnosis evolved into the dominant clone at resistance. Conclusion In summary, by exploring the impact of the FLT3-ITD diversity on clinical prognosis and the evolutionary trajectory of mFLT3-ITD, the FLT3-ITD number may be a biomarker to refine the risk stratification and further identify adverse populations among FLT3-ITD positive AML patients.
Introduction The SET binding protein 1 (SETBP1) gene is an oncogene located on chromosome 18q12.3, which is related to DNA replication and gene transcription regulation. Variants in SETBP1 are ...involved in germline and somatic mutations, leading to extremely different pathologic consequences. Germline mutations in SETBP1 are associated with Schinzel-Giedion syndrome (SGS) and SETBP1 Haploinsufficiency Disorder. In contrast, somatic mutations in SETBP1 are linked with myeloid malignancies and clonal hematopoiesis. The vast majority of reported germline SETBP1 mutations were located in the SKI homologous region (codons 868-871). However, germline SETBP1 mutations outside the hotspot region were rarely reported and the potential carcinogenicity remained unclear. Methods Patients from 2018-2022 at the Hennan Cancer Hospital were identified. Bone marrow samples at diagnosis of 285 sporadic patients with myeloid malignancies were sequenced using next generation sequencing (NGS). The candidate SETBP1 mutations were validated by Sanger sequencing from bone marrow and exfoliated buccal epithelial cell samples. Whole exome sequencing (WES) was performed on patient 5 and her parents from the family with SETBP1 mutations. Results In our study, 8 (2.8%) patients (6 AML and 2 MDS) were identified with germ line SETBP1 mutations (Table 1, Figure 1). Importantly, patient 2 and patient 5 carried the same germ line SETBP1 p.Ser373Ala mutation. Meanwhile, 4 patients had somatic SETBP1 mutations at hotspots (p.Asp868Asn in 1 patient and p.Gly870Ser in 3 patients). None of these germ line SETBP1 mutations was detected in 597 healthy Chinese individuals except p.Ser567Phe (2 out of 597) (Table 1). Minimum allele frequencies (MAF) of the germ line SETBP1 mutations were negligible in public databases (Table 1). A significant difference ( p＜0.05) was observed in the minimum allele frequency (MAF) of germ line SETBP1 mutations between sporadic MDS/AML patients and healthy controls, which suggested that germ line SETBP1 mutations should be closely related to MDS/AML. Furthermore, we investigated the family history of the patients with germ line SETBP1 mutation. The father of patient 5 was diagnosed with MDS and carried germ line SETBP1 p.Ser373Ala mutation. Known germ line mutations or somatic mutations associated with myeloid malignancies were not detected in the family of patient 5 by WES. Patient 2, who also carried the germ line SETBP1 p.Ser373Ala mutation, had no family history of myeloid disorders. The elder sister (carrier) of patient 2 had persistent abnormal CBC while the little sister (carrier) had normal CBC. Somatic SETBP1 mutations conveyed a poor prognosis in myeloid malignancies. And in our data, patient 5 and patient 2 both appeared to be induction failure and early relapse. Then patient 2 underwent HLA-full-matched allo-HSCT in the second remission and the doner was his little sister. Unfortunately, after allo-HSCT the CR only maintained 2 months. None of the other 6 sporadic MDS/AML patients with germ line SETBP1 mutation had a family history of hematologic disorders. Many family members were detected to carry germ line SETBP1 mutations but they did not show the characteristics of myeloid disorders other than abnormal percentages of neutrophils and lymphocytes. Conclusion In our study, we identified novel germ line SETBP1 mutations in 8 sporadic MDS/AML patients, and a family history of MDS/AML was noted in one. Germ line SETBP1 mutations are not infrequent among non-familial MDS/AML patients. Identification of these cases is imperative especially in patients who are candidates for HSCT from a family donor, since the association between germ line SETBP1 mutations and recipient outcomes was uncertain.
N6-Methyladenosine (m6A) on mRNAs mediates different biological processes and its dysregulation contributes to tumorigenesis. How m6A dictates its diverse molecular and cellular effects in leukemias ...remains unknown. We found that YTHDC1 is the essential m6A reader in myeloid leukemia from a genome-wide CRISPR screen and that m6A is required for YTHDC1 to undergo liquid-liquid phase separation and form nuclear YTHDC1-m6A condensates (nYACs). The number of nYACs increases in acute myeloid leukemia (AML) cells compared with normal hematopoietic stem and progenitor cells. AML cells require the nYACs to maintain cell survival and the undifferentiated state that is critical for leukemia maintenance. Furthermore, nYACs enable YTHDC1 to protect m6A-mRNAs from the PAXT complex and exosome-associated RNA degradation. Collectively, m6A is required for the formation of a nuclear body mediated by phase separation that maintains mRNA stability and control cancer cell survival and differentiation.
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•YTHDC1 is required for AML cell survival, differentiation state, and leukemogenesis•YTHDC1 binds to m6A and forms nuclear condensates (nYACs) mediated by LLPS•nYACs are more abundant in AML cells compared with normal blood cells•nYACs protect mRNAs (i.e., MYC and others) from degradation by the PAXT complex
Using AML cell lines and patient samples Cheng et al. identify a requirement for YTHDC1 in myeloid leukemogenesis. YTHDC1 undergoes liquid-liquid phase separation by binding to m6A to form dynamic nuclear condensates. These nuclear bodies are increased in myeloid leukemia cells and protect mRNAs from the PAXT-exosome complex.
Esophageal squamous cell carcinoma (ESCC) is a poor-prognostic cancer type with extensive intra- and inter-patient heterogeneity in both genomic variations and tumor microenvironment (TME). However, ...the patterns and drivers of spatial genomic and microenvironmental heterogeneity of ESCC remain largely unknown. Here, we generated a spatial multi-omic atlas by whole-exome, transcriptome, and methylome sequencing of 507 tumor samples from 103 patients. We identified a novel tumor suppressor
, accounting for 22% of ESCCs with frequent somatic mutations or hyper-methylation, which promoted migration and invasion of ESCC cells
. Analysis of the TME and quantification of subclonal expansion indicated that ESCCs undergo spatially directed evolution, where subclones mostly originated from the tumor center but had a biased clonal expansion to the upper direction of the esophagus. Interestingly, we found upper regions of ESCCs often underwent stronger immunoediting with increased selective fitness, suggesting more stringent immune selection. In addition, distinct TMEs were associated with variable genomic and clinical outcomes. Among them, hot TME was associated with high immune evasion and subclonal heterogeneity. We also found that immunoediting, instead of CD8
T cell abundance, acts as an independent prognostic factor of ESCCs. Importantly, we found significant heterogeneity in previously considered potential therapeutic targets, as well as BRCAness characteristics in a subset of patients, emphasizing the importance of focusing on heterogeneity in ESCC targeted therapy. Collectively, these findings provide novel insights into the mechanisms of the spatial evolution of ESCC and inform precision therapeutic strategies.
Main conclusion
SR proteins from sweet potato have conserved functional domains and similar gene structures as that of Arabidopsis and rice in general. However, expression patterns and alternative ...splicing regulations of SR genes from different species have changed under stresses. Novel alternative splicing regulations were found in sweet potato SR genes.
Serine/arginine-rich (SR) proteins play important roles in plant development and stress response by regulating the pre-mRNA splicing process. However, SR proteins have not been identified so far from an important crop sweet potato. Through bioinformatics analysis, our study identified 24 SR proteins from sweet potato, with comprehensively analyzing of protein characteristics, gene structure, chromosome localization, and
cis
-acting elements in promotors. Salt, heat, and mimic drought stresses triggered extensive but different expressional regulations on sweet potato SR genes. Interestingly, heat stress caused the most active disturbances in both gene transcription and pre-mRNA alternative splicing (AS). Tissue and species-specific transcriptional and pre-mRNA AS regulations in response to stresses were found in sweet potato, in comparison with Arabidopsis and rice. Moreover, novel patterns of pre-mRNA alternative splicing were found in SR proteins from sweet potato. Our study provided an insight into similarities and differences of SR proteins in different plant species from gene sequences to gene structures and stress responses, indicating SR proteins may regulate their downstream genes differently between different species and tissues by varied transcriptional and pre-mRNA AS regulations.
Extreme high temperature at the meiosis stage causes a severe decrease in spikelet fertility and grain yield in rice. The rice variety grain size on chromosome 2 (GS2) contains sequence variations of
...OsGRF4
(
Oryza sativa
growth-regulating factor 4;
OsGRF4
AA
), escaping the microRNA miR396-mediated degradation of this gene at the mRNA level. Accumulation of
OsGRF4
enhances nitrogen usage and metabolism, and increases grain size and grain yield. In this study, we found that pollen viability and seed-setting rate under heat stress (HS) decreased more seriously in GS2 than in its comparator, Zhonghua 11 (ZH11). Transcriptomic analysis revealed that, following HS, genes related to carbohydrate metabolic processes were expressed and regulated differentially in the anthers of GS2 and ZH11. Moreover, the expression of genes involved in chloroplast development and photosynthesis, lipid metabolism, and key transcription factors, including eight male sterile genes, were inhibited by HS to a greater extent in GS2 than in ZH11. Interestingly, pre-mRNAs of
OsGRF4
, and a group of essential genes involved in development and fertilization, were differentially spliced in the anthers of GS2 and ZH11. Taken together, our results suggest that variation in
OsGRF4
affects proper transcriptional and splicing regulation of genes under HS, and that this can be mediated by, and also feed back to, carbohydrate and nitrogen metabolism, resulting in a reduction in the heat tolerance of rice anthers.
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