scholarly journals Somatic mutations of activated signaling genes, transcription factors, or tumor suppressors are a precondition for leukemic transformation from myelodysplastic syndromes: a sequencing analysis of 64 paired samples

2021 ◽  
Author(s):  
Xiao Li ◽  
Chun-Kang Chang ◽  
Feng Xu ◽  
Ling-Yun Wu ◽  
Juan Guo ◽  
...  

The transformation biology of secondary AML from MDS is still not fully understood. Here, we performed a large cohort of paired sequences including target, whole-exome and single cell sequencing to search AML transformation- related mutations (TRM). The results showed that fifty-five out of the 64 (85.9%) patients presented presumptive TRM involving activated signaling, transcription factors, or tumor suppressors. Most of TRM (63.6%, 35 cases) emerged at the leukemia transformation point. All five of the remaining nine patients analyzed by paired whole exome sequencing showed TRM which are not included in the reference targets. Single-cell sequencing indicated that the activated cell signaling route was related to TRM which take place prior to phenotypic development. Of note, defined TRM was limited to a small set of genes (less than ten, in the order: NRAS/KRAS, CEBPA, TP53, FLT3, RUNX1, CBL, PTPN11 and WT1, accounted for 91.0% of the mutations). In conclusion, somatic mutations involving in activated signaling, transcription factors, or tumor suppressors appeared to be a precondition for AML transformation from myelodysplastic syndromes. The TRM may be considered as new therapy targets.

2022 ◽  
Author(s):  
Feng Xu ◽  
Ling-Yun Wu ◽  
Juan Guo ◽  
Qi He ◽  
Zheng Zhang ◽  
...  

Abstract Background The transformation biology of secondary AML from MDS is still not fully understood. Here, we performed a large cohort of paired self-controlled sequences including target, whole-exome and single cell sequencing to search AML transformation-related mutations (TRMs). Methods 39 target genes from paired samples from 72 patients with MDS who had undergone AML transformation were analyzed by next generation target sequencing. Whole exome and single-cell RNA sequencing were used to verify the dynamics of transformation. Results The target sequencing results showed that sixty-four out of the 72 (88.9%) patients presented presumptive TRMs involving activated signaling, transcription factors, or tumor suppressors. Of the 64 patients, most of TRMs (62.5%, 40 cases) emerged at the leukemia transformation point. All three of the remaining eight patients analyzed by paired whole exome sequencing showed TRMs which are not included in the reference targets. No patient with MDS developed into AML only by acquiring mutations involved in epigenetic modulation or RNA splicing. Single-cell sequencing in one pair sample indicated that the activated cell signaling route was related to TRMs which take place prior to phenotypic development. Of note, target sequencing defined TRMs were limited to a small set of seven genes (in the order: NRAS/KRAS, CEBPA, TP53, FLT3, CBL, PTPN11 and RUNX1, accounted for nearly 90.0% of the TRMs). Conclusions Somatic mutations involving in signaling, transcription factors, or tumor suppressors appeared to be a precondition for AML transformation from MDS. The TRMs may be considered as new therapy targets.


2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Yasunobu Nagata ◽  
Hideki Makishima ◽  
Cassandra M. Kerr ◽  
Bartlomiej P. Przychodzen ◽  
Mai Aly ◽  
...  

AbstractMyelodysplastic syndromes (MDS) arise in older adults through stepwise acquisitions of multiple somatic mutations. Here, analyzing 1809 MDS patients, we infer clonal architecture by using a stringent, the single-cell sequencing validated PyClone bioanalytic pipeline, and assess the position of the mutations within the clonal architecture. All 3,971 mutations are grouped based on their rank in the deduced clonal hierarchy (dominant and secondary). We evaluated how they affect the resultant morphology, progression, survival and response to therapies. Mutations of SF3B1, U2AF1, and TP53 are more likely to be dominant, those of ASXL1, CBL, and KRAS are secondary. Among distinct combinations of dominant/secondary mutations we identified 37 significant relationships, of which 12 affect clinical phenotypes, 5 cooperatively associate with poor prognosis. They also predict response to hypomethylating therapies. The clonal hierarchy has distinct ranking and the resultant invariant combinations of dominant/secondary mutations yield novel insights into the specific clinical phenotype of MDS.


BMC Cancer ◽  
2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Keiichi Akizuki ◽  
Masaaki Sekine ◽  
Yasunori Kogure ◽  
Takuro Kameda ◽  
Kotaro Shide ◽  
...  

Abstract Background The occurrence of a mediastinal germ cell tumor (GCT) and hematological malignancy in the same patient is very rare. Due to its rarity, there have been only two reports of the concurrent cases undergoing detailed genetic analysis with whole-exome sequencing (WES), and the possible clonal relationship between the both tumors remained not fully elucidated. Methods We performed whole-exome sequencing analysis of mediastinal GCT and acute myeloid leukemia (AML) samples obtained from one young Japanese male adult patient with concurrent both tumors, and investigated the possible clonal relationship between them. Results Sixteen somatic mutations were detected in the mediastinal GCT sample and 18 somatic mutations in the AML sample. Mutations in nine genes, including TP53 and PTEN both known as tumor suppressor genes, were shared in both tumors. Conclusions All in our case and in the previous two cases with concurrent mediastinal GCT and AML undergoing with whole-exome sequencing analysis, TP53 and PTEN mutations were commonly shared in both tumors. These data not only suggest that these tumors share a common founding clone, but also indicate that associated mediastinal GCT and AML harboring TP53 and PTEN mutations represent a unique biological entity.


2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Jiasheng Xu ◽  
Kaili Liao ◽  
Xi Yang ◽  
Chengfeng Wu ◽  
Wei Wu ◽  
...  

AbstractCirculating tumor cells are tumor cells with high vitality and high metastatic potential that invade and shed into the peripheral blood from primary solid tumors or metastatic foci. Due to the heterogeneity of tumors, it is difficult for high-throughput sequencing analysis of tumor tissues to find the genomic characteristics of low-abundance tumor stem cells. Single-cell sequencing of circulating tumor cells avoids interference from tumor heterogeneity by comparing the differences between single-cell genomes, transcriptomes, and epigenetic groups among circulating tumor cells, primary and metastatic tumors, and metastatic lymph nodes in patients' peripheral blood, providing a new perspective for understanding the biological process of tumors. This article describes the identification, biological characteristics, and single-cell genome-wide variation in circulating tumor cells and summarizes the application of single-cell sequencing technology to tumor typing, metastasis analysis, progression detection, and adjuvant therapy.


2021 ◽  
Vol 10 (Supplement_1) ◽  
pp. S14-S14
Author(s):  
K E Ocwieja ◽  
T K Hughes ◽  
J M Antonucci ◽  
A L Richards ◽  
A C Stanton ◽  
...  

Abstract Background The molecular mechanisms underpinning the neurologic and congenital pathologies caused by Zika virus (ZIKV) infection remain poorly understood. It is also unclear why congenital ZIKV disease was not observed prior to the recent epidemics in French Polynesia and the Americas, despite evidence that the Zika virus has actively circulated in parts of Africa and Asia since 1947 and 1966, respectively. Methods Due to advances in stem cell-based technologies, we can now model ZIKV infections of the central nervous system in human stem cell-derived neuroprogenitor cells and cerebral organoids, which recapitulate complex three-dimensional neural architecture. We apply Seq-Well—a simple, portable platform for massively parallel single-cell RNA sequencing—to characterize these neural models infected with ZIKV. We detect and quantify host mRNA transcripts and viral RNA with single-cell resolution, thereby defining transcriptional features of both uninfected and infected cells. Results In neuroprogenitor cells, single-cell sequencing reveals that while uninfected bystander cells strongly upregulate interferon pathway genes, these are largely suppressed in cells infected with ZIKV within the same culture dish. In our organoid model, single-cell sequencing allows us to identify multiple cellular populations, including neuroprogenitor cells, intermediate progenitor cells, and terminally differentiated neurons. In this model of the developing brain, we identify preferred tropisms of ZIKV infection. Our data additionally reveal differences in cell-type frequencies and gene expression within organoids infected by historic and contemporary ZIKV strains from a variety of geographic locations. Conclusions These findings may help explain phenotypic differences attributed to the viruses, including variable propensities to cause microcephaly. Overall, our work provides insight into normal and diseased human brain development and suggests that both virus replication and host response mechanisms underlie the neuropathology of ZIKV infection.


2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Andrew P. Hutchins

AbstractRecent innovations in single cell sequencing-based technologies are shining a light on the heterogeneity of cellular populations in unprecedented detail. However, several cellular aspects are currently underutilized in single cell studies. One aspect is the expression and activity of transposable elements (TEs). TEs are selfish sequences of DNA that can replicate, and have been wildly successful in colonizing genomes. However, most TEs are mutated, fragmentary and incapable of transposition, yet they are actively bound by multiple transcription factors, host complex patterns of chromatin modifications, and are expressed in mRNAs as part of the transcriptome in both normal and diseased states. The contribution of TEs to development and cellular function remains unclear, and the routine inclusion of TEs in single cell sequencing analyses will potentially lead to insight into stem cells, development and human disease.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. SCI-7-SCI-7
Author(s):  
Ralf Küppers

The genetic analysis of the Hodgkin and Reed/Sternberg (HRS) tumor cells in Hodgkin lymphoma (HL) is very much hampered by the rarity of these cells, typically accounting for only about 1% of cells in the lymphoma tissue. Moreover, only very few cell lines were established from HL, partly with an uncertain origin. Thus, for the identification of somatic mutations in HRS cells, methods had to be established to isolate the rare HRS cells by microdissection from tissue sections or by cell sorting from cell suspensions. Initial studies were focussed on candidate gene approaches, often inspired by results from the prior analysis of HL cell lines. These early studies revealed numerous recurrent mutations in members of the NF-κB and JAK/STAT pathways, causing or at least contributing to the constitutive activation of these signaling pathways.1 The pathobiological relevance of the constitutive activation of NF-κB and JAK/STAT factors was validated by functional studies with HL cell lines. A first whole exome sequencing analysis of flow-sorted HRS cells was published by Reichel and colleagues.2 B2M was found to be inactivated by somatic mutations in 7/10 cases, and caused loss of major histocompatibility complex 1 expression. Although later studies with larger case series identified such mutations in only about 20-30% of cases,3,4 B2M inactivation is nevertheless an important factor for immune evasion of HRS cells and a frequently mutated gene in HL. A second exome sequencing study of HRS cells used microdissected tumor cells and revealed as a major novel finding frequent somatic mutations in the STAT6 gene (ca. 30% of cases).3 The genetic lesions in STAT6 are gain-of-function mutations. Overall nearly 90% of HL cases show genetic alterations in members of the JAK/STAT pathway, further demonstrating the major role of this pathway in HL pathogenesis. Our group is currently performing studies of microdissected HRS cells by whole genome sequencing, aiming to identify further genetic lesions in HRS cells beyond those affecting exons. An alternative attractive approach to uncover mutations in HRS cells is the genetic analysis of circulating DNA in plasma, because HRS cell-derived DNA fragments can be identified in most patients at the time of diagnosis. A targeted sequencing study of circulating tumor DNA showed the feasibility of this approach and validated, for example, the frequent occurrence of STAT6 mutations in HL. In rare instances, a HL can co-occur with another lymphoma in the same patient. Such composite lymphomas frequently show a common clonal origin of both lymphomas from a mature B cell.5 Composite lymphomas are therefore elegant models to study the multi-step transformation process in lymphomagenesis. We are currently performing a whole exome sequencing analysis of composite classical HL and B-cell Non-Hodgkin lymphomas, to reveal the pattern of early shared mutations and later distinct mutations. In each of the cases under investigations, such shared and distinct mutations were indeed identified. Küppers R, Engert A, Hansmann ML. Hodgkin lymphoma. J Clin Invest. 2012; 122: 3439. Reichel J, Chadburn A, Rubinstein PG, et al. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015; 125: 1061. Tiacci E, Ladewig E, Schiavoni G, et al. Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma. Blood. 2018; 131: 2454. Spina V, Bruscaggin A, Cuccaro A, et al. Circulating tumor DNA reveals genetics, clonal evolution, and residual disease in classical Hodgkinlymphoma. Blood. 2018; 131: 2413. Küppers R, Dührsen U, Hansmann ML. Pathogenesis, diagnosis, and treatment of composite lymphomas. Lancet Oncol. 2014; 15: e435. Disclosures No relevant conflicts of interest to declare.


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