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Two mycobacteriophages were administered intravenously to a male with treatment-refractory Mycobacterium abscessus pulmonary infection and severe cystic fibrosis lung disease. The phages were engineered to enhance their capacity to lyse M. abscessus and were selected specifically as the most effective against the subject's bacterial isolate. In the setting of compassionate use, the evidence of phage-induced lysis was observed using molecular and metabolic assays combined with clinical assessments. M. abscessus isolates pre and post-phage treatment demonstrated genetic stability, with a general decline in diversity and no increased resistance to phage or antibiotics. The anti-phage neutralizing antibody titers to one phage increased with time but did not prevent clinical improvement throughout the course of treatment. The subject received lung transplantation on day 379, and systematic culturing of the explanted lung did not detect M. abscessus. This study describes the course and associated markers of a successful phage treatment of M. abscessus in advanced lung disease.

Significance The ontogeny of B cells in the bone marrow is regulated by a complex network of proteins and signaling pathways. Regulation of gene expression through transcriptional activation and repression is necessary for establishing and maintaining appropriate transcriptomes in cellular development. Here we show that CHD4, a protein that combines epigenetic reader and nucleosome mobilizing functions, is indispensable for early B cell lineage specification and progression. CHD4 is required for IL-7 receptor signaling and efficient V(D)J recombination. Furthermore, CHD4 is essential for repression of non-B lineage gene transcription during B lymphopoiesis. Together, our findings define the importance of a key epigenetic regulator in B cell development and gene expression., Cell lineage specification is a tightly regulated process that is dependent on appropriate expression of lineage and developmental stage-specific transcriptional programs. Here, we show that Chromodomain Helicase DNA-binding protein 4 (CHD4), a major ATPase/helicase subunit of Nucleosome Remodeling and Deacetylase Complexes (NuRD) in lymphocytes, is essential for specification of the early B cell lineage transcriptional program. In the absence of CHD4 in B cell progenitors in vivo, development of these cells is arrested at an early pro-B-like stage that is unresponsive to IL-7 receptor signaling and unable to efficiently complete V(D)J rearrangements at Igh loci. Our studies confirm that chromatin accessibility and transcription of thousands of gene loci are controlled dynamically by CHD4 during early B cell development. Strikingly, CHD4-deficient pro-B cells express transcripts of many non-B cell lineage genes, including genes that are characteristic of other hematopoietic lineages, neuronal cells, and the CNS, lung, pancreas, and other cell types. We conclude that CHD4 inhibits inappropriate transcription in pro-B cells. Together, our data demonstrate the importance of CHD4 in establishing and maintaining an appropriate transcriptome in early B lymphopoiesis via chromatin accessibility.

In contrast to responses against infectious challenge, T cell responses induced via adjuvanted subunit vaccination are dependent on interleukin-27 (IL-27). We show that subunit vaccine-elicited cellular responses are also dependent on IL-15, again in contrast to the infectious response. Early expression of interferon regulatory factor 4 (IRF4) was compromised in either IL-27- or IL-15-deficient environments after vaccination but not infection. Because IRF4 facilitates metabolic support of proliferating cells via aerobic glycolysis, we expected this form of metabolic activity to be reduced in the absence of IL-27 or IL-15 signaling after vaccination. Instead, metabolic flux analysis indicated that vaccine-elicited T cells used only mitochondrial function to support their clonal expansion. Loss of IL-27 or IL-15 signaling during vaccination resulted in a reduction in mitochondrial function, with no corresponding increase in aerobic glycolysis. Consistent with these observations, the T cell response to vaccination was unaffected by in vivo treatment with the glycolytic inhibitor 2-deoxyglucose, whereas the response to viral challenge was markedly lowered. Collectively, our data identify IL-27 and IL-15 as critical to vaccine-elicited T cell responses because of their capacity to fuel clonal expansion through a mitochondrial metabolic program previously thought only capable of supporting quiescent naïve and memory T cells.

MiSeq, Illumina's integrated next generation sequencing instrument, uses reversible-terminator sequencing-by-synthesis technology to provide end-to-end sequencing solutions. The MiSeq instrument is one of the smallest benchtop sequencers that can perform onboard cluster generation, amplification, genomic DNA sequencing, and data analysis, including base calling, alignment and variant calling, in a single run. It performs both single- and paired-end runs with adjustable read lengths from 1 × 36 base pairs to 2 × 300 base pairs. A single run can produce output data of up to 15 Gb in as little as 4 h of runtime and can output up to 25 M single reads and 50 M paired-end reads. Thus, MiSeq provides an ideal platform for rapid turnaround time. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing and target enrichment), metagenomics, and gene expression studies. For these reasons, MiSeq has become one of the most widely used next generation sequencing platforms. Here, we provide a protocol to prepare libraries for sequencing using the MiSeq instrument and basic guidelines for analysis of output data from the MiSeq sequencing run.

RNA sequencing (RNA-seq) has become an important tool for examining the role of the transcriptome to biological processes. While RNA-seq has been widely adopted as a popular approach in many experimental designs, from gene discovery to mechanistic validation of targets, technical issues have largely limited the use of this technique to abundantly available sample sources. However, RNA-seq is becoming increasingly utilized for more specialized applications, such as flow cytometry-sorted cells and clinical specimens, due to protocol advances enabling the use of very low input material ranging from 10 pg to 10 ng of total RNA or 1-1000 intact cells. In this chapter, we present an optimized and detailed approach to RNA-seq for use with low abundance samples.

RNA sequencing (RNA-seq) has become an important tool for examining the role of the transcriptome to biological processes. While RNA-seq has been widely adopted as a popular approach in many experimental designs, from gene discovery to mechanistic validation of targets, technical issues have largely limited the use of this technique to abundantly available sample sources. However, RNA-seq is becoming increasingly utilized for more specialized applications, such as flow cytometry-sorted cells and clinical specimens, due to protocol advances enabling the use of very low input material ranging from 10 pg to 10 ng of total RNA or 1-1000 intact cells. In this chapter, we present an optimized and detailed approach to RNA-seq for use with low abundance samples.

MiSeq, Illumina's integrated next generation sequencing instrument, uses reversible-terminator sequencing-by-synthesis technology to provide end-to-end sequencing solutions. The MiSeq instrument is one of the smallest benchtop sequencers that can perform onboard cluster generation, amplification, genomic DNA sequencing, and data analysis, including base calling, alignment and variant calling, in a single run. It performs both single- and paired-end runs with adjustable read lengths from 1 × 36 base pairs to 2 × 300 base pairs. A single run can produce output data of up to 15 Gb in as little as 4 h of runtime and can output up to 25 M single reads and 50 M paired-end reads. Thus, MiSeq provides an ideal platform for rapid turnaround time. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing and target enrichment), metagenomics, and gene expression studies. For these reasons, MiSeq has become one of the most widely used next generation sequencing platforms. Here, we provide a protocol to prepare libraries for sequencing using the MiSeq instrument and basic guidelines for analysis of output data from the MiSeq sequencing run.

Chromodomain Helicase DNA-binding protein 4 (CHD4, or Mi-2β) is a catalytic core subunit of Nucleosome Remodeling and Deacetylase (NuRD) complexes, which regulate chromatin structure and transcription in lymphocytes. CHD4 activities include ATP-dependent mobilization of nucleosomes, DNA binding and binding to histone tails. Here, we investigated requirements for CHD4 in B cell development in a mouse model system. We utilized Chd4flox/flox:Cd79a-Cre (Chd4 cko) mice, which inactivate Chd4 genes selectively in early B cell progenitors. These mice confirmed that CHD4 is essential for B lymphopoiesis. Following the loss of CHD4 expression, B cell development is arrested at the pro-B cell stage. Peripheral B220+ cells were nearly absent. To address the basis of the observed developmental arrest, we measured effects of the lack of CHD4 on proliferation and Igh gene rearrangements. CHD4-deficient pro-B cells fail to proliferate in response to IL-7. Furthermore, pro-B cells lacking CHD4 complete proximal VH to DJH rearrangements, but rearrange distal VH segments only rarely. Overall, our data demonstrate that CHD4 and NuRD complexes are essential for multiple aspects of early B cell development, including V(D)J recombination, proliferation and survival of pro-B cells.

Memory phenotype (MP), CD44hi CD49dlo CD8 T cells are found in nearly all mice—lymphoreplete, pathogen naïve, and even TCR transgenics. The presence of MP was long thought to be due to environmental pathogen exposure (or, in the case of transgenics, heterologous immunity to same), but studies establishing the presence of these cells in germ-free mice suggested that this was not the case. These cells, dubbed Virtual Memory (VM), are of special relevance due to their increased effector functioning, and, in contrast to other MP CD8 T cells, develop in the periphery with a dependence on IL-15. Our recent studies have determined that VM cells develop in a manner reminiscent of lymphopenic homeostatic expansion, whereby the highest self-affinity T cells (as measured by CD5) interact with available IL-15 to turn into VM cells. This indicates that the naïve CD8 T cell pool is not as homogeneous as usually assumed, and RNA sequencing has further confirmed the heterogeneity of the CD8 naïve T cell pool (separated on CD5). The sequencing has further implicated VM cells in mediating CD8 bystander protection, and ongoing studies suggest that this is indeed the case, with the VM bystander effects being IL-15 dependent.