Fig. 6
From: Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes
SQUID-predicted cell-type abundances identified outcomes-predictive subclones in pediatric AML and neuroblastoma diagnostic biopsies. A Clusters identified in scRNA-seq profiles of paired diagnostic and relapse samples from 6 pediatric AML patients included the cluster AML-X. B AML-X cells were present in the diagnostic biopsies of 3 patients and their abundance increased at relapse. C SQUID-predicted AML-X abundances in TARGET-profiled diagnostic AML biopsies were predictive of patient outcomes. D The cancer lncRNAs MALAT1 and NEAT1 and E their direct targets were upregulated in AML-X and were predicted to regulate chemoresistance in AML. F Clusters identified in scRNA-seq profiles of neuroblastoma samples included NB-s1 and NB-s2. G SQUID-predicted abundances of both NB-s1 and NB-s2 in TARGET-profiled diagnostic biopsies were predictive of patient outcomes. H Upregulated genes in NB-s1 included SEMA3D and HRAS, and upregulated genes in NB-s2 (I) included SEMA3D and other semaphorin family members