araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: Lysosomal Movement and Anabolic Resistance

Summary: Age-associated loss of muscle mass, termed sarcopenia, is strongly associated with functional impairment and physical disability in the elderly. Maintenance or growth of muscle mass is mainly driven by increased muscle protein synthesis (i.e. the generation of new muscle protein) in response to exercise and feeding. However, several investigations have shown that elderly individuals have a blunted protein synthetic response following protein intake. This inability of the elderly to properly respond to growth stimuli has been termed anabolic resistance and plays a significant role in the development of sarcopenia. However, the precise mechanisms underpinning anabolic resistance are unknown.
  It is well established that muscle protein synthesis at the molecular level is regulated by a cellular protein complex called mTORC1. When exposed to a growth stimulus, mTORC1 has been shown to associate with lysosomes, i.e. the intracellular organelles responsible for the breakdown of cellular proteins, and subsequently moving towards the cell periphery.
  This movement of lysosome-associated mTORC1 within the cell is believed to be vital for the activation of protein synthesis, as inhibition of lysosomal movement blunts mTORC1 activation in response to amino acids. Thus, dysregulation of lysosomal movement in ageing muscle may represent an underlying mechanism in the development of anabolic resistance. However, this area of research is unexplored in the context of human skeletal muscle. The investigators hypothesize that dysregulation of lysosomal movement plays a central role in the development of age-associated skeletal muscle anabolic resistance.


Eligibility: Inclusion Criteria:
  Be a non-smoking male within the specified age range for each group (young; 18-35 yrs, old; 65-75 yrs)
  Have a BMI (body mass index, body weight/height in m2) between 18 and 25 kg/m2, which is considered a normal body mass index.
  Be in good general health: no cardiovascular diseases or metabolic diseases.
  Exclusion Criteria:
  Health problems such as: heart disease , metabolic disease such as phenylketonuria, rheumatoid arthritis, uncontrolled hypertension, poor lung function, or any health condition that might put the participant at risk when participating in this study.
  Generalized neuromuscular disease (such as Parkinson's disease or motorneuron disease).
  Involvement in regular structured resistance exercise training at the time of the study.
  Consumption of any analgesic drugs, anti-inflammatory drugs, or medication that is known to affect protein metabolism (beta-blockers, corticosteroids, NSAIDs).
  Participants who have undergone muscle biopsy testing or isotope infusion procedures within the last 5 years.
  Allergic to lidocaine

Relevance to patient case: not relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: Study of 1cm Versus 2cm Margins for the Surgical Treatment of cT2N0M0 Melanoma

Summary: This is a randomized non-blinded pilot study for patients with melanoma staging cT2N0M0 who are candidates for surgical resection. The primary objective is to determine the feasibility of randomizing participants with cT2N0M0 malignant melanoma to surgical treatment with 1cm versus 2cm margins. Study will try to determine overall survival for cT2N0M0 malignant melanoma after surgical treatment with 1cm versus 2cm margins.

Detailed description: After randomization, participants will undergo surgery with wide local excision with either 1cm or 2cm margins. The margin will be based upon the previous biopsy site or area of pigmentation. The skin and subcutaneous tissue (down to fascia) will be resected. Closure considerations may require removal of additional tissue for non-oncologic purposes. As per standard of care, sentinel lymph node biopsy will be performed using a dual tracer technique (technetium radiolabeled sulfur colloid and isosulfan blue) with or without lymphoscintigraphy.

Eligibility: Inclusion Criteria:
  -  Biopsy proven T2 malignant melanoma.
  -  Eastern Cooperative Oncology Group (ECOG) score of 0-2.
  Exclusion Criteria:
  -  Visible additional disease that suggests a greater than T2 malignant melanoma
  -  Unable to tolerate general anesthesia
  -  Evidence of distant metastatic disease
  -  Melanoma located on face or digits

Relevance to patient case: not relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: Exercise Duration Models, in Middle-aged Men

Summary: Duration of exercise is an important factor among the medical guides for weight loss. However, there is still little knowledge about other its models in middle-aged and older men. The present study aimed to determine the effects of the interval training on weight loss and lipid profile, and to compare its efficiency with the continuous training.

Detailed description: Participants included sedentary men (age 45-75 years) with overweight or obesity (n= 82). They were randomly divided into two groups including continuous exercise, and interval exercise. The weight assessment parameters including change in weight and body composition, blood sample tests were performed pre- and three month post-intervention.

Eligibility: Inclusion Criteria:
  -  Sedentary lifestyle
  -  Good Health
  -  Weight stability
  Exclusion Criteria:
  Abnormality or history of Disease

Relevance to patient case: not relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: Phase 1B Study in Subjects With Small to Medium Primary Choroidal Melanoma

Summary: The primary objective is to assess the safety, immunogenicity and preliminary efficacy of a single treatment of one of two dose levels of Light-activated AU-011 for the treatment of subjects with primary choroidal melanoma.

Detailed description: This is a phase 1B open-label, single ascending dose clinical trial designed to evaluate the safety of two dose levels of Light-activated AU-011 for the treatment of subjects with small to medium primary choroidal melanoma.
  Throughout the study, subjects will be monitored through medical and ophthalmic assessments. Subjects will be followed for a total of 2 years.

Eligibility: Inclusion Criteria:
  -  Diagnosis of uveal melanoma
  Exclusion Criteria:
  -  Have known contraindications or sensitivities to the study drug

Relevance to patient case: not relevant
Patient case: 72-year-old male with melanoma; genetic feature: TP53 loss of function

Clinical trial: The LD Lync Study - Natural History Study of Genetic Lipodystrophy Syndromes

Summary: Genetic lipodystrophy syndromes are extremely rare, orphan diseases with overall estimated prevalence of less than 2,000 in the United States. These rare disorders characterized by selective loss of adipose tissue and predisposition to insulin resistance and its metabolic complications diabetes, dyslipidemia and hepatic steatosis. Due to these metabolic problems, atherosclerotic vascular disease, recurrent episodes of acute pancreatitis, cirrhosis and other morbidities complicate the lives of these patients.
  In the last few years, several genes for CGL (AGPAT2, BSCL2, CAV1 and PTRF); FPL (LMNA, PPARG, AKT2, CIDEC, LIPE, PLIN1, PCYT1A and ADRA2A); MAD (LMNA and ZMPSTE24); APS (LMNA); autoinflammatory (PSMB8); NPS (FBN1, CAV1); SHORT syndrome (PIK3R1); and MDP syndrome (POLD1) have been identified. However, there is paucity of information about the natural history of these rare syndromes, especially genotype-specific causes of morbidity and mortality.
  To overcome the problems outlined above, we propose a multicenter, collaborative, prospective, observational natural history cohort study of patients with genetic lipodystrophies. We propose to follow approximately 500 patients with genetic lipodystrophies on a yearly basis for approximately 4 years and collect robust clinical, metabolic, morbidity and mortality data.
  Medical history and patient questionnaires will be completed on a yearly basis by patients registered in the study. Clinical data such as vitals, laboratory results and anthropometric measurements will also be collected from patients' medical records if available.


Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of genetic lipodystrophy Supportive data: 1) Presence of biallelic known disease-causing variants in the genes for autosomal recessive lipodystrophy syndromes; 2) Presence of a known (or de novo loss of function) disease-causing variant in the genes for autosomal dominant lipodystrophy syndromes.
  Exclusion Criteria:
  -  HIV-infected patients with lipodystrophies
  -  Autoimmune lipodystrophy
  -  Drug-induced localized lipodystrophy

Relevance to patient case: not relevant
Patient case: 48-year-old female with melanoma; genetic feature: tumor cells with >50% membranous PD-L1 expression

Clinical trial: Detection of Melanoma Markers in Lymph Nodes or Peripheral Blood of Patients With Melanoma

Summary: RATIONALE: Diagnostic procedures may improve the ability to detect the presence or recurrence of disease.
  PURPOSE: Diagnostic trial to detect melanoma markers in the lymph nodes or peripheral blood of patients who have melanoma.

Detailed description: OBJECTIVES:
  -  Determine the feasibility of performing reverse transcriptase-polymerase chain reaction (RT-PCR) for five different tumor antigen genes using lymph node samples or peripheral blood from patients with melanoma.
  -  Determine the ability of PCR-positive lymph nodes or peripheral blood to predict relapse of disease in these patients.
  -  Determine the correlation of positive PCR results from peripheral blood with disease stage.
  OUTLINE: Lymph node biopsies or peripheral blood are obtained from patients. These specimens are examined by nested reverse transcriptase-polymerase chain reaction (RT-PCR) and analyzed for various tumor antigens.
  Patients may choose to be told the results of this testing, but the results do not influence or change the planned therapy. Brief counseling is required to discuss the results and their potential implications.
  Patients are followed for at least 2 years.
  PROJECTED ACCRUAL: A total of 30 patients for the lymph node portion and 80 patients (20 per stage of disease) for the peripheral blood portion will be accrued for this study within 3 years.

Eligibility: DISEASE CHARACTERISTICS:
  -  Clinically proven melanoma with indication to perform sentinel lymph node biopsy or elective lymph node dissection OR
  -  Histologically proven or diagnosis highly suspicious for melanoma
  PATIENT CHARACTERISTICS:
  Age:
  -  Any age
  Performance status:
  -  Not specified
  Life expectancy:
  -  Not specified
  Hematopoietic:
  -  Platelet count greater than 50,000/mm^3
  -  Hemoglobin greater than 7 g/dL
  Hepatic:
  -  PT less than 15 sec
  -  PTT less than 30 sec
  Renal:
  -  Not specified
  Other:
  -  No psychiatric illness that precludes compliance
  -  No other concurrent malignancy
  PRIOR CONCURRENT THERAPY:
  Biologic therapy
  -  Not specified
  Chemotherapy
  -  Not specified
  Endocrine therapy
  -  Not specified
  Radiotherapy
  -  Not specified
  Surgery
  -  Not specified

Relevance to patient case: not relevant
Patient case: 48-year-old female with melanoma; genetic feature: tumor cells with >50% membranous PD-L1 expression

Clinical trial: Vaccine Therapy in Treating Patients With Stage IIIB, Stage IIIC, or Stage IV Melanoma

Summary: RATIONALE: Vaccines may make the body build an immune response to kill tumor cells.
  PURPOSE: This randomized phase I/II trial is studying three different doses of a vaccine and comparing them to see how well they work in treating patients with stage IIIB, stage IIIC, or stage IV melanoma.

Detailed description: OBJECTIVES:
  -  Determine the immune response in patients with stage IIIB, IIIC, or IV melanoma treated with vaccine comprising multiple synthetic melanoma peptides, Montanide ISA-51, and sargramostim (GM-CSF).
  OUTLINE: This is a randomized study. Patients are randomized to 1 of 3 treatment arms.
  -  Arm I: Patients receive vaccine comprising low-dose multiple synthetic melanoma peptides, Montanide ISA-51, and sargramostim (GM-CSF) on days 1, 8, 15, 29, 36, and 43.
  -  Arm II: Patients receive vaccine comprising medium-dose multiple synthetic melanoma peptides, Montanide ISA-51, and GM-CSF as in arm I.
  -  Arm III: Patients receive vaccine comprising high-dose multiple synthetic melanoma peptides, Montanide ISA-51, and GM-CSF as in arm I.
  On day 22, the lymph node draining the vaccination site is removed to determine whether the immune system is responding to the vaccine.
  PROJECTED ACCRUAL: A maximum of 38 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of stage IIIB, IIIC, or IV melanoma
  -  HLA-DR1, -DR4, -DR11, -DR13, or -DR15 positive
  -  Brain metastases allowed at the discretion of the principle investigator
  PATIENT CHARACTERISTICS:
  Age
  -  18 and over
  Performance status
  -  ECOG 0-1
  Life expectancy
  -  Not specified
  Hematopoietic
  -  Absolute neutrophil count > 1,000/mm^3
  -  Platelet count > 100,000/mm ^3
  -  Hemoglobin > 9 g/dL
  Hepatic
  -  Liver function tests ≤ 2.5 times upper limit of normal (ULN)
  Renal
  -  Creatinine ≤ 1.5 times ULN
  Cardiovascular
  -  No New York Heart Association class III or IV heart disease
  Other
  -  Prior diagnosis of other cancer allowed
  -  Not pregnant or nursing
  -  Weight ≥ 110 pounds
  -  No uncontrolled diabetes
  PRIOR CONCURRENT THERAPY:
  Biologic therapy
  -  More than 4 weeks since prior growth factors
  -  More than 4 weeks since prior allergy shots
  -  More than 12 weeks since prior melanoma vaccine therapy* NOTE: *Prior melanoma vaccine allowed only for patients with disease progression during or after administration of the vaccine
  -  No prior vaccination with any of the peptides used in this study
  Chemotherapy
  -  More than 4 weeks since prior chemotherapy
  Endocrine therapy
  -  More than 4 weeks since prior steroids
  Radiotherapy
  -  More than 4 weeks since prior radiotherapy
  Surgery
  -  Not specified
  Other
  -  More than 1 month since prior investigational drugs or therapies
  -  No other concurrent investigational drugs or therapies

Relevance to patient case: not relevant
Patient case: 48-year-old female with melanoma; genetic feature: tumor cells with >50% membranous PD-L1 expression

Clinical trial: Universal Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF)-Producing and CD40L Expressing Bystander Cell Line for Tumor Vaccine in Melanoma

Summary: The purpose of this study is to find out what effects (good and/or bad) this new cancer vaccine has on the patient and their cancer, whether it is safe and whether it can help get rid of their cancer (malignant melanoma). We want to check how the patient's immune system reacts, both before and after the vaccine treatment.

Detailed description: The vaccine will be made by mixing two kinds of cells: 1) some of the patient's own malignant melanoma cells which were removed by surgery and then processed in the Cell Therapy Laboratory, and 2) experimental "bystander" cells. All the cells in the vaccine will be treated with high-dose X-rays to make sure that none of them grow and cause more cancer. The bystander cells, called "GM.CD40L", are human cells that have been genetically changed. The original cells, called K562, had the genes for human GM-CSF and CD40L inserted into them. These changes are designed to help boost the patient's immune system to better fight the cancer in their body.

Eligibility: Inclusion Criteria:
  -  Histologically confirmed stage IIIC or stage IV melanoma
  -  Measurable disease
  -  Age 18 or older
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1
  -  No radiation therapy within 2 weeks prior to first vaccine administration
  -  No chemotherapy within 4 weeks prior to first vaccine administration
  -  No steroid therapy within 4 weeks prior to first vaccine administration
  -  No surgery within 10 days prior to first vaccine administration
  -  Patient's written informed consent
  -  Patient's ability to comply with the visit schedule and assessments required by the protocol
  -  Adequate organ function (measured within a week of beginning treatment):
  -  White blood count (WBC) > 3,000/mm^3 and absolute neutrophil count (ANC) >1500/mm^3
  -  Platelets > 100,000/mm^3
  -  Hematocrit > 25% and Hgb > 8 g/dL
  -  Bilirubin < 2.0 mg/dL
  -  Creatinine < 2.0 mg/dL, or creatinine clearance > 60 mL/min
  Exclusion Criteria:
  -  Symptomatic or untreated brain metastasis
  -  Any serious ongoing infection
  -  Current corticosteroid or other immunosuppressive therapy
  -  Any other pre-existing immunodeficiency condition (including known HIV infection)
  -  Pregnant or lactating women -- Patients in reproductive age must agree to use contraceptive methods for the duration of the study (*A pregnancy test will be obtained before treatment)
  -  ECOG performance status of 2, 3, or 4
  -  Any second active primary cancer

Relevance to patient case: not relevant
Patient case: 48-year-old female with melanoma; genetic feature: tumor cells with >50% membranous PD-L1 expression

Clinical trial: Anti-Tumor Activity Of SB-485232 In Patients With Previously Untreated Metastatic Melanoma

Summary: This Phase II study is designed to evaluate the anti-tumor activity of three dose groups of SB-485232 (0.01, 0.1, and 1.0 mg/kg/day) administered intravenously as a single agent in subjects with previously untreated metastatic melanoma.


Eligibility: Inclusion criteria:
  -  Patients must have melanoma that has spread beyond the original location and has not yet been treated.
  -  Tissue from the spreading melanoma should have been tested to confirm it is melanoma.
  Exclusion criteria:
  -  Patients having hepatitis or HIV infection.
  -  Taking corticosteroids.
  -  Patients with the primary site being occular melanoma or patients with melanoma of the brain.

Relevance to patient case: not relevant
Patient case: 48-year-old female with melanoma; genetic feature: tumor cells with >50% membranous PD-L1 expression

Clinical trial: Survivin Peptide Vaccination for Patients With Advanced Melanoma, Pancreatic, Colon and Cervical Cancer

Summary: This study evaluates the safety, the immunological response and the clinical outcome of a vaccination with survivin peptides for patients with advanced melanoma, pancreatic, colon and cervical carcinoma.

Detailed description: As prognosis of advanced melanoma, pancreatic, colon and cervical cancer remains gloomy, new therapeutic modalities have to be developed to improve the patient´s clinical outcome. Immunotherapy, which targets tumor associated antigens of tumor cells or tumor stroma, is currently an intensively investigated, novel therapeutic option. As survivin is expressed both by neoplastic cells as well as by endothelial cells of the tumor vasculature, this antigen is an intriguing target molecule. Spontaneous cytotoxic T-cell responses against different survivin epitopes in cancer patients underline the relevance of survivin-directed immunological trials. This study is comprised of a peptide vaccine with HLA-A1, -A2 and -B35 restricted survivin epitopes in Montanide ISA-51 for patients with stage IV melanoma, advanced pancreatic, colon and cervical carcinoma. The vaccine is applicated as a deep subcutaneous injection. Vaccination is administered for the first 2 months weekly, afterwards every 4 weeks. Standard staging examinations are performed every three months. Clinical, laboratory and immunological monitoring is done every month.Diagnostic leucapheresis is performed before first vaccination and afterwards every 2 months.

Eligibility: Inclusion Criteria:
  -  Advanced melanoma, pancreatic, colon and cervical cancer
  -  At least 1 prior postoperative conventional therapy (chemotherapy, radiation, immunotherapy)
  -  HLA-A1, -A2, -B35
  -  More than 4 weeks since last chemo-, immune- or radiotherapy
  -  ECOG-PS (Eastern Cooperative Oncology Group- Performance Status) of 0-1
  -  Sufficient renal, hepatic and bone marrow function: thrombocytes > 75.000/ul; hb > 9 g/dl; leucocytes > 2.500/ul; creatinine < 2 mg/dl; GOT/GPT < twice the normal value
  -  negative for HIV and Hbs
  -  Older than 18 years
  -  Informed consent
  Exclusion Criteria:
  -  Acute/chronic infections
  -  Positive for HIV, Hbs
  -  Autoimmune disorders
  -  Pregnancy, breast feeding

Relevance to patient case: not relevant
Patient case: 48-year-old female with melanoma; genetic feature: tumor cells with >50% membranous PD-L1 expression

Clinical trial: Immunotherapy of Stage III/IV Melanoma Patients

Summary: The purpose of this study is to determine whether vaccination with melanoma antigen peptides [Melan-A/Mart-1 (both EAA and ELA), NY-ESO-1b analog, Long NY-ESO-1 LP and MAGE-A10] and Montanide, CpG adjuvants and low dose rIL-2 can induce an immune response in melanoma patients and to assess the safety of this vaccination.

Detailed description: Current peptide vaccines suffer from low efficiency, since they induce only weak immune activation. We have recently confirmed that in humans the immune response was readily detectable in local lymph nodes while no or only weak activation could be identified in circulating lymphocytes. Increased doses of antigen and adjuvant allow a better extension from local to systemic immune responses.
  -  Group 1 : vaccination with Melan-A analog (ELA) peptide + Montanide
  -  Group 2 : vaccination with Melan-A analog (ELA), NY-ESO-1b analog and MAGE-A10 peptides + Montanide
  -  Group 3: vaccination with Melan-A analog (both EAA and ELA), Mage-A10, NY-ESO-1 peptides+ Montanide + CpG adjuvant
  -  Group 4: vaccination with Melan-A (ELA), Mage-A10,long NY-ESO-1LP peptides + Montanide + CpG
  -  Group 5: vaccination with Melan-A(both EAA and ELA), Mage-A10, long NY-ESO-1 LP peptides + Montanide + CpG + low dose rIL-2

Eligibility: Inclusion Criteria:
  -  Histologically confirmed stage III or stage IV melanoma
  -  Tumor expression of Melan-A +/- one of the tumor antigens MAGE-A10, NY-ESO-1, or LAGE-1
  -  Human leukocyte antigen-A2 (HLA-A2) positive
  Exclusion Criteria:
  -  Clinically significant heart disease
  -  Serious illnesses, eg, serious infections requiring antibiotics, uncontrolled peptic ulcer, or central nervous system disorders
  -  History of immunodeficiency disease or autoimmune disease
  -  Coagulation or bleeding disorders

Relevance to patient case: not relevant
Patient case: 48-year-old female with melanoma; genetic feature: tumor cells with >50% membranous PD-L1 expression

Clinical trial: Safety and Efficacy Study of INGN 241 Gene Therapy in Patients With In Transit Melanoma

Summary: This is a research study to look at the ways in which a treatment called INGN241 can kill melanoma cells or help the patient's immune system kill melanoma cells.

Detailed description: INGN 241 is an adenoviral vector carrying the MDA-7 cDNA. MDA-7 is a novel tumor suppressor molecule with cytokine properties, recently designated as IL-24. Over expression of MDA-7 in melanoma cells in vitro has been shown to inhibit cellular proliferation and induce apoptosis. Loss of MDA-7 expression in human melanomas has been shown to correlate with invasion and metastasis. The INGN 241 gene transfer construct has been previously used in human subjects in an ongoing open label Phase I study using intratumoral administration, and has been well tolerated to date. The primary objectives of the present study are to determine if INGN 241, injected into a melanoma in transit lesion, can induce apoptosis in regional uninjected lesions and initiate systemic immune activation. Secondary objectives include examination of specific immunity and of clinical response and toxicity.

Eligibility: Inclusion Criteria:
  -  Histologically proven melanoma, must have 3 regional metastatic lesions that are in transit
  Exclusion Criteria:
  -  Central nervous system involvement by melanoma

Relevance to patient case: not relevant