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• Count Me In (CMI): The Metastatic Prostate Cancer (MPC) Project (CMI-MPCproject)

  Count Me In - The Metastatic Prostate Cancer Project: A Patient-Driven Research Initiative to Accelerate Metastatic Prostate Cancer Research The Metastatic Prostate Cancer Project (MPCproject; http://mpcproject.org/) is a research study that empowers men with metastatic and advanced prostate cancer to partner directly with researchers by sharing their samples and clinical information, with the ultimate goal of accelerating scientific discoveries that have clinical impact. The MPCproject enables any man with metastatic or advanced prostate cancer in the US and Canada to participate in cutting-edge genomic and molecular research, regardless of where they live. Metastatic or advanced prostate cancer patients visit the project website and complete an online questionnaire of basic information about themselves and their cancer. Enrolled patients are mailed saliva and blood draw kits, which can be used to extract germline DNA and cell-free DNA (cfDNA), respectively. The study team contacts participants' healthcare institutions to obtain medical records and a portion of archived tumor samples. Whole exome sequencing is performed on tumor DNA, germline DNA, and cfDNA, and transcriptome sequencing is performed on tumor RNA. De-identified data, including linked genomic, clinical, and patient-reported data, are shared via public databases on a recurring pre-publication basis. Participants are regularly provided with updates on the study.

  Study phs001939

• Immunoprotective mechanisms and microbiota interplay in Salmonella Typhi infection

  Vaccine development against Salmonella enterica serovar Typhi (S. Typhi) requires a better understanding of interaction between human host and the resident microbial consortia in gastrointestinal tract. Healthy adult volunteers received either Ty21a, M01ZH09 or placebo, and underwent challenges with wt S. Typhi. Stool samples were collected at the screening interview (Baseline 1), prior to the first vaccination visit (Baseline 2), during vaccination (Day -28 and -26 for placebo and M01ZH09 groups; Day -32, -30, -28, -26 for Ty21a group), prior to challenge with S. Typhi (Day 0), and after challenge (day 0 12h, day 1, day 3, day 7, and day 10). 16S rRNA and messenger RNA were extracted from stool and sequenced on the Illumina Miseq and HiSeq 2000 platforms, respectively.

  Study phs001521

• RNA-seq of atypical 3q26 samples

  RNA was isolated using phenol-chloroform extraction followed by DNase digestion or using the Qiagen Allprep DNA/RNA kit and protocol (Qiagen, #80204). cDNA synthesis was done using the SuperScript II Reverse Transcriptase kit (Invitrogen). Quantitative real-time PCR was performed by using primers as described previously13,21 on the 7500 Fast Real-time PCR System (Applied Biosystems). Relative levels of gene expression were calculated using the ΔΔCt method

  Dataset EGAD00001006106

• Botensilimab, an Fc-enhanced Anti-CTLA-4 Antibody, is Effective Against Tumors Poorly Responsive to Conventional Immunotherapy

  This study explores the genomic landscape associated with a novel Fc-engineered anti-CTLA-4 antibody (botensilimab) in advanced solid tumors. We seek to understand if enhancing the Fc-region affinity of anti-CTLA-4 antibodies can improve anti-tumor efficacy and expand clinical benefit to tumors poorly responsive to conventional immunotherapy. As part of an ongoing open-label, Phase 1, multicenter study, we conducted an exploratory sub-analysis of genomics data. The primary study evaluates the safety, tolerability, pharmacokinetics, and pharmacodynamics of botensilimab monotherapy and in combination with an anti-PD-1 antibody (balstilimab) in participants with advanced solid tumors. RNA from formalin-fixed paraffin-embedded (FFPE) tumor biopsies and matched normal blood samples were isolated and subjected to RNA-sequencing using the Personalis ImmunoID NeXT Platform. We demonstrated that anti-CTLA-4 engineered for enhanced FcγR affinity leverages FcγR-dependent mechanisms to potentiate T cell responsiveness, reduce intratumoral Tregs, and enhance antigen presenting cell activation. This genomic analysis contributes to our understanding of the molecular mechanisms underlying patient responses to Fc-engineered anti-CTLA-4 therapy and may inform future strategies to expand the clinical benefit of immune checkpoint blockade in cancer immunotherapy.

  Study phs003704

• Fgl2 Regulates FcγRIIB+ CD8+ T Cell Responses during Infection

  While the inhibitory receptor FcγRIIB has been shown to be upregulated on activated CD8+ T cells in both mice and humans, its impact on T cell fate during infection has not been fully elucidated. We identified an increase in FcγRIIB-expressing CD8+ T cells in COVID patients relative to healthy controls, and in mouse models of viral infection. Despite its well-known role as an Fc receptor, FcγRIIB also ligates the immunosuppressive cytokine Fgl2, resulting in CD8+ T cell apoptosis. Both chronic LCMV infection in mice and COVID in humans resulted in a significant increase in plasma Fgl2. Further, plasma Fgl2 was directly proportional to CD8+ T cell lymphopenia in COVID patients. To further understand the association of Fgl2 and CD8+ T cell lymphopenia following COVID infection, we assessed the transcriptomic profiles of PBMCs with high (≥ 9.153 ng/ml) vs low (defined as

  Study phs003870

• Defining Cutaneous Gene Expression Signatures in Juvenile Dermatomyositis

  Skin inflammation in juvenile dermatomyositis (JDM) can signal disease onset or flare up and prevent complete disease remission. Our objective was to evaluate JDM cutaneous expression signatures through tape stripping in both lesional and non-lesional skin and as compared to paired blood. A total of 28 JDM and 20 control (CTL) patients participated in the study. All patients had tape strip sampling of non-lesional (NL) skin at enrollment visit. Within our JDM cohort, paired lesional (L) skin was additionally sampled if rash was present. 16/28 of JDM patients had at least one additional skin sample associated with a follow-up (FU) visit (total number of follow-up samples included = 26 NL and 4 L). We identified a common innate immune signature in both lesional and non-lesional JDM skin. Using unsupervised hierarchical clustering of skin expression data, we distinguished a JDM molecular subgroup characterized by a mitochondrial dysfunction signature. In comparison to blood expression data, we determined that skin may more effectively highlight the JDM subgroup characterized by a mitochondrial dysfunction expression signature. Data available include bulk RNA-sequencing data from tape strips and blood of the JDM and control patients from this study.

  Study phs003884

• Cross-Sectional Characterization of Idiopathic Bronchiectasis

  This GDMCC protocol will study adult patients with non-CF, idiopathic bronchiectasis, whose genetic etiologies are not known. Idiopathic bronchiectasis is reportedly more common in females with certain tall, thin body types and associated with environmental organisms, such as nontuberculous mycobacterium (NTM). The other susceptibility factors predisposing to bronchiectasis or acquisition of NTM are unclear. The study will attempt to broaden the understanding of this disease by comparing gender-associated factors and NTM status. A relatively equal number of both females/males and NTM/non-NTM infected subjects will be enrolled. Approximately 300 people may be screened to find 260 eligible subjects, since a small number (e.g., 40 patients) may be diagnosed with PCD, vCF, or other known etiology as an explanation for the bronchiectasis. This single-visit protocol will use a systematic approach to characterize the physical features, radiographic patterns, and associated lower airway microbial flora. There is no natural history of disease course follow-up component to this protocol. Participants will have one outpatient clinic visit for evaluation with a physical examination including detailed body size measurements, medical history, collection of blood samples for routine lab tests and genetic analyses, and a chest X-ray if no recent one is available. Participants will also have tests of lung function, and measurement of a gas called nitric oxide in the nose. Participants whose initial tests show abnormal results may also be asked to have a nasal scrape to collect cell samples and/or a skin sweat test to measure salt concentrations. Participants will also have a sputum specimen collected during the visit and will be asked to collect two additional early morning sputum samples and a mouth rinse at home within 2 weeks of the clinic visit, and mail the sample collection materials to the research team. Careful evaluation and characterization of the physical and clinical characteristics will guide the genetic characterization of idiopathic bronchiectasis, and likely lead to an improved diagnostic approach. Identification of disease causing genes may provide new therapeutic targets.

  Study phs001279

• Data Access Committee KCL FC

  Dac EGAC00001000386

• MCF10A 12h IL6 classical signaling

  Gene expression after cell culture, 12h IL6+sgp130-Fc stimulated

  Dataset EGAD00010001970

• MCF10A 24h IL6 classical signaling

  Gene expression after cell culture, 24h IL6+sgp130-Fc stimulated

  Dataset EGAD00010001963