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Article ; Online: The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction.

Moshiri, Niema / Fisch, Kathleen M / Birmingham, Amanda / DeHoff, Peter / Yeo, Gene W / Jepsen, Kristen / Laurent, Louise C / Knight, Rob

Scientific reports

2022 Volume 12, Issue 1, Page(s) 5077

Abstract: Throughout the COVID-19 pandemic, massive sequencing and data sharing efforts enabled the real-time surveillance of novel SARS-CoV-2 strains throughout the world, the results of which provided public health officials with actionable information to ... ...

Abstract	Throughout the COVID-19 pandemic, massive sequencing and data sharing efforts enabled the real-time surveillance of novel SARS-CoV-2 strains throughout the world, the results of which provided public health officials with actionable information to prevent the spread of the virus. However, with great sequencing comes great computation, and while cloud computing platforms bring high-performance computing directly into the hands of all who seek it, optimal design and configuration of a cloud compute cluster requires significant system administration expertise. We developed ViReflow, a user-friendly viral consensus sequence reconstruction pipeline enabling rapid analysis of viral sequence datasets leveraging Amazon Web Services (AWS) cloud compute resources and the Reflow system. ViReflow was developed specifically in response to the COVID-19 pandemic, but it is general to any viral pathogen. Importantly, when utilized with sufficient compute resources, ViReflow can trim, map, call variants, and call consensus sequences from amplicon sequence data from 1000 SARS-CoV-2 samples at 1000X depth in < 10 min, with no user intervention. ViReflow's simplicity, flexibility, and scalability make it an ideal tool for viral molecular epidemiological efforts.
MeSH term(s)	COVID-19/epidemiology ; Genome, Viral/genetics ; Humans ; Pandemics ; SARS-CoV-2/genetics ; Software
Language	English
Publishing date	2022-03-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-09035-w
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Article ; Online: An iPSC line derived from a human acute myeloid leukemia cell line (HL-60-iPSC) retains leukemic abnormalities and displays myeloid differentiation defects.

Yamasaki, Amanda E / Warshaw, Jane N / Kyalwazi, Beverly L / Matsui, Hiroko / Jepsen, Kristen / Panopoulos, Athanasia D

Stem cell research

2020 Volume 49, Page(s) 102096

Abstract: Cancer-derived iPSCs have provided valuable insight into oncogenesis, but human cancer cells can often be difficult to reprogram, especially in cases of complex genetic abnormalities. Here we report, to our knowledge, the first successful generation of ... ...

Abstract	Cancer-derived iPSCs have provided valuable insight into oncogenesis, but human cancer cells can often be difficult to reprogram, especially in cases of complex genetic abnormalities. Here we report, to our knowledge, the first successful generation of an iPSC line from a human immortalized acute myeloid leukemia (AML) cell line, the cell line HL-60. This iPSC line retains a majority of the leukemic genotype and displays defects in myeloid differentiation, thus providing a tool for modeling and studying AML.
MeSH term(s)	Cell Differentiation ; HL-60 Cells ; Hematopoiesis ; Humans ; Induced Pluripotent Stem Cells ; Leukemia, Myeloid, Acute/genetics
Language	English
Publishing date	2020-11-23
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1876-7753
ISSN (online)	1876-7753
DOI	10.1016/j.scr.2020.102096
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Article ; Online: The unfolded protein response links tumor aneuploidy to local immune dysregulation.

Xian, Su / Dosset, Magalie / Almanza, Gonzalo / Searles, Stephen / Sahani, Paras / Waller, T Cameron / Jepsen, Kristen / Carter, Hannah / Zanetti, Maurizio

EMBO reports

2021 Volume 22, Issue 12, Page(s) e52509

Abstract: Aneuploidy is a chromosomal abnormality associated with poor prognosis in many cancer types. Here, we tested the hypothesis that the unfolded protein response (UPR) mechanistically links aneuploidy and local immune dysregulation. Using a single somatic ... ...

Abstract	Aneuploidy is a chromosomal abnormality associated with poor prognosis in many cancer types. Here, we tested the hypothesis that the unfolded protein response (UPR) mechanistically links aneuploidy and local immune dysregulation. Using a single somatic copy number alteration (SCNA) score inclusive of whole-chromosome, chromosome arm, and focal alterations in a pan-cancer analysis of 9,375 samples in The Cancer Genome Atlas (TCGA) database, we found an inverse correlation with a cytotoxicity (CYT) score across disease stages. Co-expression patterns of UPR genes changed substantially between SCNA
MeSH term(s)	Aneuploidy ; Humans ; Neoplasms/genetics ; Tumor Microenvironment ; Unfolded Protein Response
Language	English
Publishing date	2021-10-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.202152509
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Zs.A 5433: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Two iPSC lines generated from the bone marrow of a relapsed/refractory AML patient display normal karyotypes and myeloid differentiation potential.

Yamasaki, Amanda E / King, Nicholas E / Matsui, Hiroko / Jepsen, Kristen / Panopoulos, Athanasia D

Stem cell research

2019 Volume 41, Page(s) 101587

Abstract: Using iPSCs to study cancer has been complicated by the fact that many cancer cells are difficult to reprogram, which has been attributed to the genomic abnormalities present. Acute Myeloid Leukemia (AML) is a complex disease that presents with various ... ...

Abstract	Using iPSCs to study cancer has been complicated by the fact that many cancer cells are difficult to reprogram, which has been attributed to the genomic abnormalities present. Acute Myeloid Leukemia (AML) is a complex disease that presents with various types of genomic aberrations that affect prognosis. Here we reprogrammed CD34+ cells from an AML patient containing a rare der(7)t(7;13) translocation associated with poor prognosis, who had relapsed and was refractory to current treatments. The generated AML-iPSCs displayed normal karyotypes and myeloid differentiation potential. These findings have implications for modeling and treating AML disease.
MeSH term(s)	Aged ; Bone Marrow/pathology ; Cell Differentiation ; Drug Resistance, Neoplasm ; Humans ; Induced Pluripotent Stem Cells/pathology ; Karyotype ; Leukemia, Myeloid, Acute/pathology ; Male ; Myeloid Cells/pathology ; Neoplasm Recurrence, Local/pathology ; Tumor Cells, Cultured
Language	English
Publishing date	2019-10-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1876-7753
ISSN (online)	1876-7753
DOI	10.1016/j.scr.2019.101587
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Article ; Online: Nuclear corepressors NCOR1/NCOR2 regulate B cell development, maintain genomic integrity and prevent transformation.

Lee, Robin D / Knutson, Todd P / Munro, Sarah A / Miller, Jeffrey T / Heltemes-Harris, Lynn M / Mullighan, Charles G / Jepsen, Kristen / Farrar, Michael A

Nature immunology

2022 Volume 23, Issue 12, Page(s) 1763–1776

Abstract: The nuclear corepressors NCOR1 and NCOR2 interact with transcription factors involved in B cell development and potentially link these factors to alterations in chromatin structure and gene expression. Herein, we demonstrate that Ncor1/2 deletion limits ... ...

Abstract	The nuclear corepressors NCOR1 and NCOR2 interact with transcription factors involved in B cell development and potentially link these factors to alterations in chromatin structure and gene expression. Herein, we demonstrate that Ncor1/2 deletion limits B cell differentiation via impaired recombination, attenuates pre-BCR signaling and enhances STAT5-dependent transcription. Furthermore, NCOR1/2-deficient B cells exhibited derepression of EZH2-repressed gene modules, including the p53 pathway. These alterations resulted in aberrant Rag1 and Rag2 expression and accessibility. Whole-genome sequencing of Ncor1/2 DKO B cells identified increased number of structural variants with cryptic recombination signal sequences. Finally, deletion of Ncor1 alleles in mice facilitated leukemic transformation, whereas human leukemias with less NCOR1 correlated with worse survival. NCOR1/2 mutations in human leukemia correlated with increased RAG expression and number of structural variants. These studies illuminate how the corepressors NCOR1/2 regulate B cell differentiation and provide insights into how NCOR1/2 mutations may promote B cell transformation.
MeSH term(s)	Mice ; Humans ; Animals ; Co-Repressor Proteins ; Hematopoiesis ; Signal Transduction ; Cell Nucleus ; Genomics ; Nuclear Receptor Co-Repressor 2/genetics ; Nuclear Receptor Co-Repressor 1/genetics
Chemical Substances	Co-Repressor Proteins ; NCOR2 protein, human ; Nuclear Receptor Co-Repressor 2 ; NCOR1 protein, human ; Nuclear Receptor Co-Repressor 1 ; Ncor1 protein, mouse
Language	English
Publishing date	2022-10-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2016987-5
ISSN	1529-2916 ; 1529-2908
ISSN (online)	1529-2916
ISSN	1529-2908
DOI	10.1038/s41590-022-01343-7
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Zs.A 5294: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Extracellular vesicles produced in B cells deliver tumor suppressor miR-335 to breast cancer cells disrupting oncogenic programming in vitro and in vivo.

Almanza, Gonzalo / Rodvold, Jeffrey J / Tsui, Brian / Jepsen, Kristen / Carter, Hannah / Zanetti, Maurizio

Scientific reports

2018 Volume 8, Issue 1, Page(s) 17581

Abstract: The successful implementation of miRNA (miR) therapies in humans will ultimately rely on the use of vehicles with improved cellular delivery capability. Here we tested a new system that leverages extracellular vesicles (EVs) laden with a tumor suppressor ...

Abstract	The successful implementation of miRNA (miR) therapies in humans will ultimately rely on the use of vehicles with improved cellular delivery capability. Here we tested a new system that leverages extracellular vesicles (EVs) laden with a tumor suppressor miRNA (miR-335) produced in B cells by plasmid DNA induction (iEVs). We demonstrate that iEVs-335 efficiently and durably restored the endogenous miR-335 pool in human triple negative breast cancer cells, downregulated the expression of the miR-335 target gene SOX4 transcription factor, and markedly inhibited tumor growth in vivo. Remarkably, iEVs-335 mediated transcriptional effects that persisted in tumors after 60 days post orthotopic implantation. Genome-wide RNASeq analysis of cancer cells treated in vitro with iEVs-335 showed the regulation of a discrete number of genes only, without broad transcriptome perturbations. This new technology may be ideally suited for therapies aimed to restore tumor suppressor miRNAs in cancer cells, disrupting the oncogenic program established after escape from miRNA control.
MeSH term(s)	Animals ; B-Lymphocytes/metabolism ; Carcinogenesis/drug effects ; Cell Line, Tumor ; Extracellular Vesicles/metabolism ; Gene Expression Regulation, Neoplastic ; Genes, Tumor Suppressor ; Humans ; Mice ; Mice, Inbred NOD ; MicroRNAs/genetics ; SOXC Transcription Factors/metabolism ; Signal Transduction/drug effects ; Triple Negative Breast Neoplasms/genetics ; Triple Negative Breast Neoplasms/therapy ; Xenograft Model Antitumor Assays
Chemical Substances	MIRN335 microRNA, human ; MicroRNAs ; SOX4 protein, human ; SOXC Transcription Factors
Language	English
Publishing date	2018-12-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-35968-2
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Article: The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ.

Nachmanson, Daniela / Officer, Adam / Mori, Hidetoshi / Gordon, Jonathan / Evans, Mark F / Steward, Joseph / Yao, Huazhen / O'Keefe, Thomas / Hasteh, Farnaz / Stein, Gary S / Jepsen, Kristen / Weaver, Donald L / Hirst, Gillian L / Sprague, Brian L / Esserman, Laura J / Borowsky, Alexander D / Stein, Janet L / Harismendy, Olivier

NPJ breast cancer

2022 Volume 8, Issue 1, Page(s) 6

Abstract: Microenvironmental and molecular factors mediating the progression of Breast Ductal Carcinoma In Situ (DCIS) are not well understood, impeding the development of prevention strategies and the safe testing of treatment de-escalation. We addressed ... ...

Abstract	Microenvironmental and molecular factors mediating the progression of Breast Ductal Carcinoma In Situ (DCIS) are not well understood, impeding the development of prevention strategies and the safe testing of treatment de-escalation. We addressed methodological barriers and characterized the mutational, transcriptional, histological, and microenvironmental landscape across 85 multiple microdissected regions from 39 cases. Most somatic alterations, including whole-genome duplications, were clonal, but genetic divergence increased with physical distance. Phenotypic and subtype heterogeneity was frequently associated with underlying genetic heterogeneity and regions with low-risk features preceded those with high-risk features according to the inferred phylogeny. B- and T-lymphocytes spatial analysis identified three immune states, including an epithelial excluded state located preferentially at DCIS regions, and characterized by histological and molecular features of immune escape, independently from molecular subtypes. Such breast pre-cancer atlas with uniquely integrated observations will help scope future expansion studies and build finer models of outcomes and progression risk.
Language	English
Publishing date	2022-01-13
Publishing country	United States
Document type	Journal Article
ISSN	2374-4677
ISSN	2374-4677
DOI	10.1038/s41523-021-00365-y
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Article: Differential blood DNA methylation across Lewy body dementias.

Nasamran, Chanond A / Sachan, Anubhav Nikunj Singh / Mott, Jennifer / Kuras, Yuliya I / Scherzer, Clemens R / Study, Harvard Biomarkers / Ricciardelli, Eugenia / Jepsen, Kristen / Edland, Steven D / Fisch, Kathleen M / Desplats, Paula

Alzheimer's & dementia (Amsterdam, Netherlands)

2021 Volume 13, Issue 1, Page(s) e12156

Abstract: Introduction: Dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are characterized by cognitive alterations, visual hallucinations, and motor impairment. Diagnosis is based on type and timing of clinical manifestations; however, ... ...

Abstract	Introduction: Dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are characterized by cognitive alterations, visual hallucinations, and motor impairment. Diagnosis is based on type and timing of clinical manifestations; however, determination of clinical subtypes is challenging. The utility of blood DNA methylation as a biomarker for Lewy body disorders (LBD) is mostly unexplored. Methods: We performed a cross-sectional analysis of blood methylation in 42 DLB and 50 PDD cases applying linear models to compare groups and logistic least absolute shrinkage and selection operator regression to explore the discriminant power of methylation signals. Results: DLB blood shows differential methylation compared to PDD. Some methylation changes associate with core features of LBD. Sets of probes show high predictive value to discriminate between variants. Discussion: Our study is the first to explore LBD blood methylation. Despite overlapping clinical presentation, we detected differential epigenetic signatures that, if confirmed in independent cohorts, could be developed into useful biomarkers.
Language	English
Publishing date	2021-02-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2832898-X
ISSN	2352-8729
ISSN	2352-8729
DOI	10.1002/dad2.12156
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Article ; Online: Mutational profiling of micro-dissected pre-malignant lesions from archived specimens.

Nachmanson, Daniela / Steward, Joseph / Yao, Huazhen / Officer, Adam / Jeong, Eliza / O'Keefe, Thomas J / Hasteh, Farnaz / Jepsen, Kristen / Hirst, Gillian L / Esserman, Laura J / Borowsky, Alexander D / Harismendy, Olivier

BMC medical genomics

2020 Volume 13, Issue 1, Page(s) 173

Abstract: Background: Systematic cancer screening has led to the increased detection of pre-malignant lesions (PMLs). The absence of reliable prognostic markers has led mostly to over treatment resulting in potentially unnecessary stress, or insufficient ... ...

Abstract	Background: Systematic cancer screening has led to the increased detection of pre-malignant lesions (PMLs). The absence of reliable prognostic markers has led mostly to over treatment resulting in potentially unnecessary stress, or insufficient treatment and avoidable progression. Importantly, most mutational profiling studies have relied on PML synchronous to invasive cancer, or performed in patients without outcome information, hence limiting their utility for biomarker discovery. The limitations in comprehensive mutational profiling of PMLs are in large part due to the significant technical and methodological challenges: most PML specimens are small, fixed in formalin and paraffin embedded (FFPE) and lack matching normal DNA. Methods: Using test DNA from a highly degraded FFPE specimen, multiple targeted sequencing approaches were evaluated, varying DNA input amount (3-200 ng), library preparation strategy (BE: Blunt-End, SS: Single-Strand, AT: A-Tailing) and target size (whole exome vs. cancer gene panel). Variants in high-input DNA from FFPE and mirrored frozen specimens were used for PML-specific variant calling training and testing, respectively. The resulting approach was applied to profile and compare multiple regions micro-dissected (mean area 5 mm Results: Using low-input FFPE DNA, BE and SS libraries resulted in 4.9 and 3.7 increase over AT libraries in the fraction of whole exome covered at 20x (BE:87%, SS:63%, AT:17%). Compared to high-confidence somatic mutations from frozen specimens, PML-specific variant filtering increased recall (BE:85%, SS:80%, AT:75%) and precision (BE:93%, SS:91%, AT:84%) to levels expected from sampling variation. Copy number alterations were consistent across all tested approaches and only impacted by the design of the capture probe-set. Applied to DNA extracted from 9 micro-dissected regions (8 PML, 1 normal epithelium), the approach achieved comparable performance, illustrated the data adequacy to identify candidate driver events (GATA3 mutations, ERBB2 or FGFR1 gains, TP53 loss) and measure intra-lesion genetic heterogeneity. Conclusion: Alternate experimental and analytical strategies increased the accuracy of DNA sequencing from archived micro-dissected PML regions, supporting the deeper molecular characterization of early cancer lesions and achieving a critical milestone in the development of biology-informed prognostic markers and precision chemo-prevention strategies.
MeSH term(s)	Benchmarking ; Biological Specimen Banks ; Breast Neoplasms/genetics ; Carcinoma, Intraductal, Noninfiltrating/genetics ; Clone Cells ; DNA Copy Number Variations ; DNA Fragmentation ; DNA Mutational Analysis/methods ; Dissection/methods ; Female ; Gene Library ; Genes, erbB-2 ; Genetic Heterogeneity ; Humans ; INDEL Mutation ; Mutation ; Paraffin Embedding ; Polymorphism, Single Nucleotide ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; Specimen Handling ; Tissue Fixation
Language	English
Publishing date	2020-11-18
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1755-8794
ISSN (online)	1755-8794
DOI	10.1186/s12920-020-00820-y
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Article ; Online: IRE1α regulates macrophage polarization, PD-L1 expression, and tumor survival.

Batista, Alyssa / Rodvold, Jeffrey J / Xian, Su / Searles, Stephen C / Lew, Alyssa / Iwawaki, Takao / Almanza, Gonzalo / Waller, T Cameron / Lin, Jonathan / Jepsen, Kristen / Carter, Hannah / Zanetti, Maurizio

PLoS biology

2020 Volume 18, Issue 6, Page(s) e3000687

Abstract: In the tumor microenvironment, local immune dysregulation is driven in part by macrophages and dendritic cells that are polarized to a mixed proinflammatory/immune-suppressive phenotype. The unfolded protein response (UPR) is emerging as the possible ... ...

Abstract	In the tumor microenvironment, local immune dysregulation is driven in part by macrophages and dendritic cells that are polarized to a mixed proinflammatory/immune-suppressive phenotype. The unfolded protein response (UPR) is emerging as the possible origin of these events. Here we report that the inositol-requiring enzyme 1 (IRE1α) branch of the UPR is directly involved in the polarization of macrophages in vitro and in vivo, including the up-regulation of interleukin 6 (IL-6), IL-23, Arginase1, as well as surface expression of CD86 and programmed death ligand 1 (PD-L1). Macrophages in which the IRE1α/X-box binding protein 1 (Xbp1) axis is blocked pharmacologically or deleted genetically have significantly reduced polarization and CD86 and PD-L1 expression, which was induced independent of IFNγ signaling, suggesting a novel mechanism in PD-L1 regulation in macrophages. Mice with IRE1α- but not Xbp1-deficient macrophages showed greater survival than controls when implanted with B16.F10 melanoma cells. Remarkably, we found a significant association between the IRE1α gene signature and CD274 gene expression in tumor-infiltrating macrophages in humans. RNA sequencing (RNASeq) analysis showed that bone marrow-derived macrophages with IRE1α deletion lose the integrity of the gene connectivity characteristic of regulated IRE1α-dependent decay (RIDD) and the ability to activate CD274 gene expression. Thus, the IRE1α/Xbp1 axis drives the polarization of macrophages in the tumor microenvironment initiating a complex immune dysregulation leading to failure of local immune surveillance.
MeSH term(s)	Animals ; B7-H1 Antigen/metabolism ; CD11b Antigen/metabolism ; Cell Line, Tumor ; Cell Polarity ; Cell Proliferation ; Cell Survival ; Endoribonucleases/metabolism ; Gene Expression Regulation, Neoplastic ; Humans ; Inflammation/pathology ; Linear Models ; Macrophages/metabolism ; Mice, Inbred C57BL ; Mice, Knockout ; Myeloid Cells/metabolism ; Neoplasms/metabolism ; Neoplasms/pathology ; Phenotype ; Protein Serine-Threonine Kinases/metabolism ; Unfolded Protein Response ; X-Box Binding Protein 1/metabolism
Chemical Substances	B7-H1 Antigen ; CD11b Antigen ; CD274 protein, human ; Cd274 protein, mouse ; X-Box Binding Protein 1 ; Xbp1 protein, mouse ; ERN1 protein, human (EC 2.7.11.1) ; Ern1 protein, mouse (EC 2.7.11.1) ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Endoribonucleases (EC 3.1.-)
Language	English
Publishing date	2020-06-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3000687
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