The authors would like to thank Dr Rita Shaknovich and members of Elemento lab, Melnick lab, and Tam lab for thoughtful discussions. We would also like to thank the Genomics Resources Core Facility at Weill Cornell Medical College for performing the VDJ-sequencing. YJ was supported by ASH Scholar Award. WT and OE are supported by Weill Cornell Cancer Center Pilot Grant. OE is supported by the NSF CAREER award, the Starr Cancer Consortium and the Hirschl Trust. We would also like to thank Katherine Benesch, JD, MPH for her generous support to this project.

<ol>
	<li>Nowell, P. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+clonal+evolution+of+tumor+cell+populations.">The clonal evolution of tumor cell populations.</a> Science. 194 (4260), 23-28 (1976).</li><li>Greaves, M., Maley, C. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clonal+evolution+in+cancer.">Clonal evolution in cancer.</a> Nature. 481 (7381), 306-313 (2012).</li><li>Ding, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clonal+evolution+in+relapsed+acute+myeloid+leukaemia+revealed+by+whole-genome+sequencing.">Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing.</a> Nature. 481 (7382), 506-510 (2012).</li><li>Jiao, W., Vembu, S., Deshwar, A. G., Stein, L., Morris, Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inferring+clonal+evolution+of+tumors+from+single+nucleotide+somatic+mutations.">Inferring clonal evolution of tumors from single nucleotide somatic mutations.</a> BMC bioinformatics. 15, 35 (2014).</li><li>Schatz, D. G., Ji, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recombination+centres+and+the+orchestration+of+V(D)J+recombination.">Recombination centres and the orchestration of V(D)J recombination.</a> Nature reviews immunology. 11 (4), 251-263 (2011).</li><li>Jacob, J., Kelsoe, G., Rajewsky, K., Weiss, U. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intraclonal+generation+of+antibody+mutants+in+germinal+centres.">Intraclonal generation of antibody mutants in germinal centres.</a> Nature. 354 (6352), 389-392 (1991).</li><li>Coiffier, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CHOP+chemotherapy+plus+rituximab+compared+with+CHOP+alone+in+elderly+patients+with+diffuse+large-B-cell+lymphoma.">CHOP chemotherapy plus rituximab compared with CHOP alone in elderly patients with diffuse large-B-cell lymphoma.</a> N Engl J Med. 346 (4), 235-242 (2002).</li><li>Larouche, J. F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lymphoma+recurrence+5+years+or+later+following+diffuse+large+B-cell+lymphoma:+clinical+characteristics+and+outcome.">Lymphoma recurrence 5 years or later following diffuse large B-cell lymphoma: clinical characteristics and outcome.</a> J Clin Oncol. 28 (12), 2094-2100 (2010).</li><li>Friedberg, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relapsed/refractory+diffuse+large+B-cell+lymphoma.">Relapsed/refractory diffuse large B-cell lymphoma.</a> Hematology Am Soc Hematol Educ Program. 2011, 498-505 (2011).</li><li>Gisselbrecht, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Salvage+regimens+with+autologous+transplantation+for+relapsed+large+B-cell+lymphoma+in+the+rituximab+era.">Salvage regimens with autologous transplantation for relapsed large B-cell lymphoma in the rituximab era.</a> J Clin Oncol. 28 (27), 4184-4190 (2010).</li><li>Lefranc, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IMGT,+the+International+ImMunoGeneTics+Information+System+for+Immunoinformatics+:+methods+for+querying+IMGT+databases,+tools,+and+web+resources+in+the+context+of+immunoinformatics.">IMGT, the International ImMunoGeneTics Information System for Immunoinformatics : methods for querying IMGT databases, tools, and web resources in the context of immunoinformatics.</a> Molecular biotechnology. 40 (1), 101-111 (2008).</li><li>Jiang, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deep+sequencing+reveals+clonal+evolution+patterns+and+mutation+events+associated+with+relapse+in+B-cell+lymphomas.">Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas.</a> Genome biology. 15 (8), 432 (2014).</li><li>Hanna, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+reprogramming+of+terminally+differentiated+mature+B+lymphocytes+to+pluripotency.">Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency.</a> Cell. 133 (2), 250-264 (2008).</li></ol>

The authors have no conflicts of interest to disclose.

בגלל המספר כמעט בלתי מוגבל של חזרות של רצף מידע המקודד על ידי סידור מחדש VDJ וSHM במוקד IGH של תאי B אנושיים, בדיקה של כל רפרטואר IGH ידי תפוקה גבוהה עמוק רצף הוכיחה להיות דרך יעילה ומקיפה להתוות משובט ואוכלוסיות B-תא תת-משובטים. יתר על כן, אסטרטגיה זו יכולה לשמש כדי לחקור את נ?...

הסרטן הוא מחלה משובט. מאז לפני שלושים שנה, כאשר פיטר ג Nowell הציע מודל התפתחות הסרטן המשובט 1, מחקרים רבים ניסו לנתח אוכלוסיות משובטים בתוך דגימות גידול ולשחזר דפוסי התרחבות והתפתחות משובטים העומדים בבסיס תהליך יצירת הגידולים 2. לאחרונה, רצף הגנום אפשר חוקרים ליסתכל עמוק בהטרוגניות והאבולוציה 3,4 המשובטים. עם זאת, בשל חוסר סמנים צייתן בסוגי תאים רבים, קשה להסיק ארכיטקטורה משובט המדויקת ומסלול האבולוציוני. למרבה המזל, יש סמן clonality טבעי בתאי B הבוגרים ממנו רבות ממאירות הלימפה, כולל DLBCL, מקורן. בתגובה לגירוי אנטיגן, כל תא B יכול ליצור רצף IGH VDJ יחיד יצרני על ידי הצטרפות H V (משתנה), D (גיוון), וH J (הצטרפות) קטע יחד ממאגר גדול של מגזרים אלו. במהלך יחסי ציבור זהocess, מנות קטנות של הרצף המקורי עשויים להימחק ונוקלאוטידים שאינן בתבניות נוספות ניתן להוסיף ליצור סידור מחדש VDJ ייחודי. סידור מחדש VDJ ספציפי זה יכול להיות בירושה בכל הצאצאים של תאי B זה, ולכן תיוג B-תא בוגר פרט וצאצאיה 5. יתר על כן, SHM מתרחש על רצפי VDJ recombined בתגובה הבאה מרכז נבטי (GC) להציג מוטציות נוספות להרחבת בריכת הנוגדן ושיפור של זיקת נוגדן 6. לכן, על ידי השוואה והנגדה דפוסים של דגימות לימפומה שעברו תהליכים אלה VDJ וSHM, ההטרוגניות תוך גידול יכולה להיות שמסומן ונתיב התפתחות משובט של המחלה ניתן ללמוד. בעבר, סידור מחדש VDJ וSHM יכולים להיות מזוהה על ידי PCR הגברת אזורי recombined, שיבוט מוצרי ה- PCR, ולאחר מכן רצף סנגר לקבל מידע רצף. אני גישה זוזה נמוך תפוקה ותשואה נמוכה, אחזור רק חלק קטן מרפרטואר VDJ recombined כל, ומעכב את האפיון של הייצוג הכולל של האוכלוסייה המשובט בתוך מדגם נתון. גישה שונה נוצרה על ידי יצירת אינדקס NGS ספריות רצף ממוצרי VDJ PCR וביצוע רצף נ&quot;ב 2x150 PE להשיג יותר מחצי מיליון רצפי VDJ recombined לדגימה. בנוסף, צינור מותאם אישית פותח כדי לבצע בקרת איכות (QC), ליישר, רצף VDJ המסנן קורא לזהות rearrangements וSHMs של כל קריאה, ולבצע ניתוח פילוגנטי על הארכיטקטורה המשובט של כל דגימה. בנוסף, גישה חדשה הוקמה כדי להמשיך ולאפיין את דפוסי התפתחות המשובטים לדגימות שנאספו בשלבי מחלה שונים. יש לנו ליישם את הטכניקה הזו לדגימות חולה DLBCL. DLBCL הוא צורה אגרסיבית של לימפומה שאינה הודג&#39;קין עם הישנות תכופה בה עד אחדIRD של החולים 7. התקפי DLBCL בדרך כלל להתרחש מוקדם, בתוך 2 עד 3 שנים של האבחון הראשוני, למרות שחלקם מתרחש לאחר 5 שנים 8. הפרוגנוזה של חולי הישנות היא עניה, עם רק 10% השיג 3 שנות הישרדות ללא התקדמות מחלה בשל אפשרויות טיפול מוגבלות. זהו הבסיס לצורך הדחוף בגישות חדשות לטיפול בהישנות DLBCL 9,10. עם זאת, מנגנונים מולקולריים הקשורים בהישנות DLBCL עדיין במידה רבה לא ידועים. במיוחד, התפקיד של ההטרוגניות משובט באבחון ואבולוציה משובט במהלך פיתוח הישנות DLBCL הוא כיום uncharacterized, ולכן קשה להגדיר סמן ביולוגי מדויק ושימושי לחזות הישנות. כדי לענות על שאלות אלה, יישמנו גישת VDJ-הרצף שלנו בזוגות רבים של זוגות מדגם DLBCL אבחון הישנות ראשונית מתאימים. שני תרחישים האבולוציונית משובטים מובהקים של הישנות יצאו מההשוואה של הארכיטקטורות המשובטים בין האבחון וSAMP הישנותles שמציע מנגנונים מולקולריים מרובים עשוי להיות מעורב בהישנות DLBCL.

<table border="0" cellpadding="0" cellspacing="0" width="841">
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		<tr height="60">
			<td height="60" style="height:60px;width:359px;">Ethanol</td>
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			<td>VWR</td>
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			<td>500 ml</td>
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			<td>100 mg</td>
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			<td height="40" style="height:40px;width:359px;">Deoxynucleotide triphosphate (dNTP) Solution Mix</td>
			<td>Promega</td>
			<td style="width:123px;">U1515</td>
			<td style="width:197px;">10 mM each nucleotide</td>
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			<td height="20" style="height:20px;">10x PCR Buffer&#160;</td>
			<td>Roche</td>
			<td>11699105001</td>
			<td>Without MgCl2</td>
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			<td height="46" style="height:46px;width:359px;">AmpliTaq Gold DNA Polymerase with Gold Buffer and MgCl2</td>
			<td style="width:163px;">Life Technonogies</td>
			<td style="width:123px;">4311806</td>
			<td>50 &#181;l at 5 U/&#181;l</td>
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			<td>2-096-0020</td>
			<td>33 reactions</td>
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			<td height="80" style="height:80px;width:359px;">IGH Somatic Hypermutation Assay v2.0 - Gel Detection</td>
			<td style="width:163px;">Invivoscribe Technologies&#160;</td>
			<td style="width:123px;">5-101-0030</td>
			<td style="width:197px;">33 reactions, Mix 2 for IGVHFR1 detection</td>
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			<td style="width:163px;">Invivoscribe Technologies&#160;</td>
			<td>1-101-0020</td>
			<td style="width:197px;">33 reactions, Tube B for IGVHFR2 detection</td>
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			<td height="20" style="height:20px;">GoTaq Flexi DNA Polymerase</td>
			<td>Promega</td>
			<td style="width:123px;">M8291</td>
			<td>20 &#181;l at 5 U/&#181;l</td>
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			<td height="20" style="height:20px;">10X Tris-Borate-EDTA (TBE) buffer</td>
			<td>Corning (cellgro)</td>
			<td style="width:123px;">46-011-CM</td>
			<td style="width:197px;">6x1 L</td>
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			<td height="20" style="height:20px;">50X TAE BUFFER&#160;&#160;</td>
			<td>VWR</td>
			<td>101414-298</td>
			<td style="width:197px;">1 L</td>
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			<td height="20" style="height:20px;">Ethidium bromide solution</td>
			<td>Sigma-Aldrich</td>
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			<td style="width:197px;">10 mg/ml</td>
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			<td height="40" style="height:40px;">25 bp DNA Ladder</td>
			<td>Life Technologies</td>
			<td>10597011</td>
			<td style="width:197px;">1 &#181;g/&#181;l</td>
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			<td height="20" style="height:20px;">100 bp DNA Ladder</td>
			<td>Life Technologies</td>
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			<td>Life Technologies</td>
			<td>16500-500</td>
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			<td>Bio-Rad Laboratories</td>
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			<td height="40" style="height:40px;">QIAquick Gel Extraction Kit</td>
			<td>Qiagen</td>
			<td>28704</td>
			<td style="width:197px;">50 columns</td>
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		<tr height="60">
			<td height="60" style="height:60px;width:359px;">Agencourt AMPure XP</td>
			<td style="width:163px;">Beckman Coulter</td>
			<td style="width:123px;">A63881</td>
			<td style="width:197px;"></td>
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			<td height="20" style="height:20px;width:359px;">Qubit dsDNA High Sensitivity Assay Kit</td>
			<td style="width:163px;">Life Technologies</td>
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			<td height="40" style="height:40px;width:359px;">High Sensitivity DNA Kit</td>
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			<td height="20" style="height:20px;width:359px;">PhiX Control v3</td>
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			<td height="20" style="height:20px;width:359px;">MiSeq</td>
			<td style="width:163px;">Illumina</td>
			<td></td>
			<td style="width:197px;"></td>
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			<td height="20" style="height:20px;">Qubit 2.0 Fluorometer</td>
			<td>Life Technologies</td>
			<td>Q32872</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:359px;">Resuspension buffer (Illumina TruSeq DNA Sample Preparation Kit v2)</td>
			<td style="width:163px;">Illumina</td>
			<td>FC-121-2001</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:359px;">End repair mix (Illumina TruSeq DNA Sample Preparation Kit v2)</td>
			<td style="width:163px;">Illumina</td>
			<td>FC-121-2001</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:359px;">A-tailing mix (Illumina TruSeq DNA Sample Preparation Kit v2)</td>
			<td style="width:163px;">Illumina</td>
			<td>FC-121-2001</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:359px;">Ligation mix (Illumina TruSeq DNA Sample Preparation Kit v2)</td>
			<td style="width:163px;">Illumina</td>
			<td>FC-121-2001</td>
			<td style="width:197px;"></td>
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		<tr height="60">
			<td height="60" style="height:60px;width:359px;">DNA adaptor index (Illumina TruSeq DNA Sample Preparation Kit v2)</td>
			<td style="width:163px;">Illumina</td>
			<td>FC-121-2001</td>
			<td style="width:197px;"></td>
		</tr>
		<tr height="60">
			<td height="60" style="height:60px;width:359px;">Stop ligation buffer (Illumina TruSeq DNA Sample Preparation Kit v2)</td>
			<td style="width:163px;">Illumina</td>
			<td>FC-121-2001</td>
			<td style="width:197px;"></td>
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		<tr height="60">
			<td height="60" style="height:60px;width:359px;">PCR primer cocktail (Illumina TruSeq DNA Sample Preparation Kit v2)</td>
			<td style="width:163px;">Illumina</td>
			<td>FC-121-2001</td>
			<td style="width:197px;"></td>
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			<td style="width:163px;">Illumina</td>
			<td>FC-121-2001</td>
			<td style="width:197px;"></td>
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			<td align="right">4457858</td>
			<td></td>
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			<td>170-8370</td>
			<td></td>
		</tr>
	</tbody>
</table>

vdj-seq: deep sequencing analysis of rearranged immunoglobulin heavy chain gene to reveal clonal evolution patterns of b cell lymphoma

clonality גידול הבנה הוא קריטי להבנת המנגנונים המעורבים בהתקדמות tumorigenesis ומחלה. בנוסף, הבנת שינויי ההרכב המשובטים המתרחשים בתוך גידול בתגובה למייקרו-סביבה או טיפולים מסוימים עלולה להוביל לעיצוב של גישות יותר מתוחכמות ויעילות למיגור תאים סרטניים. עם זאת, תת-אוכלוסיות משובטים גידול מעקב היו מאתגרות בשל חוסר הסמנים להבחין. כדי לטפל בבעיה זו, פרוטוקול VDJ-seq נוצר כדי להתחקות אחרים דפוסי התפתחות המשובטים של לימפומה B תא הגדולה הישנות מפוזרת (DLBCL) על ידי ניצול רקומבינציה VDJ וhypermutation הגופני (SHM), שתי תכונות ייחודיות של לימפומות תאי B. בפרוטוקול זה, ספריות רצף של הדור הבא (NGS) עם פוטנציאל לאינדקס נבנו משרשרת מוגברת אימונוגלובולינים מחדש כבדה (IGH) אזור VDJ מזוגות של אבחון ראשוני וSAMP DLBCL הישנותles. על יותר מממוצע חצי מיליון רצפי VDJ למדגם התקבלו לאחר רצף, המכיל שני VDJ התארגנות ומידע SHM. בנוסף, צינורות ביואינפורמטיקה מותאמים אישית פותחו לנצל מידע רצף לאפיון של רפרטואר IGH-VDJ בתוך דגימות אלה באופן מלא. יתר על כן, הצינור מאפשר שחזור והשוואה של הארכיטקטורה המשובט של גידולים בודדים, המאפשרת הבחינה של ההטרוגניות המשובט בתוך גידולי האבחון וניכוי דפוסי התפתחות משובטים בין האבחון וזוגות גידול הישנות. כאשר מיישמים את הניתוח הזה לכמה זוגות אבחון הישנות, אנחנו חשפנו ראיות מרכזיות שדפוסים אבולוציוניים גידול ייחודי מרובים עלולים להוביל לנסיגת DLBCL. בנוסף, גישה זו יכולה להיות מורחבת להיבטים קליניים אחרים, כגון זיהוי של מחלה שיורית מינימאלית, מעקב אחר התקדמות הישנות ותגובה לטיפול, וחקירה של רפרטואר חיסוניes בהקשרים שאינם לימפומה.

ההליך הכולל של רצף VDJ (VDJ-seq), כולל מיצוי DNA, recombined הגברה VDJ אזור וטיהור, בניית ספריית רצף, קורא עיבוד, וניתוח פילוגנטי, מיוצג באיור 1. באופן שגרתי 5-200 מיקרוגרם DNA יכול להאסף מ חלקים קפואים רקמות מוצקות או 0.5-20 מיקרוגרם DNA מסעיפי רקמות מוטבע פרפין-קבוע פורמלין. בהתאם ?...

Watch this Scientific Journal Video about VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma at JoVE.com

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

This protocol describes an approach to interrogate the recombined immunoglobulin heavy chain VDJ regions of lymphomas by deep-sequencing and retrieve VDJ rearrangement and somatic hypermutation status to delineate clonal architecture of individual tumor. Comparing clonal architecture between paired diagnosis and relapse samples reveals lymphoma relapse clonal evolution modes.

VDJ-Seq: ניתוח רצף עמוק של ג&#39;ין שרשרת מחדש Immunoglobulin כבד לחשוף את דפוסים משובטים אבולוציה של לימפומה B הסלולרי

Understanding tumor clonality is critical to understanding the mechanisms involved in tumorigenesis and disease progression. In addition, understanding ...

vdj-seq-deep-sequencing-analysis-rearranged-immunoglobulin-heavy

Research

JoVE Journal

Medicine

26.5K Views.  Weill Cornell Medical College. This protocol describes an approach to interrogate the recombined immunoglobulin heavy chain VDJ regions of lymphomas by deep-sequencing and retrieve VDJ rearrangement and somatic hypermutation status to delineate clonal architecture of individual tumor. Comparing clonal architecture between paired diagnosis and relapse samples reveals lymphoma relapse clonal evolution modes. 

Video: VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Dissection of Human Vitreous Body Elements for Proteomic Analysis

The vitreous is an optically clear, collagenous extracellular matrix that fills the inside of the eye and overlies the retina. 1,2 Abnormal interactions between vitreous substructures and the retina underlie several vitreoretinal diseases, including retinal tear and detachment, macular pucker, macular hole, age-related macular degeneration, vitreomacular traction, proliferative vitreoretinopathy, proliferative diabetic retinopathy, and inherited vitreoretinopathies. 1,2 The molecular composition of the vitreous substructures is not known. Since the vitreous body is transparent with limited surgical access, it has been difficult to study its substructures at the molecular level. We developed a method to separate and preserve these tissues for proteomic and biochemical analysis. The dissection technique in this experimental video shows how to isolate vitreous base, anterior hyaloid, vitreous core, and vitreous cortex from postmortem human eyes. One-dimensional SDS-PAGE analyses of each vitreous component showed that our dissection technique resulted in four unique protein profiles corresponding to each substructure of the human vitreous body. Identification of differentially compartmentalized proteins will reveal candidate molecules underlying various vitreoretinal diseases.

This video shows an effective technique for differentiating and dissecting the various semi-transparent structures of the human vitreous body in post mortem eyes.

Dissection של גוף האדם אלמנטים הזגוגיות לניתוח proteomic

The vitreous is an optically clear, collagenous extracellular matrix that fills the inside of the eye and overlies the retina. 1,2 Abnormal interactions ...

Establishment and Propagation of Human Retinoblastoma Tumors in Immune Deficient Mice

Culturing retinoblastoma tumor cells in defined stem cell media gives rise to primary tumorspheres that can be grown and maintained for only a limited time. These cultured tumorspheres may exhibit markedly different cellular phenotypes when compared to the original tumors. Demonstration that cultured cells have the capability of forming new tumors is important to ensure that cultured cells model the biology of the original tumor. 
Here we present a protocol for propagating human retinoblastoma tumors in vivo using Rag2-/- immune deficient mice. Cultured human retinoblastoma tumorspheres of low passage or cells obtained from freshly harvested human retinoblastoma tumors injected directly into the vitreous cavity of murine eyes form tumors within 2-4 weeks. These tumors can be harvested and either further passaged into murine eyes in vivo or grown as tumorspheres in vitro. Propagation has been successfully carried out for at least three passages thus establishing a continuing source of human retinoblastoma tissue for further experimentation. 
Wesley S. Bond and Lalita Wadhwa are co-first authors.

A method is described to propagate human retinoblastoma tumors in mice. Tumor cells are directly injected into the eyes of immune deficient mice. Secondary tumors have been successfully established using both cells directly harvested from human tumors and cultured tumorspheres.

הקמה התפשטות של גידולים רטינובלסטומה האדם עכברים החיסון לקויה

Culturing retinoblastoma tumor cells in defined stem cell media gives rise to primary tumorspheres that can be grown and maintained for only a limited ...

Production and Detection of Reactive Oxygen Species (ROS) in Cancers

Reactive oxygen species include a number of molecules that damage DNA and RNA and oxidize proteins and lipids (lipid peroxydation). These reactive molecules contain an oxygen and include H2O2 (hydrogen peroxide), NO (nitric oxide), O2- (oxide anion), peroxynitrite (ONOO-), hydrochlorous acid (HOCl), and hydroxyl radical (OH-).
Oxidative species are produced not only under pathological situations (cancers, ischemic/reperfusion, neurologic and cardiovascular pathologies, infectious diseases, inflammatory diseases 1, autoimmune diseases 2, etc&hellip;) but also during physiological (non-pathological) situations such as cellular metabolism 3, 4. Indeed, ROS play important roles in many cellular signaling pathways (proliferation, cell activation 5, 6, migration 7 etc..). ROS can be detrimental (it is then referred to as "oxidative and nitrosative stress") when produced in high amounts in the intracellular compartments and cells generally respond to ROS by upregulating antioxidants such as superoxide dismutase (SOD) and catalase (CAT), glutathione peroxidase (GPx) and glutathione (GSH) that protects them by converting dangerous free radicals to harmless molecules (i.e. water). Vitamins C and E have also been described as ROS scavengers (antioxidants).
Free radicals are beneficial in low amounts 3. Macrophage and neutrophils-mediated immune responses involve the production and release of NO, which inhibits viruses, pathogens and tumor proliferation 8. NO also reacts with other ROS and thus, also has a role as a detoxifier (ROS scavenger). Finally NO acts on vessels to regulate blood flow which is important for the adaptation of muscle to prolonged exercise 9, 10. Several publications have also demonstrated that ROS are involved in insulin sensitivity 11, 12.
Numerous methods to evaluate ROS production are available. In this article we propose several simple, fast, and affordable assays; these assays have been validated by many publications and are routinely used to detect ROS or its effects in mammalian cells. While some of these assays detect multiple ROS, others detect only a single ROS.

Production and Detection of Reactive Oxygen Species ROS in Cancers

Here we propose simple methods to test and evaluate the presence of reactive oxygen species in cells.

הפקה וזיהוי של מינים חמצן תגובתי (ROS) סרטן

Reactive oxygen species include a number of molecules that damage DNA and RNA and oxidize proteins and lipids (lipid peroxydation). These reactive ...

DNA Vector-based RNA Interference to Study Gene Function in Cancer

RNA interference (RNAi) inhibits gene expression by specifically degrading target mRNAs. Since the discovery of double-stranded small interference RNA (siRNA) in gene silencing1, RNAi has become a powerful research tool in gene function studies. Compared to genetic deletion, RNAi-mediated gene silencing possesses many advantages, such as the ease with which it is carried out and its suitability to most cell lines. Multiple studies have demonstrated the applications of RNAi technology in cancer research. In particular, the development of the DNA vector-based technology to produce small hairpin RNA (shRNA) driven by the U6 or H1 promoter has made long term and inducible gene silencing possible2,3. Its use in combination with genetically engineered viral vectors, such as lentivirus, facilitates high efficiencies of shRNA delivery and/or integration into genomic DNA for stable shRNA expression. 
We describe a detailed procedure using the DNA vector-based RNAi technology to determine gene function, including construction of lentiviral vectors expressing shRNA, lentivirus production and cell infection, and functional studies using a mouse xenograft model. 
Various strategies have been reported in generating shRNA constructs. The protocol described here employing PCR amplification and a 3-fragment ligation can be used to directly and efficiently generate shRNA-containing lentiviral constructs without leaving any extra nucleotide adjacent to a shRNA coding sequence. Since the shRNA-expression cassettes created by this strategy can be cut out by restriction enzymes, they can be easily moved to other vectors with different fluorescent or antibiotic markers. Most commercial transfection reagents can be used in lentivirus production. However, in this report, we provide an economic method using calcium phosphate precipitation that can achieve over 90% transfection efficiency in 293T cells. Compared to constitutive shRNA expression vectors, an inducible shRNA system is particularly suitable to knocking down a gene essential to cell proliferation. We demonstrate the gene silencing of Yin Yang 1 (YY1), a potential oncogene in breast cancer4,5, by a Tet-On inducible shRNA system and its effects on tumor formation. Research using lentivirus requires review and approval of a biosafety protocol by the Biosafety Committee of a researcher's institution. Research using animal models requires review and approval of an animal protocol by the Animal Care and Use Committee (ACUC) of a researcher's institution.

RNA interference (RNAi) possesses many advantages over gene knockout and has been broadly used as a tool in gene functional studies. The invention of DNA vector-based RNAi technology has made long term and inducible gene knockdown possible, and also increased the feasibility of gene silencing in vivo.

וקטור מבוסס DNA התערבות RNA ללמוד לתפקד גנים סרטן

RNA interference (RNAi) inhibits gene expression by specifically degrading target mRNAs. Since the discovery of double-stranded small interference RNA ...

Deep Neuromuscular Blockade Leads to a Larger Intraabdominal Volume During Laparoscopy

Shoulder pain is a commonly reported symptom following laparoscopic procedures such as myomectomy or hysterectomy, and recent studies have shown that lowering the insufflation pressure during surgery may reduce the risk of post-operative pain. In this pilot study, a method is presented for measuring the intra-abdominal space available to the surgeon during laproscopy, in order to examine whether the relaxation produced by deep neuromuscular blockade can increase the working surgical space sufficiently to permit a reduction in the CO2 insufflation pressure. Using the laproscopic grasper, the distance from the promontory to the skin is measured at two different insufflation pressures: 8 mm Hg and 12 mm Hg. After the initial measurements, a neuromuscular blocking agent (rocuronium) is administered to the patient and the intra-abdominal volume is measured again. Pilot data collected from 15 patients shows that the intra-abdominal space at 8 mm Hg with blockade is comparable to the intra-abdominal space measured at 12 mm Hg without blockade. The impact of neuromuscular blockade was not correlated with patient height, weight, BMI, and age. Thus, using neuromuscular blockade to maintain a steady volume while reducing insufflation pressure may produce improved patient outcomes.

This article presents a method for measuring the working abdominal volume during laproscopic myomectomy using the surgical grasper, and applies this technique to obtain pilot data on whether deep neuromuscular blockade (NMB) can enable the use of lower insufflation pressure. Reduced insufflation pressure during laproscopic surgery has been shown to reduce post-operative pain, and thus the use of NMB during surgery may enable improved patient outcomes.

מצור Neuromuscular עמוק מוביל לנפח גדול יותר במהלך Intraabdominal פרוסקופיה

Shoulder pain is a commonly reported symptom following laparoscopic procedures such as myomectomy or hysterectomy, and recent studies have shown that ...

Detection of Architectural Distortion in Prior Mammograms via Analysis of Oriented Patterns

We demonstrate methods for the detection of architectural distortion in prior mammograms of interval-cancer cases based on analysis of the orientation of breast tissue patterns in mammograms. We hypothesize that architectural distortion modifies the normal orientation of breast tissue patterns in mammographic images before the formation of masses or tumors. In the initial steps of our methods, the oriented structures in a given mammogram are analyzed using Gabor filters and phase portraits to detect node-like sites of radiating or intersecting tissue patterns. Each detected site is then characterized using the node value, fractal dimension, and a measure of angular dispersion specifically designed to represent spiculating patterns associated with architectural distortion.
Our methods were tested with a database of 106 prior mammograms of 56 interval-cancer cases and 52 mammograms of 13 normal cases using the features developed for the characterization of architectural distortion, pattern classification via quadratic discriminant analysis, and validation with the leave-one-patient out procedure. According to the results of free-response receiver operating characteristic analysis, our methods have demonstrated the capability to detect architectural distortion in prior mammograms, taken 15 months (on the average) before clinical diagnosis of breast cancer, with a sensitivity of 80% at about five false positives per patient.

Detection of Architectural Distortion in Prior Mammograms via Analysis of Oriented Patterns

We demonstrate methods for the detection of architectural distortion in prior mammograms. Oriented structures are analyzed using Gabor filters and phase portraits to detect sites of radiating tissue patterns. Each site is characterized and classified using measures to represent spiculating patterns. The methods should assist in the detection of breast cancer.

זיהוי של דיסטורשן אדריכלי בממוגרפיה לפני<em&gt; דרך</em&gt; ניתוח דפוסי Oriented

We demonstrate methods for the detection of architectural distortion in prior mammograms of interval-cancer cases based on analysis of the orientation of ...

Gene-environment Interaction Models to Unmask Susceptibility Mechanisms in Parkinson's Disease

Lipoxygenase (LOX) activity has been implicated in neurodegenerative disorders such as Alzheimer&#39;s disease, but its effects in Parkinson&#39;s disease (PD) pathogenesis are less understood. Gene-environment interaction models have utility in unmasking the impact of specific cellular pathways in toxicity that may not be observed using a solely genetic or toxicant disease model alone.&#160;To evaluate if distinct LOX isozymes selectively contribute to PD-related neurodegeneration, transgenic (i.e. 5-LOX and 12/15-LOX deficient) mice can be challenged with a toxin that mimics cell injury and death in the disorder.&#160;Here we describe the use of a neurotoxin, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), which produces a nigrostriatal lesion to elucidate the distinct contributions of LOX isozymes to neurodegeneration related to PD. The use of MPTP in mouse, and nonhuman primate, is well-established to recapitulate the nigrostriatal damage in PD.&#160;The extent of MPTP-induced lesioning is measured by HPLC analysis of dopamine and its metabolites and semi-quantitative Western blot analysis of striatum for tyrosine hydroxylase (TH), the rate-limiting enzyme for the synthesis of dopamine. To assess inflammatory markers, which may demonstrate LOX isozyme-selective sensitivity, glial fibrillary acidic protein (GFAP) and Iba-1 immunohistochemistry are performed on brain sections containing substantia nigra, and GFAP Western blot analysis is performed on striatal homogenates.&#160;This experimental approach can provide novel insights into gene-environment interactions underlying nigrostriatal degeneration and PD.

Gene-environment Interaction Models to Unmask Susceptibility Mechanisms in Parkinson&#039;s Disease

Lipoxygenase (LOX) isozymes can generate products that may increase or decrease neuroinflammation and neurodegeneration.&#160;A gene-environment interaction study could identify LOX isozyme-specific effects. Using the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model of nigrostriatal damage in two LOX isozyme-deficient transgenic lines allows for comparison of the contribution of LOX isozymes on dopaminergic integrity and inflammation.

מודלים לאינטראקציה בין סביבת גנים כדי לחשוף מנגנוני רגישות במחלת פרקינסון

Lipoxygenase (LOX) activity has been implicated in neurodegenerative disorders such as Alzheimer&#39;s disease, but its effects in Parkinson&#39;s disease ...

Focus Formation: A Cell-based Assay to Determine the Oncogenic Potential of a Gene

Malignant transformation of cells is typically associated with increased proliferation, loss of contact inhibition, acquisition of anchorage-independent growth potential, and the ability to form tumors in experimental animals1. In NIH 3T3 cells, the Ras signal transduction pathway is known to trigger many of these events, what is known as Ras transformation. The introduction of an overexpressed gene in NIH 3T3 cells may promote morphological transformation and loss of contact inhibition, which can help determine the oncogenic potential of that gene of interest. An assay that provides a straightforward method to assess one aspect of the transforming potential of an oncogene is the Focus Formation Assay (FFA)2. When NIH 3T3 cells divide normally in culture, they do so until they reach a confluent monolayer. However, in the presence of an overexpressed oncogene, these cells can begin to grow in dense, multilayered foci1 that can be visualized and quantified by crystal violet or Hema 3 staining. In this article we describe the FFA protocol with retroviral transduction of the gene of interest into NIH 3T3 cells, and how to quantify the number of foci through staining. Retroviral transduction offers a more efficient method of gene delivery than transfection, and the use of an ecotropic murine retrovirus provides a biosafety control when working with potential human oncogenes.

The Focus Formation Assay provides a straightforward method to assess the transforming potential of a candidate oncogene.

להתמקד גיבוש: Assay מבוסס תאים כדי לקבוע את הפוטנציאל שבעור של ג&#39;ין

Malignant transformation of cells is typically associated with increased proliferation, loss of contact inhibition, acquisition of anchorage-independent ...

Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

Here we outline a next-generation RNA sequencing protocol that enables de novo assemblies and intra-host variant calls of viral genomes collected from clinical and biological sources. The method is unbiased and universal; it uses random primers for cDNA synthesis and requires no prior knowledge of the viral sequence content. Before library construction, selective RNase H-based digestion is used to deplete unwanted RNA &#8212; including poly(rA) carrier and ribosomal RNA &#8212; from the viral RNA sample. Selective depletion improves both the data quality and the number of unique reads in viral RNA sequencing libraries. Moreover, a transposase-based &#39;tagmentation&#39; step is used in the protocol as it reduces overall library construction time. The protocol has enabled rapid deep sequencing of over 600 Lassa and Ebola virus samples-including collections from both blood and tissue isolates-and is broadly applicable to other microbial genomics studies.

This protocol describes a rapid and broadly applicable method for unbiased RNA-sequencing of viral samples from human clinical isolates.

רצף עמוק משוחד של RNA וירוסי ממדגמים קליניים

Here we outline a next-generation RNA sequencing protocol that enables de novo assemblies and intra-host variant calls of viral genomes collected from ...

Application of Biochip Microfluidic Technology to Detect Serum Allergen-specific Immunoglobulin E (sIgE)

Allergic disease is common in both adults and children. Identification of the causative allergens is significant in disease management and prevention. However, a specific immunoglobulin E (IgE) measurement system with a high price-performance ratio is lacking in mainland China, especially in the primary care hospitals. This paper describes the principle and operation procedures of using a microfluidic cartridge-based chemiluminescence system to detect allergen-specific IgE in serum. The results were compared with those from ImmunoCAP (System 1), the industrial standard, and the reproducibility of the system to detect patients sensitized to common allergens is evaluated. The results showed that in comparison with ImmunoCAP (System 1), the BioIC System (System 2) has good precision and sensitivity in detecting serum-specific IgE against various inhalant and food allergens but with a significantly lower cost. It can serve as a good alternative to System 1 in primary care hospitals in mainland China who have lower financial affordability.

Application of Biochip Microfluidic Technology to Detect Serum Allergen-specific Immunoglobulin E sIgE

This paper presents a protocol for detecting serum-specific immunoglobulin E with a microfluidic cartridge-based chemiluminescence system and the evaluation of its usefulness in allergy diagnoses.

יישום של טכנולוגיה Microfluidic ביו-שבב על סרום לזהות אלרגן ספציפיים אימונוגלובולין E (sIgE)

Allergic disease is common in both adults and children. Identification of the causative allergens is significant in disease management and prevention. ...